cord-007373-livz5zuu	2006	authors: Gayathri, P.; Satheshkumar, P.S.; Prasad, K.; Nair, Smita; Savithri, H.S.; Murthy, M.R.N. title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket In the present study, the crystal structure of SeMV protease domain was determined to a resolution of 2.4 Å by multiple isomorphous replacement coupled with anomalous scattering, with a view to identify the residues involved in substrate binding as well as protease -VPg interactions. The absence of well-defined density for F301 in SeMV protease suggests that its side chain might undergo substantial displacement on binding of the substrate or on conformational changes induced by the interaction of the protease domain with VPg. TEV and equine arteritis virus proteases, in which a serine residue occurs at the position corresponding to F301, are active in trans.
cord-008407-jbp8bxjz	1995	During serial undiluted passage of rubella virus (RUB) in Vero cells, two species of defective-interfering (DI) RNAs of approximately 7000 and 800 nucleotides (nts) in length were generated (Frey, T. Finally, to determine whether the majority of DI RNAs present in P12 RNA contained a deletion in the SP-ORF, an oligonucleotide probe which is complementary to a sequence located within the E1 protein coding region (nts 8472 to 8488, eligonucleotide 83, Fig. 3E ) that was deleted in all three cDNA clones was hybridized to P12 RNA. Analysis of the 5'' terminus of DI RNA generated during serial passage As shown in Figure 3A , oligonucleotide probes complementary to the exact 5'' terminal sequences of the RUB genome hybridized to the large DI RNAs. To confirm that these DI RNAs contained the authentic 5'' end of the genome, primer extension was performed on intraceilular RNA from standard RUB-infected cells and P12 RNA.
cord-008426-ktn8c0zx	1995	From a comparison of the predicted sequences of the ORFs of these three sobemoviruses and of the noncoding regions, it is suggested that the two SBMV strains differ from one another as much as they do from RYMV and that they should be considered as different viruses. Southern bean mosaic virus (SBMV) is the type member of the sobemovirus group of small icosahedral positive-strand RNA viruses (for reviews see Sehgal, 1981 ; Tremaine and Hamilton, 1983; Hull, 1988) . The recently published nucleotide sequence (4450 nt) of rice yellow mottle virus (RYMV), another sobemovirus (Ngon A Yassi et aL, 1994) , shows that it has a similar genome organization to SBMV-C (Fig. 1) . Amino acid sequence of southern bean mosaic virus coat protein and its relation to the three dimensional structure of the virus
cord-252397-qlu7dilh	2015	Results from a natural history study of MERS-CoV-infected rhesus monkeys indicated that intratracheal inoculation induced a non-lethal disease with limited pathology observed in recovering animals at 28 days post-inoculation and infectious virus could be recovered from lung but not other tissues assayed (Yao et al., 2014) . One subject in the MERS-EMC inoculated group appeared to develop a secondary infection observed by CT that increased to study end, day 25 post-exposure. With the use of CT, we observed that IT inoculation of common marmosets with MERS-JOR or MERS-EMC isolates resulted in a non-lethal disease characterized by limited clinical signs and moderate consolidative lung pathology that did not completely resolve by study end. In this experiment, we sought to determine if there were virus specific differences in disease progression following intratracheal inoculation of common marmosets with Middle Eastern Respiratory Syndrome Coronavirus, commonly known as MERS-CoV, with two common laboratory viral isolates (MERS-EMC and MERS-Jordan).
cord-252615-ajyv95pu	2016	Although 3A protein had no effect on the expression of ATP1B3, EV71 infection resulted in elevated expression of ATP1B3 in RD cell line, both on messenger RNA (mRNA) and protein levels. Our study demonstrated that ATP1B3 inhibit EV71 replication by enhancing the production of type-I interferons, which could act as a potential therapeutic target in EV71 infection. We observed that both the mRNA and protein levels of ATP1B3 in RD cells were positively correlated with the infection doses of EV71 (Fig. 3B) . We infected ATP1B3 overpression cells or vector controls with EV71 at an MOI of 1, cultured cells with anti-human interferon-α1/β antibodies or isotype control IgG, and examined the viral replication using RT-PCR assay. Previous studies have shown that EV71 infection can induce IFN-β production which is dependent on the infectious dose, but the interferon is not cell type specific (Lu et al., 2012) .
cord-253024-b393ea2u	1992	Six RNA+ mutants that reside within a single complementation group mapping within the S glycoprotein gene of MHV-A59 were isolated which did not cause syncytium at the restrictive temperature. Since these mutants do not produce syncytium at the restrictive temperature ( Fig. 1) and sequence analysis of RNA recombinant viruses suggested that the defect in LA7 mapped within the first 1 .l kb of the S glycoprotein gene (Banner et al., 1990; Keck eta/., 1987 Keck eta/., , 1988a Makino eta/., 1986b Makino eta/., , 1987 , these data provided an anchor for mapping the location of the remaining group F RNA+ mutants. Since the distance between the group Fl and F2 mutants would have required sizable deletions (>lOO bp) to result in ts+ virus (Fig. 4) these data suggested that large deletions were rare events in these crosses, and did not contribute to an increase in the recombination frequency within the S glycoprotein gene.
cord-253351-b36g09r0	1998	Similar substitutions within PEP2 result in a fusion-negative phenotype; however, these mutant S proteins also exhibit defects in protein processing and surface expression which likely explain the loss of the ability to induce fusion. To determine the importance of the asymmetric distribution of hydrophobicity in the induction of cell-to-cell fusion, as predicted by the ability to model this peptide as a sided ␣ helix ( Fig. 2A) , nonconservative and conservative amino acid substitutions were introduced in PEP1 to target representative bulky hydrophobic residues (F977K, F977L, L981K, L981I) and polar or charged residues (S975D, N978D, N978L, D986V-D989V). All mutant PEP1 S proteins were assayed for fusion using both in situ and quantitative fusion assays, performed as shown in Fig. 3 , using the vTF7-3-infected and wild-type S gene-transfected cells as positive controls and vTF7-3-infected and mock-transfected cells as negative controls.
cord-253894-4u5yt7b7	2011	VACV, by far the most intensively studied poxvirus, replicates entirely in the cytoplasm of infected cells and encodes many of the proteins required for its growth as well as numerous proteins modulating virus-host interactions. Here we provide a detailed computational analysis of the F16 protein indicating that it is unlikely to have serine recombinase activity, and experimental data showing that the F16L gene is not required for virus growth in cell culture. F16-3xflag was detected by Western blotting at 2 h after infection, only slightly increased in amount between 4 and 24 h, and accumulated in the presence of cytosine arabinoside (araC), an inhibitor of DNA synthesis that prevents VACV intermediate and late gene expression. Two other VAC proteins, I3 and B1, containing a C-terminal 3xflag tag and expressed from a transfected plasmid under the control of the CMV promoter were analyzed in parallel with F16-3xflag, and no nucleolar or nuclear membrane staining was detected (not shown).
cord-254558-gvo0gwjf	2003	The infected SB cells underwent DNA fragmentation and stained positive in terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) assay, suggesting that GGNNV infection induced apoptosis in SB cells. To determine if GGNNV induces apoptosis in fish cells through the CD95 apoptotic pathway, infected SB cells were harvested at 24 PI and 48 h PI, and cell lysates were analyzed for IETDase activity, using IETD as the substrate for caspase-8. To determine which protein encoded by betanovirus GGNNV might be responsible for inducing apoptosis, the transient expression of viral proteins A and ␣ in SB and Cos-7 cells was carried out. The results that GGNNV infection induced activation of caspase-3-like proteases and GGNNV-induced apoptosis could be inhibited by DEVD-CHO indicate that fish caspases are important mediators of virus-induced cell death. Here, protein ␣ of GGNNV was demonstrated to be capable of inducing apoptosis by DNA fragmentation and TUNEL staining in transfected SB and Cos-7 cells at 48 h post-transfection.
cord-254747-vox5xsgd	2018	Overall, current evidence indicates that the EndoU activity of CoV nsp15 is dispensable for viral RNA synthesis and virus replication in cell culture. It was first discovered that the EndoU activity of nsp15 mediates the evasion of host recognition of viral dsRNA by infecting primary macrophages with EndoU-deficient CoVs (Deng et al., 2017; Kindler et al., 2017) . Moreover, treatment with the PKR inhibitor did not affect IFN induction or RNase L-mediated ribosomal RNA degradation in the EndoU-deficient CoV infected-macrophages (Deng et al., unpublished data) . Macrophages infected by the EndoU-deficient CoVs exhibited an early, RNase L-mediated degradation of ribosomal RNA, demonstrating that the OAS-RNase L system was activated (Deng et al., 2017; Kindler et al., 2017) . Lack of MDA5 expression or treatment with the PKR inhibitor did not affect virus-induced RNA degradation (Deng et al., 2017; Kindler et al., 2017) , suggesting that the nsp15-mediated blockage of OAS-RNase L activation is independent of the MDA5-IFN and PKR pathways.
cord-254950-y6kayxie	1988	Abstract Mouse thymic virus (MTLV; murid herpesvirus 3) is a lymphotropic herpesvirus that cytolytically infects developing T lineage lymphocytes in the thymus of neonatal mice. In order to determine whether T lineage lymphocytes are required for infection, young adult athymic nude (nulnu) mice and euthymic littermates were infected with MTLV and tested for virus shedding. To determine whether MTLV infection requires thymus-derived lymphocytes, 4-week-old female ICR Swiss athymic nude (nulnu) and euthymic (+lnu) littermate controls (four each; Memorial Sloan-Kettering Cancer Center nude mouse breeding colony) were inoculated intraperitoneally with either 40 or 200 IDS0 of MTLV and virus shedding was tested by mouth swabs beginning 6 days after infection. litters available did not allow every negative sample to be tested, additional litters of normal newborn mice were inoculated with fresh homogenates (1 O-20%, w/v) of randomly selected negative thymuses and salivary glands, representing various test dates up to Day 48, from 14 assay litters that had received swab fluids from nude mice.
cord-255453-7e40rj1y	2006	The relationship of Bo/Newbury1/1976/UK with members of the Caliciviridae Although many features of the Newbury1 genome organization were consistent with the Caliciviridae, the Newbury1 genome had low nucleotide (≤47%) and amino acid (≤39%) identities to all representative viruses of the 4 Caliciviridae genera by comparison of complete non-structural genes (2Chelicase, 3C-protease, 3D-polymerase), complete capsids, capsid subdomains and the 3′ terminal ORF genes ( Table 2 ). Newbury1 failed to group phylogenetically with the 4 recognized Caliciviridae genera but formed a separate clade with NB virus by UPGMA, Fitch-Margoliash, parsimony and maximum likelihood analyses of the nucleotide and translated amino acids of ORF1 (excluding the capsid gene), the individual regions that encoded the 2C-helicase, 3C-protease, 3D-polymerase and complete capsid genes (not shown). The distant relationship of Newbury1 to the 4 recognized Caliciviridae genera was confirmed using additional phylogenetic analyses based on amino acid alignments generated from homology models of structurally conserved regions of the partial polymerase and the capsid S-domain (Fig. 3) .
cord-255738-r8zfdsix	2007	Sequence analysis of the replicon RNA purified from SCR-1 cells soon after selection in blasticidin (passage number 6) found no sequence differences compared with the published sequence of SARS-CoV strain SIN2774 (GenBank Accession Number AY283798). Baric''s group constructed a transmissible gastroenteritis virus (TGEV) replicon for the expression of heterologous GFP gene (Curtis et al., 2002) and Thiel''s group generated a non-cytopathic, selectable replicon RNA (based on HCoV 229E) for the identification of coronavirus replicase inhibitors (Hertzig et al., 2004) . Compared to anti-viral agent identification systems based on purified proteins or nucleic acids, our SARS-CoV replicon cell line has two advantages: first, if a candidate inhibitor can inhibit replication of our replicon RNA, which occurs intracellularly, it thus demonstrates that this agent can permeate the cell. To obtain the complete sequence of the SARS-CoV replicon persisting in the SCR-1 cells, the total cellular RNAs isolated from SRC-1 cells at passage number 6 and 40 were used as the templates.
cord-255773-b4re5bky	2016	title: Suppression of type I interferon production by porcine epidemic diarrhea virus and degradation of CREB-binding protein by nsp1 We showed that PEDV suppressed the type I interferon production and ISGs expression in these cells, and identified nsp1, nsp3, nsp7, nsp14, nsp15, nsp16, E, M, N and ORF3 as the viral IFN antagonists. The CBP degradation is a novel mechanism of coronavirus nsp1 for IFN suppression and our study provides a new insight into the immune modulation and evasion strategy of PEDV. MARC-145 cells have been used to study type I IFN signaling of porcine arterivirus (Kim et al., 2010; Overend et al., 2007; Patel et al., 2010) , and thus infection of these cells One μg of each of the cloned genes was transfected to HeLa cells in 12-well plates, and protein expression was determined by immunofluorescence (B) and
cord-255828-jrqdyfbg	2012	title: Glycosyl-phosphatidylinositol (GPI)-anchored membrane association of the porcine reproductive and respiratory syndrome virus GP4 glycoprotein and its co-localization with CD163 in lipid rafts The porcine reproductive and respiratory syndrome virus (PRRSV) glycoprotein 4 (GP4) resembles a typical type I membrane protein in its structure but lacks a hydrophilic tail at the C-terminus, suggesting that GP4 may be a lipid-anchored membrane protein. Mutational studies for residues adjacent to the GPI modification site and characterization of respective mutant viruses generated from infectious cDNA clones show that the ability of GP4 for membrane association corresponded to virus viability and growth characteristics. The depletion of cholesterol from the plasma membrane of cells reduced the virus production, suggesting a role of lipid rafts in PRRSV infection. 7C, D) .These data indicate that the reduction of virus production by MβCD was due to the depletion of cholesterol from the cells and this effect was reversible, suggesting a role of lipid rafts in PRRSV infection.
cord-255841-3laov764	2005	A striking arrangement of conserved asparagine and glutamine residues of HR1 propagates from two central chloride ions, providing hydrogen-bonding "zippers" that strongly constrain the path of the HR2 main chain, forcing it to adopt an extended conformation at either end of a short HR2 α-helix. We and others have previously shown that, analogous to other class I fusion proteins, peptides corresponding to the HR regions of the mouse hepatitis coronavirus (MHV, Bosch et al., 2003) and SARS-CoV (Bosch et al., 2004; Ingallinella et al., 2004; Xu et al., 2004a; Tripet et al., 2004) can fold into a stable rod-like structure, consisting of three HR1 helices in association with three HR2 peptides in antiparallel orientation. As expected, there is essentially one side chain per turn of the HR1 a-helix participating to the central hydrophobic core of the molecule, resulting in 23 amino acids from each chain (labeled to the left of Fig. 2A ) interacting with their symmetry mates at the central 3-fold axis.
cord-256036-gd53s4dv	2013	In contrast to human hepatocytes, murine cells do not support HCV entry thereby creating a first and important barrier for a broader host tropism of the virus. Utilizing blocking antibodies specific to CD81 or the viral envelope protein E2, expression of entry factor mutants and mice with a targeted disruption of the SCARB1 gene validated uptake of HCV into murine hepatocytes in an HCV glycoprotein-mediated fashion. Taking advantage of the high mutational plasticity of HCV, three adaptive mutations in the viral glycoproteins E1 and E2 were identified that allowed the virus to enter cells expressing human SCARB1, CLDN1, OCLN and mouse CD81. Recently, a genetically humanized mouse model was constructed utilizing cell culture produced recombinant hepatitis C virus to activate a cellular encoded reporter (Dorner et al., 2011, in press ). Human occludin is a hepatitis C virus entry factor required for infection of mouse cells A humanized mouse model to study Hepatitis C virus infection, immune response, and liver disease
cord-256316-1odgm6hm	1992	
cord-256703-eaj63c2k	1988	On the basis of genetic recombination and sequence analysis, it has been concluded that the S RNA encodes the nucleocapsid protein N and a nonstructural protein NS,; the M RNA encodes two glycoproteins Gl and G2 and in some genera a nonstructural protein, NS,; and the L RNA probably contains the information for the viral transcriptase (Bishop et al., 1982; Bouloy et a/., 1984; Cabradilla et al., 1983; Collett et a/., 1985; Eshita and Bishop, 1984; Fuller et al., 1983; lhara et a/., 1985; Lees et al., 1986; Ronnholm and Pettersson, 1987; Schmaljohn et a/., 1987 , 1982, 1984) . To compare the levels of PlV glycoprotein synthesis, monolayers of CV-1 cells were infected with wildtype vaccinia virus, PTV, or the vaccinia recombinants described above which contain the PTV glycoprotein gene with the different sequences in the translation initiation region. We have constructed vaccinia virus recombinants containing a partial cDNA clone of the M genome segment of PTV, which encodes the Gl and G2 glycoproteins.
cord-256737-ptjng78b	2010	The SARS-CoV spike (S) protein mediates virus entry by binding cellular receptors and inducing fusion between the viral envelope and the host cell membrane. Importantly, we show that SARS-CoV S palmitoylation is not necessary for efficient interaction with SARS-CoV M, which differs from published experiments for MHV (Thorp et al., 2006) and suggests a significant difference between the two viruses that may have important implications for virus assembly and infectivity. To determine if SARS-CoV S becomes palmitoylated in a pre-medial Golgi compartment, HEK293T cells exogenously expressing SARS-CoV S were labeled for 30 min with 35 S-methionine/ cysteine to measure total protein expression or 3 H-palmitic acid to measure palmitoylated protein. Although both SARS-CoV S and S PN were present at the cell surface, it is possible that there could be a difference in the amount of protein at the plasma membrane at steady state if palmitoylation affects a post-Golgi trafficking step.
cord-256769-flfycl7i	2011	
cord-258232-br4z3na6	1999	The present study demonstrated that mouse hepatitis virus (MHV) E protein was released as an integral membrane protein in lipid vesicles from E-protein-expressing mammalian cells, in the absence of other MHV proteins. Complementation studies using two defective interfering (DI) RNAs of a prototypic coronavirus, mouse hepatitis virus (MHV), showed that E and M proteins are both required for the production of MHV particles containing the viral nucleocapsid (5) . To establish the buoyant density of released E protein, culture fluids from E-protein-expressing cells were applied onto a discontinuous sucrose gradient and centrifuged as described above. The release of E-protein-containing membrane vesicles from MHV-infected cells and E-protein-expressing cells further emphasized the pivotal role of E protein in coronavirus assembly. Furthermore, sucrose gradient centrifugation of MHV particles showed two E protein radioactive peaks, whereas N protein had only one peak corresponding to the MHV buoyant density (Fig. 3) , indicating that membrane vesicles containing only E protein do not include nucleocapsid.
cord-258286-lodjcj8c	1997	Previous studies have shown that immunocoma large plaque variant derived from the parental JHM petent mice infected with MHV exhibited increased exstrain (Stohlman et al., 1982) ; the small plaque variant pression of a number of cytokines, including IL-1, IL-6, DS (Stohlman et al., 1982) ; the neutralization-escape mu-TNF-a, and IFN-g, in the CNS at the time of viral cleartant 2.2-V-1 (Fleming et al., 1987; Wang et al., 1992) , and ance (Pearce et al., 1994) . The expressed IFNg exhibited antiviral activity, prevented virus spread in layers of DBT cells grown at approximately 70% confluence in 60-mm petri dishes were infected with MHV at vitro, and altered viral pathogenesis in mice. Expression of IFN-g using an MHV DI RNA vector cell metabolism prior to infection or it may be that interferon acts at an early stage of viral replication.
cord-258327-03vk6enj	1991	The purified HE protein retained acetylesterase activity and was able to function as a receptor-destroying enzyme rendering red blood cells resistant against agglutination by both coronaviruses. However, it was found to recognize glycoconjugates containing N-acetyl-9-O-acetylneuraminic acid as indicated by a binding assay with rat serum proteins blotted to nitrocellulose and by its ability to inhibit the hemagglutinating activity of BCV, HEV, and influenza C virus. The virus pellet was resuspended in PBS and used for (i) analysis by polyacrylamide gel electrophoresis ; (ii) determination of the esterase activity ; (iii) hemagglutination and hemagglutination-inhibition assays ; and (iv) purification of the viral glycoproteins . These erythrocytes and control cells, which had been incubated with PBS, were used to determine the HA titer of BCV, HEV, and influenza C virus . As shown in Table 1 , incubation of erythrocytes with purified acetylesterase from either BCV or HEV rendered the cells resistant to agglutination by both coronaviruses as well as by influenza C virus .
cord-258379-v3lceirh	1991	There was considerably less evidence of contaminating cellular proteins in this gradient, and the relative proportion of the 12K protein to the other virion proteins appeared similar to that observed at the previous stage in purification, strongly supporting the idea of a specific association between the 12K protein and virus particles. In order to establish the identity of the 12K polypeptide as the product of the 3c gene, and to examine the possibility that IBV virions might contain other new virus polypeptides in amounts too small to detect directly, we next carried out immunoprecipitation experiments using monospecific antisera directed against the predicted products of the 3a, 3b, 3c, 5a, and 5b ORFs (17, 18, 23) . Messenger RNA 4 of mouse hepatitis virus (MHV) is known to encode a 15K polypeptide, the predicted amino acid sequence of which contains a highly hydrophobic region from residues 8 to 41 (9, 22) , although the protein has not so far been found in virions.
cord-258691-cd83w9o6	2009	IFN-γ-mediated control of JHMV replication is dampened in glial cultures derived from the neural progenitor cells of type I receptor knock-out mice. These data indicate that JHMV is capable of infecting glial cells generated from neural progenitor cells and that IFN-γ-mediated control of viral replication is dependent, in part, on type I IFN secretion. In the present study, we demonstrate that primary cultures of glia derived from neural progenitor cells are susceptible to JHMV infection and support viral replication. Therefore, these findings provide, to our knowledge, the first demonstration that glia-committed cells derived from neural precursors are susceptible to JHMV infection as well as identify a potential mechanism responsible for controlling viral replication. These findings indicate that differentiated cells derived from neural progenitors are susceptible to JHMV infection and are capable of supporting replicating virus which results in extensive cytopathology.
cord-259095-mfptcw8t	1997	Numbering of amino acid residues within MHV 3CLpro is based The linear schematic of the MHV genome shows the organization of Ser 1 (Lu et al., 1995) Site-directed mutagenesis of pGpro with bovine chymotrypsin (Gorbalenya and Koonin, 1993) , 3Cpro of human rhinovirus 14 (Matthews et al., 1994) , and hepatitis A virus Asp53 and Asp65 were mutagenized by the Chame-3Cpro (Allaire et al., 1994) . The comparison of the were checked for residual expression and processing from the pGpro construct by the addition of [ 35 S]-four coronavirus 3CLpro sequences revealed two potential cleavage sites present only in MHV, QS 3554-5 , and methionine to an aliquot of the unlabeled reaction mixture after treatment with RNase and cycloheximide and QG 3607-8 . Mutation of Asp65 to Pro or Ala (D65P and D65A) MHV-A59, IBV, HCV-229E, and TGEV revealed no completely conserved Asp or Glu residues at positions analo-resulted in a proteinase with activity comparable to that expressed from wild-type pGpro (Fig. 3B, lanes 3 and 4) .
cord-259500-ndjbrtrv	2003	title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli These data demonstrate that, when hosts are sufficiently susceptible for infection by transcripts of reduced specific infectivity, introduction of frameshift mutations at "slippery sequences" near toxic regions of viral cDNAs can be used as an additional strategy to clone recalcitrant viral sequences in high-copy-number plasmids for reverse genetics. A similar frameshift mutation was also found in the derivative replicon pCTV-⌬Cla. However, the sequence of the progeny virion RNA of CTV9 from infected protoplasts or citrus plants did not contain the additional nt at position 3732 that occurred in the cDNA clones, suggesting that the frameshift mutation present in the original cDNA clone was repaired either during the in vitro transcription or during replication in the protoplasts.
cord-259717-e8ljkv2y	2014	Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). Because previous metagenomic studies demonstrated significant virus diversity in patients with diarrhea (Finkbeiner et al., 2008) we focused this study on comparing the eukaryotic virus populations in stools of children with diarrhea collected from two different locations, Melbourne, Australia and the Northern Territory, Australia. In order to independently confirm the sequencing results, we used PCR to define the prevalence of the most frequently detected viruses for which pan-family or pan-genus primers could be used including: adenovirus, astrovirus, enterovirus, norovirus, and rotavirus.
cord-260108-osg8q89i	2012	Here, we report the entire 26,340-bp genome of a novel adenovirus, detected by PCR, in tissues of six of nine South Polar skuas (Catharacta maccormicki), collected in Lake King Sejong, King George Island, Antarctica, from 2007 to 2009. The DNA polymerase, penton base, hexon and fiber genes of the South Polar skua adenovirus (SPSAdV) exhibited 68.3%, 75.4%, 74.9% and 48.0% nucleotide sequence similarity with their counterparts in turkey hemorrhagic enteritis virus. Phylogenetic analysis based on the entire genome revealed that SPSAdV belonged to the genus Siadenovirus, family Adenoviridae. Using newly designed primers based on the obtained sequence, the full genome of the novel adenovirus (SPSAdV) was extended from the left-end inverted terminal repeat (ITR) region to the right-end ITR region. At the nucleotide level, the SPSAdV pol, penton base and hexon genes exhibited somewhat higher sequence similarity of 73.8%, 79.2% and 77.5% with RAdV-1 than with THEV (68.3%, 75.4% and 74.9%) ( Table 4 ).
cord-260177-xu0elmak	1982	title: Monoclonal antibodies to murine hepatitis virus-4 (strain JHM) define the viral glycoprotein responsible for attachment and cell-cell fusion Abstract Hybridoma cell lines producing monoclonal antibodies to the JHM strain of mouse hepatitis virus-4 (MHV-4) were established. A third set of monoclonal antibodies reacted both in the cytoplasm and on the surface of infected cells and precipitated the 25,000d viral glycoprotein (GP-5) and its precursor VP-6 (23,000d). MHV-4 polypeptide specificities of monoclonal antibodies were determined by immune precipitation of [35S]methionine-labeled viral proteins from infected L-241 cells. Only incubation with monoclonal antibodies to GP-1 resulted in inhibition in plaque and syncytium number (Fig. 5) , indicating involvement of that polypeptide in cell to cell spread of infection by fusion. When we examined our collection of monoclonal antibodies for the ability to inhibit spread of infection, only anti-GP-1 was effective, suggesting that the virion peplomer contains the active site for cell-cell co % fusion.
cord-260376-29ih5c9v	2004	title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases We synthesized on cellulose membranes 4942 ten-amino-acid peptides which included all of the sequences predicted for the severe acute respiratory syndrome (SARS) corona virus. Peptides incorporating all of the sequences predicted in the open reading frames of the SARS-CoV genome were prepared on derivatized cellulose membranes using a robotic peptide synthesizer (Autospot ASP 222, Intavis Bioanalytical Instruments, Lagenfeld, Germany). These data indicate that the four recovered cases developed antibodies with viral neutralizing potency between the time of acute and convalescent serum sampling. Therefore, those peptides strongly recognized on membranes probed with convalescent sera, but not with acute or control sera, should be the most immunodominant and may include SARS-CoV epitopes that are vulnerable to neutralization by antibody. Shown in Table 2 are the 24 overlapping membrane peptides that were recognized exclusively, or much more strongly, in multiple pairs of convalescent compared with the respective acute sera.
cord-260695-qwepi0we	2017	Of the host-encoded lncRNAs reported to be differentially expressed upon HIV-1 infection, only nuclear enriched abundant transcript 1 (NEAT1) and noncoding repressor of nuclear factor of activated T cells (NRON) have been functionally characterized (Lazar et al., 2016) . In this report, we describe a meta-analysis of two independent RNA-seq studies of HIV-1-infected cells and show that, unexpectedly, only three lncRNAs are differentially expressed in both of these datasets (Chang et al., 2011; Mohammadi et al., 2013) . To obtain an unbiased understanding of any changes in lncRNA expression during HIV-1 infection, we performed a meta-analysis of two independent RNA-seq studies conducted by two different groups using two different virus strains ( Supplementary Fig. S1 ) (Chang et al., 2011; Mohammadi et al., 2013) . To validate the results of the in silico analysis of lnc173 expression, we isolated RNA from 4 human cell lines and probed for the presence of both transcript variants by quantitative RT-PCR (qRT-PCR; Fig. 3A -D).
cord-260782-1lm8tzbc	2018	title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) The aim of the current study was to describe histological lesions and viral RNA levels in tissues from possum experimentally infected with WPDV. Histology of brain, kidney and liver tissue from wobbly possum disease virus (WPDV)-infected possums. Whilst RNA levels in selected tissues (liver, spleen, brain and kidney) from WPD-infected possums have been previously reported (Dunowska et al., 2013) , we have expanded both the number of possums and the tissue types tested to provide a greater understanding of the tissues targeted by the virus in-vivo. Detection of moderate to high levels of viral RNA from the sera of all but one infected possum in this study also supports the use of blood or serum samples for detection of WPDV.
cord-262226-7kwkla73	2013	
cord-262245-eb7g9p1x	1991	Abstract The intracellular RNA of two neurotropic variants of the JHM strain of mouse hepatitis virus (MHV) independently isolated from the brain and spinal cord of an infected Wistar Furth rat were compared with that of the parental virus. Both the brain and the spinal cord isolates displayed a different pattern of virus-specific mRNAs from the parental JHM virus in the infected cells (26). The size of several of these mRNAs appeared different; most notably, the mRNA 3 of the At1 lf cord isolate was smaller than those of the parental JHM strain and of the brain isolate but similar to that of JHM (2), which has a deletion of 423 nucleotides in the S gene (28). Figure 5A shows that the S protein of the At1 lf cord variant is smaller than that of the JHM parental virus, but similar in size to that of the JHM(2), which has a deletion of 153 amino acids (28).
cord-262347-ejhz9rra	2015	
cord-262441-slh52nxm	2017	To determine the crucial amino acid residue(s) in SARS-CoV nsp4 required to induce membrane rearrangements through the interaction with nsp3C, we constructed additional expression plasmids encoding deletion mutants of SARS-CoV nsp4, pCAG nsp4 Δ112-126-HA and pCAG nsp4 Δ126-164-HA, as shown in Fig. 1B . To determine the effect of the two amino acid residues, H120 and F121, in SARS-CoV nsp4 on the membrane rearrangements thorough interaction with nsp3C, 293T cells transfected with pCAG nsp4-HA or pCAG nsp4 H120N/F121L-HA together with pCAG nsp3C-3xFLAG at 30 h posttransfection were subjected to transmission electron microscopy (TEM) analysis. As we expected, expression of renilla luciferase was detected in cells transfected with pBAC-SARS-Rep-wt, but not in those with pBAC-SARS-Rep-H120N/F121L or pBAC-SARSRep-SAD (Fig. 7C) , suggesting that both H120 and F121 in SARS-CoV nsp4 play critical roles in the viral replication by remodeling the membrane through binding with nsp3.
cord-262574-gu0930s3	1985	The BALB/cV subline was used to study the molecular basis of potential virus-host interactions involving cell surface-expressed MMTV proteins. Cell surface iodination identified virus-specific proteins expressed on BALB/cv primary mammary tumor cells grown in culture. Adsorption experiments have demonstrated that the anti-gp52/gp36 serum reacts specifically with MMTV glycoproteins and envelope-related precursors and does not react with normal cell proteins of BALB/c mammary tissue (Slagle et aQ, 1985) . Primary cultures of a BALB/cV tumor were analyzed for cell surface expression of viral proteins using the same iodination procedure. Primary cultures of BALB/cV tumor cells were starved for 2 hr in methionine-free media and were then metabolically labeled for 1 hr with r5S]Met. Intact cell monolayers were rinsed with cold TBS, placed on ice, and reacted with specific antisera to detect 35S-labeled MMTV proteins expressed on the cell surface. DISCUSSION This report describes a thorough analysis of the expression of MMTV-specific proteins on the surface of BALB/cV mammary tumor cells.
cord-263302-z5uhrta5	2000	Transfection of the reporter RNA into MHV-infected cells resulted in synthesis of a CAT-specific subgenomic mRNA detected by reverse transcription-polymerase chain reaction (RT-PCR). Further sequencing on cDNA clones derived from JHM2c mRNAs by reserve transcription-polymerase chain reaction (RT-PCR) has shown that the leader-body joining sites in subgenomic mRNA2-1 are more heterogeneous . When it was placed in front of the chloramphenicol acetyl-transferase (CAT) gene in the defective-interfering (DI) RNA-CAT reporter plasmid, the IG5-1, which is devoid of any known IRES sequence, can direct the synthesis of a subgenomic CAT-containing mRNA and expression of the CAT activity, thus confirming that the IG5-1 serves as a promoter for transcription of a subgenomic mRNA. To identify the minimal sequence required for subgenomic mRNA transcription, three deletions within the 140-nt sequence were made by PCR, and the deletion fragments were cloned into the DI RNA-CAT reporter vector in place of the wild-type, full-length (140-nt) se, and MHV-1 (F), respectively.
cord-263334-wwkdum94	2014	BHK-21 cells transfected with the DDX3 shRNA were infected with JEV (MOI¼ 0.01) for 48 h, Viral titers determined by plaque formation assay at 48 hpi. (F) BHK-21 cells transfected with different amounts of DDX3 shRNA plasmid were infected with JEV (MOI ¼0.01), 48 h later, the amount of virus released into the medium was determined by plaque formation assay. In order to determine whether cellular DDX3 is involved in virus assembly or release, the BHK-21 cells were transfected with DDX3 shRNA plasmid before being infected with JEV (MOI ¼0.01). The virus titers were detected 2 days later by plaque formation assay, the results showed that overexpression of DDX3r-K230E, DDX3r-S382L and the control plasmid pcDNA3.1 after DDX3 knockdown resulted in the reduction of JEV replication for 13-fold (p o0.01), 12-fold (p o0.01) and 15-fold (p o0.01). The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3′ UTR
cord-264331-uvi8ucz4	2010	Following ex vivo co-culture with MHC matched B19/B19 APCs infected with H5N9 virus, memory responses were detected in T cell preparations obtained from all chickens receiving plasmids expressing either AIV protein by 3 weeks p.i. Since neither supernatants from the T cells cultured with uninfected APCs nor T cells from PBS inoculated birds cultured with infected MHC matched B19/B19 birds produced IFNγ (data not shown), the memory T lymphocyte activity was considered AIV specific. In order to evaluate the memory T lymphocyte responses of chickens inoculated with infectious AIV, chicks with the B19/B19 haplotype were inoculated with the low pathogenic H5N9/Turkey/Wis/68 strain and blood was collected at 5 weeks p.i. The ex vivo activation of T lymphocytes by AIV infected APCs was determined by the indirect IFNγ assay (Fig. 5) .
cord-264359-m9j3pcj1	1978	The VPl-VP3 group of poliovirion polypeptides can be resolved into multiple components by normal polyacrylamide gel electrophoresis (PAGE) in the presence of sodium dodecyl sulfate (SDS) (Vanden Berghe and Boeye, 1972) ; however, resolution into six components is achieved more easily and reproducibly in the presence of a pH gradient. In summary, fine resolution of the poliovirus capsid polypeptides was achieved by pH gradient electrophoresis and the results were independent of (i) the virus purification or (ii) protein extraction procedures, (iii) the state of maturation (procapsid or mature virion), and (iv) the serotype (type 1 or 2). DISCUSSION The improved resolution of poliovirus capsid polypeptides by pH gradient electrophoresis reported by Vrijsen and Boeye (1978) was confirmed and shown to be independent of the serotype and of the methods used for virus purification and protein extraction.
cord-265156-u1re7983	2017	Here, we investigated the CypA dependence of three distantly related nidoviruses that can all replicate in Huh7 cells: the arterivirus equine arteritis virus (EAV), the alphacoronavirus human coronavirus 229E (HCoV-229E), and the betacoronavirus Middle East respiratory syndrome coronavirus (MERS-CoV). The replication in cell culture of the arterivirus equine arteritis virus (EAV; de Wilde et al., 2013a) and the alphacoronaviruses feline coronavirus (FCoV; Tanaka et al., 2017) , human coronavirus (HCoV) NL63 (Carbajo-Lozoya et al., 2014), and HCoV-229E (von Brunn et al., 2015) was reported to be affected by CypA knockdown (KD) or knockout (KO), although the level of CypA dependence of these viruses, which was not compared directly, appeared to be quite different. Using different cell lines, the replication of two of these viruses, the arterivirus EAV (de Wilde et al., 2013a) and the alphacoronavirus HCoV-229E , was previously concluded to depend on CypA.
cord-265173-70wyecwj	2020	title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication Viruses modulate p53 functions in different manners: single-stranded RNA viruses such as the human coronavirus NL63 (HCoV-NL63) induces its degradation of p53 (Yuan et al., 2015) to ensure viral growth in infected cells (Ma-Lauer et al., 2016) , Zika (ZIKV) and West Nile (WNV) activate p53 to facilitate their replication (El Ghouzzi et al., 2016) (Teng et al., 2017) (Yang et al., 2008) while Adenovirus Even though p53 is implicated in the induction of apoptosis and in many viral infections, its role during calicivirus infection has not been studied. Here we found that p53 interacts with FCV dsRNA, the protease-polymerase NS6/7, and VP1 in the RC; moreover, knockdown of p53 resulted in a significant reduction of the NS viral protein synthesis and virus production, indicating its role for efficient viral replication.
cord-265895-ck7eto16	1987	These data, coupled with the high frequency of RNA recombination during MHV infection, suggest that the viral polymerase may pause in or around regions of secondary structure, thereby generating pools of free leader-containing RNA intermediates which can reassociate with the template, acting as primers for the synthesis of full-length or recombinant RNAs. These data suggest that MHV transcription uses a discontinuous and nonprocessive mechanism in which RNA polymerase allows the partial RNA products to be dissociated from the template temporarily during the process of transcription. These data, coupled with the presence of discrete large leader-containing RNAs which range from 84 to 1000 nucleotides in length in MHV-infected cells (Baric et a/., 1985) suggest that discontinuous RNA intermediates may be dissociated and reassert between viral RNA templates to generate recombinant viruses by a copy-choice mechanism (Makino eta/., 1986a). The leader-containing RNAs larger than 1 10 nucleotides in length detected by the leader-specific cDNA probe were more heterogeneous (Fig. 2) (Baric et al., 1985) suggesting that multiple RNA species in this size range were present.
cord-266018-8bhnlsgy	2004	The major findings of this study are (i) MHV infection of the CNS results in the appearance of two distinct populations of CD11c + cells each expressing markers characteristic of lymphoid (CD11c + CD11b À CD8a + DEC205 + ) and myeloid dendritic cells (CD11c + CD11b + CD8a À DEC205 À ), (ii) the accumulation of CD8a À DCs within the draining CLN is reduced in the absence of CCL3 signaling, (iii) expression of co-stimulatory molecules such as CD40 by CD8a À DCs within either the brain and CLN of MHV-infected CCL3 À/À mice is diminished suggesting that CCL3 signaling enhances expression of these molecules, and (iv) absence of CCL3 signaling results in the re-direction of the T cell response to viral antigens as determined by cytokine production. Our studies clearly indicate that CD8a À DCs isolated from the draining CLN of MHV-infected CCL3 +/+ mice secrete IL-12 suggesting that these cells help influence a protective Th1-mediated immune response characterized by the majority of antigen-specific T cells expressing IFN-g rather than IL-10 (Table 1 ).
cord-266230-ia04jc9j	1991	It is possible that the similar sequences at both ends of TomRSV RNA1 and RNA2 are a result of recombination between these two genomic RNA components. Beginning from the first potential in-frame initiation site at AUG,B, the N-terminal regions of the TomRSV RNA1 and RNA2 polyproteins are identical for the first 132 amino acids, and of the next 145 amino acid residues 75.3% of the positions are identical (Fig. 3A ). The fact that these regions of similarity are present only at the N-termini of the TBRV and GCMV RNAl-encoded polyproteins but are present at the N-termini of both TomRSV RNA1 -and RNA2encoded pofyproteins suggests that a large portion of coding and noncoding sequences at the 5'' terminus of TomRSV RNA1 have been duplicated and are now present at the 5'' terrnini of both RNA1 and RNA2.
cord-266585-jfjrk9gy	2007	During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation blocks the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid (Lys) affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. To further demonstrate that the failure to rescue infectious virus from the G15526C mutant transcripts is due to a defect in subgenomic RNA transcription, the full-length clones with and without the G15526C mutation were used to generate recombinant IBV expressing the enhanced green fluorescent protein (EGFP) by replacing the 5a gene with EGFP.
cord-266617-z8uecyl6	2019	Analysis of nucleotide and amino acid sequences revealed that half of overlaps undergo asymmetric evolution, as the protein from one frame shows a number of substitutions significantly higher than that of the protein from the other frame. I classified a pair of homologous overlaps as a case of symmetric evolution, if the number of amino acid substitutions in the Up1-Up2 alignment did not significantly differ from that in the Down1-Down2 alignment (chi-square < 3.84). In alternative, I classified a pair of homologous overlaps as a case of asymmetric evolution, if the number of amino acid substitutions in the Up1-Up2 alignment was significantly different from that in the Down1-Down2 alignment (chi-square > 3.84). The analysis of the pattern of nucleotide substitutions in the 75 pairs of homologous overlaps revealed 39 and 36 cases of symmetric and asymmetric evolution, respectively (Supplementary Table S2 ).
cord-266861-t5h133lp	2014	
cord-267014-3vi7pgvr	1992	Abstract The genomic organization at the 3′ end of canine coronavirus (CCV) and feline enteric coronavirus (FECV) was determined by sequence analysis and compared to that of feline infectious peritonitis virus (FIPV) and transmissible gastroenteritis virus (TGEV) of swine. Amplification of cDNA was performed by the polymerase chain reaction (PCR) as described (Kawasaki and Wang, 1989) , after the addition of synthetic oligonucleotide 178, 5''-GATGACACACAGGlTGAG-3'', which is identical to the carboxyl-terminus of the nucleocapsid (N) protein gene of FIPV (nucleotides 1945-l 962; Vennema et a/., 1991) . The nucleotide sequences flanking the ORFs 6a and 6b of FIPV and CCV and ORF 7 of TGEV were aligned to design primers for cDNA synthesis and polymerase chain reaction (PCR) amplification. The recombinant expression products were compared to the proteins produced in CCV-, FECV-, and FIPV-infected cells, which were analyzed similarly (Fig. 6) .
cord-267027-diwm1940	1992	
cord-267377-wyhsxj6g	2014	The single, large ORF encodes a polyprotein with domains specifying methyltransferase (mtr), protease (pro), helicase/NTpase (hel), and polymerase (pol) activities fused to the sequence encoding the CPs. The major and minor coat proteins map to the same CP sequence and size differences between them are potentially determined by translation initiation at two different start codons (minor, AUG 5581 and major, AUG 5710 ). Oat protoplasts were inoculated with capped transcripts of wild type clone pOBDV, major CP mutants GH1-7 (premature termination mutant) and KL1-3 (initiation codon mutant), and AB15-25 (marafibox mutant) and incubated for 40 h. Accumulation of viral coat proteins (CPs) and RNA in oat protoplasts inoculated with premature termination and initiation codon mutants of the CP gene. Oat protoplasts were inoculated with capped transcripts of wild type clone pOBDV, premature termination mutants GH1-7 and EF2-2, and initiation codon mutants IJ4-7 (minor CP), and KL1-3 and KL2-5 (major CP) and incubated for 24 h.
cord-267532-5rnqd9mb	1998	HEor CAT-specific subgenomic mRNAs were detected in the brains at days 1 and 2 p.i. but not later, indicating that the genes in the DI vector were expressed only in the early stage of viral infection. In the present study, we used this DI RNA vector system to express the viral HE gene in the CNS of mice in the presence of an HE-deficient helper virus. To determine the basis for the reduction in mortality following A59-DE-HE infection compared to other viruses ( Fig. 2) , virus titers in the brains of mice infected with A59-DE-HE were initially compared to mice infected with the parental A59 or A59-DE-CAT at 6 days p.i. Based on the survival of most mice infected with A59-DE-HE, reduced viral replication in the CNS was anticipated. IL-6 mRNA was also increased in the CNS of mice infected with A59-DE-HE virus (Fig. 5B) ; however, no differences were detected in the liver between the two groups.
cord-267718-t47i8hui	2017	An evolutionary rate of 2.61 × 10(−6) nucleotide substitutions per site per day was estimated, dating the most recent common ancestor of PPRV China 2013–2014 strains to early August 2013. Transmission network analysis revealed that all the virus sequences could be grouped into five clusters of infection, suggesting long-distance animal transmission play an important role in the spread of PPRV in China. Here we present the first intra-epidemic analysis of PPRV genome by studying viruses from 25 farms infected during the 2013-2014 PPR outbreaks in China. In this study, we constructed the transmission pathway of the spread of PPR virus basing on the fulllength genome sequences and identified five clusters of infections. Although more than 200 infected farms were reported during 20132014 PPRV epidemic in China, only 25 of them were full-genome sequenced and analyzed in this study. Full genome sequence of a peste des petits ruminants virus (PPRV) from Ghana
cord-268139-tgpsu4qz	2005	
cord-268341-103xf3dw	1997	the plaque size and pathogenesis similar to the parental During JHMV infection of the CNS there is an abrupt suckling mouse brain pool of JHMV originally described increase in mRNA encoding interleukin-1 (a and b), ILby Weiner (1973) and produces a lethal encephalomyeli-6, tumor necrosis factor (TNF)-a, and interferon (IFN)-g, tis with minimal demyelination apparent at the time of at the time of maximal decrease in virus replication and death. Similar of mice through Day 5 postinfection, consistent with the to the kinetics of IFN-g, TNF-a mRNA increased until rapid accumulation of both NK and T cells in the CNS of death of lethally infected mice. Similarly, the adoptive transfer at the time most lethally infected mice were about to succumb to infection (Day 7), there was no difference in the of virus-specific CD4 / T cells to JHMV-infected mice demonstrates that some clones protect via reducing viral peak levels of IL-10 mRNA between the two groups.
cord-268416-8hw80qx8	2018	While screening for ADP-ribosylated proteins during coronavirus (CoV) infection, we detected a ~55 kDa ADP-ribosylated protein in mouse hepatitis virus (MHV)-infected cells and in virions, which we identified as the viral nucleocapsid (N) protein. To identify potential targets of the CoV macrodomain, we analyzed infected cells for changes in ADP-ribosylation patterns utilizing antibodies specific for ADPr. We focused on cells infected with a murine CoV, mouse hepatitis virus (MHV). If the macrodomain was indeed removing the ADPr from the N protein, we would expect to see increased N protein ADP-ribosylation in cells infected with mutant virus compared to wild-type infected cells. To determine if N protein expressed in the absence of CoV infection could be ADP-ribosylated in cell culture, we transduced Vero cells with VEEV replicon particles (VRPs) encoding the MERS-CoV N protein or control GFP at different MOIs .
cord-268467-btfz6ye8	1989	The 3′-noncoding region of the genome contains an 11-nucleotide sequence, which is relatively conserved throughout the Coronavirus family and lends support to the theory that this region is important for the replication of negative-strand RNA. This result suggested that the HCV229E subgenomic mRNAs possess a nested-set structure similar to other coronaviruses and that A34 represented a cDNA clone of either the 3''-end of the genomic RNA or the leader sequence. The 3''-noncoding region contains the sequence TGGAAGAGCCA, 75 nucleotides from the 3''-end (Fig. 4) which is relatively conserved among coronaviruses and is found at approximately the same location in all of these viral genomes (Kapke and Brian, 1986; Skinner and Siddell, 1984; Armstrong et a/., 1983; Lapps et al., 1987; Kamahora et a/., 1988; Boursnell et al., 1985) ( Table 1) . Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3''end of the viral mRNA leader sequence
cord-269094-6aka052v	2007	
cord-269193-a647hwu9	1991	Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. The viral RNAs have been shown to encode information in the negative-sense (Clerx et al., 1983; Fuller et al., 1987; Freedman-Faulstich and Fuller, 1990) and it was previously shown that the Dhori nucleoprotein (encoded by RNA segment 5) shares conserved amino acid sequences with the influenza A, B, and C virus nucleoproteins (Fuller et al., 1987) . The PBl polymerase proteins are the most highly conserved among the proteins of the influenza A, B, and C viruses (Yamashita et a/,, 1989 ) and they are most likely required for nucleotide addition during viral RNA synthesis (Braam et al., 1983) .
cord-269204-kajws5xo	2008	To investigate whether EAV cell entry proceeds via endocytic uptake we first studied the involvement of clathrin-coated pits in EAV internalization using a BHK cell line that can be induced to express antisense RNA of the clathrin heavy chain (CHC) causing a selective block in clathrin-dependent endocytosis (Iversen et al., 2001) . In contrast to EAV, neither concanamycin A nor bafilomycin A1 nor monensin treatment of BHK-21 cells did affect SV5 mediated plaque formation (Fig. 3 ) consistent with the fact that infection by Parainfluenza viruses does not require a low pH compartment (Lamb and Kolakofsky, 2001) . To explore whether proteases of the late acidic compartments may play a role in fusion activation of EAV, we measured infection of BHK-21 cells upon incubation with leupeptin and E64d, which have been shown to inhibit acidic proteases in the endosomal compartment.
cord-269419-68kja6bg	2013	title: Fully human broadly neutralizing monoclonal antibodies against influenza A viruses generated from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient In this study, we used the full-length HA protein from the 2009 pandemic H1N1 influenza virus to raise fully human neutralizing mAbs. We obtained 19 monoclonal antibodies from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient and confirmed that all 19 of the monoclonal antibodies recognized the lysates of both the pandemic virus and the recently circulating seasonal H1N1 influenza virus. Interestingly, we found that most of the monoclonal antibodies, including the seven neutralizing mAbs, bound to the HA stem region (HA2), which is relatively conserved among different influenza A virus strains. These findings indicate that a broad cross-subtype neutralizing antibody response targeting the HA stem region exists in individuals vaccinated against 2009 pandemic H1N1 influenza and that these broadly reactive memory B cells may be important for protecting humans from infection with different influenza A viruses.
cord-269862-krcu3hfa	2009	
cord-269866-3tpyj04y	1992	We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera.
cord-269986-jdcw59r2	2009	
cord-270487-m770a1rl	1991	
cord-270534-ebkwv4zo	2018	title: Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model One of these candidates, MV vac2 -MERS-S(H) (Malczyk et al., 2015) , is based on the measles virus (MV) vaccine platform technology (Mühlebach, 2017) , and encodes the MERS-CoV spike protein (S) as an additional antigen in the backbone of recombinant MV vac2 (del Valle et al., 2007) resembling vaccine strain Moraten that is authorized and in use in the US since 1968. (G) Secretion of IFN-γ after antigen-specific re-stimulation of splenocytes harvested 32 days post prime immunization and after co-culture with JAWSII (left) or DC2.4 (middle) dendritic cells transgenic for MERS-N (black) or untransduced controls (NC, white). To assess the capacity of the different MV vac2 -MERS-S(H) vaccine preparations to induce MERS-CoV S-specific cellular immune responses, splenocytes of mice, which had already been tested for humoral responses ( Fig. 2A) , were isolated and analyzed 49 days after immunization for antigen(Ag)-dependent IFN-γ secretion using ELISpot assay.
cord-270586-ohs8z91m	1997	
cord-270814-krw8zmr5	1997	
cord-270929-utn21ce1	2006	
cord-271359-dpa8zzc3	1996	
cord-271526-14nfqusv	1997	To determine the specificity of the nucleocapsid pro-RNA-protein complexes (Fig. 3, lanes 8-10 and 12) , tein-Ps180 RNA interaction in UV cross-linking assays, clearly indicating that the observed supershift was not competition experiments were performed. This interaction was studied by gel retardation and UV Lysates were prepared from the virus peak fractions (pcross-linking assays using an RNA probe containing the lysate) and from the gradient bottom fractions (b-lysate; 69-nt Ps and the N protein from MHV-A59 infected cell negative control). A structural model for coronaviruses was flanked by non-MHV sequences could confer specific proposed, in which a spherical core, composed of a combination of N and M proteins, was present in addition to encapsidation to a heterologous RNA in MHV infected INTERACTION BETWEEN NUCLEOCAPSID PROTEIN AND PACKAGING SIGNAL of a murine coronavirus in the absence of helper virus.
cord-271763-cual2qv4	1990	
cord-272045-v1wt5t7m	2006	
cord-272050-0u62j7nj	2008	In contrast, cis-preferential function of the viral encoded proteins or a coupling between translation and replication has been reported for several viruses, including Alfalfa mosaic virus (AMV) (Neeleman and Bol, 1999; van Rossum et al., 1996) , Clover yellow mosaic virus (CYMV) (White et al., 1992) , Bovine coronavirus (Chang et al., 1994) , Cowpea mosaic virus (van Bokhoven et al., 1993) , Poliovirus (Hagino-Yamagishi and Nomoto, 1989; Johnson and Sarnow, 1991; Novak and Kirkegaard, 1994) , Turnip crinkle virus (TCV) (White et al., 1995) , Tobacco etch virus (Mahajan et al., 1996; Schaad et al., 1996) , Tobacco mosaic virus (TMV) (Lewandowski and Dawson, 2000) , Tomato bushy stunt virus (TBSV) (Oster et al., 1998) , Turnip yellow mosaic virus (TYMV) (Weiland and Dreher, 1993) , and Rubella virus (Liang and Gillam, 2001) . cis-Acting core RNA elements required for negative-strand RNA synthesis and cap-independent translation are separated in the 3¢-untranslated region of Red clover necrotic mosaic virus RNA1
cord-272051-arz8r204	2011	
cord-272260-88l9bq4i	2005	
cord-272437-gvzfl8c3	2020	title: Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus Avian coronavirus infectious bronchitis virus (IBV) is an important pathogen threatening poultry production worldwide. Our findings demonstrate that the replicase 1a gene of avian coronavirus IBV is a determinant of pathogenicity. In this study, we used an IBV reverse genetics system based on virulent strain Fig. 2. Recombinant live attenuated avian coronavirus 431 vaccines with deletions in the accessory genes 3ab and/or 5ab protect against infectious 432 bronchitis in chickens attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine S gene and 5a accessory gene 455 are responsible for the attenuation of virulent infectious bronchitis coronavirus
cord-272871-gu9ptt9y	1991	Abstract A small group of 1.2-kb RNAs present on polyribosoes from clover yellow mosaic virus (CYMV)-infected tissue contains sequences from the genomic RNA (gRNA) of CYMV and is encapsidated by CYMV coat protein. Figure 2 shows Northern blots of polyribosomal RNA extracted from CYMV-infected tissue containing the 1.2-kb RNAs. The 7.0-kb gRNA is identified by all probes (Fig. 2 , lanes a, c, e, g, i, and k; probes 1 to 6), but the 1 .O-kb sgRNA encoding coat protein hybridizes only to probes corresponding to the 3'' region of the gRNA (Fig. 2 , lanes i and k; probes 5 and 6). The majority of the sequence of the prototype 1.2-kb RNA (Fig. 4) and of additional 1.2-kb RNAs is identical WHITE, BANCROFT, AND MACKIE with the corresponding region of CYMV gRNA reported by Sit et al.
cord-272925-xag1yaie	2009	
cord-273246-4s54jrww	2014	title: An infectious RNA with a hepta-adenosine stretch responsible for programmed −1 ribosomal frameshift derived from a full-length cDNA clone of Hibiscus latent Singapore virus In HLSV, a À 1 PRF product, 108 kDa protein, was still detected using transcripts derived from BspHI digested pHLSV-7A, in which the far downstream HLSV sequence was cut off (Fig. 2C , fourth lane from the right). We report here the construction of HLSV biologically active full-length cDNA clones and the identification of a heptaadenosine stretch in HLSV genome as a slippery sequence responsible for À 1 PRF, independent of its downstream pseudoknot structure and the far downstream RNA sequence in vitro. Since monotonous runs of nucleotides can also cause À 2 or þ 1 PRF (Brierley et al., 1992) , we noticed that in the in vitro translation products using HLSV-8A transcripts, a 78 kDa protein was detected (Fig. 2C , first lane from the right).
cord-273379-w8vy5rl8	2000	RNase protection assays using the purified genome-length RI and two probes, which corresponded to the 5′ 300-nt region of mRNA 6 and to the same region of mRNA 7, showed the presence of nascent leader sequence-containing subgenomic mRNAs in the genome-length RI. We purified genome-length RI without contamination of any detectable level of MHV subgenomic mRNAs. We used RNase protection assays to look for nascent subgenomic mRNAs containing the leader sequence in the genome-length RI. If leader-sequence-containing subgenomic mRNA 6 elongates on the genome-length RI, then the RNase protection assay using probe 1 and purified radiolabeled genome-length RI should produce a radiolabeled 300-nt-long RNA fragment (300-nt fragment) that corresponds to the 5Ј-end 300 nt of nascent mRNA 6 (see Fig. 3A ). RNase A treatment of the gel-purified genome-length RI produced RF 1 (Fig. 2B) , and the RNase protection assay demonstrated the presence of nascent leader-sequence-containing subgenomic mRNAs in the genome-length RI.
cord-273487-nfgjz6f9	2012	
cord-273745-mwjh5se7	2014	
cord-274122-n9jnu2ah	2014	
cord-274172-3dctmmfe	1978	To investigate the replication of measles in the other non-neural and neural continuous cell lines, monolayer cultures were inoculated at 32.5" and examined for cytopathology, virus production, and development of infectious centers. Fol-With vaccinia virus, combined cell-associResults from these studies focus attention on three salient findings: (1) The strains of measles and mouse hepatitis viruses used can readily become established in a persistent form of infection in cell lines of neural and non-neural origin; (2) almost invariably when the infection is of the persistent type, virus replication becomes thermosensitive due to unknown factors under host control; the virus progeny from persistent infections are themselves not thermolabile; and (3) among the many cell types tested a rat RN2-2 Schwannoma has the unique ability to discriminate between the prototype MHV, and the neurotropic variant, JHM, supporting the persistence of only the latter.
cord-274424-juj71nc5	1991	
cord-274480-aywdmj6o	2014	Middle East respiratory syndrome coronavirus (MERS-CoV) infects host cells through binding the receptor binding domain (RBD) on its spike glycoprotein to human receptor dipeptidyl peptidase 4 (hDPP4). Previously, we have generated a panel of MERS-CoV mutant RBD proteins at the residues D539, Y499, D510, E513, L506, W553 and V555 to characterize their impacts on binding activity to hDPP4 and the entry efficiency into target cells. To study the impacts of the substitutions of the critical residues on hDPP4 described above on the interaction between MERS-CoV RBD and hDDP4, we determined the binding efficiency between these two proteins by employing SPR technique. To further study the importance of the critical residues on hDPP4 on viral entry, we measured the entry efficiency of pseudovirus into COS7 cells expressing the wide-type and mutant forms of hDPP4. These results are consistent with our findings and suggest these residues play an important role in RBD binding and viral entry, and determining the tropism to MERS-CoV infection.
cord-274673-tjzlssal	1989	authors: De Groot, Raoul J.; Van Leen, Robert W.; Dalderup, Mieke J.M.; Vennema, Harry; Horzinek, Marian C.; Spaan, Willy J.M. title: Stably expressed FIPV peplomer protein induces cell fusion and elicits neutralizing antibodies in mice Abstract We have established bovine papilloma virus (BPV)-transformed mouse C127 cell lines that synthesize the peplomer protein of the feline infectious peritonitis virus (FIPV) strain 79-1146. Mice immunized with whole lysates of the transformed cells produced FIPV-neutralizing antibodies as shown by plaque reduction. Mammalian cell lines expressing the FIPV peplomer gene would provide a convenient source of protein to dissect the role of E2 in FIP. It is shown that the expression product induces fusion of FIPV-permissive feline cells and is immunogenic in mice. (b) Glyoxal-denatured RNA extracted from noninduced (lane 2) and heat-shock-induced (lane 3) RM(-)I 7 cells was separated on 0.8% agarose gels, transferred to a nylon membrane, and hybridized to a nick-translated 4.5-kbBamHl fragment containing the complete FIPV E2 gene.
cord-275234-t6e7vr9y	1991	
cord-275348-jna496x7	2008	A SARS vaccine based on a live-attenuated vesicular stomatitis virus (VSV) recombinant expressing the SARS-CoV S protein provides long-term protection of immunized mice from SARS-CoV infection (Kapadia, S.U., Rose, J. We found that the vaccine given intramuscularly induced a neutralizing antibody response to SARS-CoV that was approximately ten-fold greater than that required for the protection from SARS-CoV infection, and significantly greater than that generated by the replication-competent vector expressing SARS-CoV S protein given by the same route. In order to evaluate this vector as a SARS vaccine candidate, we also developed a SARS-CoV neutralization assay using a pseudotyped VSV recombinant expressing a green fluorescent protein. SARS-CoV neutralizing antibody titers of these sera were determined by incubating VSVΔG-EGFP/SΔtail-HA virus with serial dilutions of these sera, and the virusserum mixtures were transferred to a monolayer of Vero E6 cells.
cord-275403-g4rohhtt	2002	To examine characteristics of putative nonstructural proteins (nsp) encoded in ORF1b, which have been identified by nucleotide similarity to domains of equine arteritis virus, defined genomic regions were cloned and expressed in the pRSET expression system. As initial proof of helicase-like activity, experiments were performed to test the ability of purified PRRSV-14 nsp10 protein to hydrolyze radiolabeled ribonucleotides in the presence or absence of polyribonucleotides. To further analyze the predicted helicase activity of the PRRSV nsp10 protein, experiments were performed using duplex substrates prepared with synthetic oligonucleotides containing single-strand regions at the 3Ј or 5Ј ends and short duplex regions (21 and 24 bp). The 5Ј-to-3Ј orientation of the unwinding activity of the PRRSV helicase was further confirmed in experiments using substrates prepared with in vitro transcribed RNA that contained singlestrand regions at the 5Ј end of both strands and duplex regions of 67 bp (5Ј5ЈDuplex #1) and 85 bp (5Ј5ЈDuplex #2), as shown in Fig. 9B .
cord-275664-qbafkxtr	2009	
cord-275993-isff6lp2	2004	
cord-276034-a8pixbuc	2005	
cord-276358-so390gp4	2015	
cord-277838-931sco95	2003	
cord-278578-vq5fy8m5	2017	In this study, we demonstrate that the fully functional HCoV-OC43 E protein (harboring specific TMD and PBM) is critical in infectious virus production and dissemination in epithelial and neuronal cell cultures and in the murine CNS and that it is a determinant of neurovirulence, a first demonstration for this coronavirus species. However, in these primary cultures, low levels of infected cells were visualized by immunofluorescence (IFA) where we detect the viral S protein, suggesting that infection was possible even for the complemented rOC/E-Stop virus but that production of new infectious progeny and eventual propagation were severely inhibited compared to wild type virus (Fig. 2C ). Infection of human LA-N-5 cells and mixed primary cultures of mouse CNS cells showed a similar virus production kinetic Infectious viral titer differences observed between experiments, revealed, by sequencing (G), the appearance of reversions at the position in the E gene where a stop codon was introduced are indicated by bold and underline.
cord-279346-7del8d2p	2007	
cord-279432-aik5bo6o	1989	
cord-279813-mrei5kih	2017	authors: Temeeyasen, G.; Sinha, A.; Gimenez-Lirola, L.G.; Zhang, J.Q.; Piñeyro, P.E. title: Differential gene modulation of pattern-recognition receptor TLR and RIG-I-like and downstream mediators on intestinal mucosa of pigs infected with PEDV non S-INDEL and PEDV S-INDEL strains The aim of this study was to investigate the differential gene modulation of pattern recognition TLR and RIG-I-like receptors and downstream mediators on the intestinal mucosa of neonatal pigs infected with PEDV non-S-INDEL and PEDV S-INDEL strains. We evaluated whether the differential modulatory effect observed in PRRs and downstream mediators in response to infection with the PEDV S-INDEL versus the non-S-INDEL strain was also translated into a differential modulation in the expression of gene coding for pro-inflammatory cytokines and type I interferons. Changes in TNF receptor associated factor (TRAF) 6 and interferon regulatory factor 7 (IRF7) genes mRNA expression induced by porcine epidemic diarrhea virus (PEDV) non S-INDEL and PEDV S-INDEL strains in intestinal mucosa (A-B).
cord-279924-09uwhxs9	2014	In this study, we demonstrate that cultured murine NPCs are infected by the neurotropic JHM strain of mouse hepatitis virus (JHMV), which induces acute encephalomyelitis and chronic demyelination when injected intracranially into immunocompetent mice. We co-cultured virus-specific CTLs at diminishing effectorto-target (E:T) ratios with NPCs pulsed with the immunodominant CD8 peptide specific for JHMV spike (S) glycoprotein spanning amino acids 510-518 (S510-518), and treated with IFN-γ to induce MHC class I expression. To confirm the role of IFN-γ as the major cytokine contributing to suppression of JHMV replication in infected NPC cultures, monoclonal antibody blockade against the IFN-γ receptor was performed on NPCs before and during treatment with virusspecific CD4þ T cell enriched media. Impaired expression of MHC class II following IFN-γ-treatment of infected NPCs may be a mechanism employed to subvert detection by infiltrating virus-specific CD4þ T cells.
cord-280287-t7uozjml	2004	We show that Ad41 infectivity is not diminished by acid exposure, a condition limiting the infectivity of the respiratory Ad. This feature can be attributed to a large extent to the global basic charge of enteric Ad virions and to the stability of Ad41 fiber, a viral protein mediating virus attachment. During cell attachment, the distal C-terminal globular head domain of the fiber protein interacts with the primary receptor, which for some human Ad serotypes is the coxsackievirus and adenovirus receptor (CAR) (Bergelson et al., 1997; Roelvink et al., 1998) . In the first attempt to understand the survival mechanism of the human enteric Ad41 under acid conditions of the stomach, we compared the predicted pI values of external structural proteins of different Ad serotypes (Table 1) .
cord-280795-wtrt13ij	2007	As a step toward better understanding the relationship between activities and structures of the helicase-like domain of BaMV replicase, we set out to investigate the importance of each signature motif to its NTPase and RNA 5′-triphosphatase activities by mutational and kinetic analyses. The apparent K i value of AMPPNP in inhibiting RNA 5′-triphosphatase activity The enzymatic activity was determined at 20°C by enzyme-coupled assay in 1 ml solution that contained 10 pmol enzyme, 0.1 to 3 mM NTP and other buffer components as described under Materials and methods except that the amounts of pyruvate kinase were increased up to 50, 75 and 300 U for GTPase, UTPase and CTPase assay, respectively, to assure the rate of NTP hydrolysis being the limiting step within the coupling reaction. The helicase-like domain of plant potexvirus replicase participates in formation of RNA 5′ cap structure by exhibiting RNA 5′-triphosphatase activity
cord-280957-cdd6ngf1	2018	
cord-281237-asnpuami	1989	The effect of peptidyl chloroalkyl ketones on the activation of the fowl plague virus hemagglutinin by the proteases specific for paired basic residues has been investigated. When virions containing uncleaved hemagglutinin were incubated with lysates of uninfected cells, cleavage was completely inhibited by peptidyl chloroalkyl ketones containing paired basic residues at a concentration of 1 mM. When dibasic peptidyl chloroalkyl ketones were added to infected cell cultures, cleavage of hemagglutinin and multiple cycles of virus replication were inhibited at 10 mM. the hemagglutinins of the pathogenic avian influenza viruses have a cleavage site consisting of several basic amino acids which can be cleaved by endoproteases present in many cells (for review see Klenk and Rott, 1988) . Table 2 shows an experiment in which a cell lysate has been first incubated with AKR-CMK as an inhibitor and subsequently with chromogenic substrates containing also two basic residues at the cleavage site.
cord-281309-c9y7m5do	2013	We found that this HP-PRRSV strain caused extreme morbidity, as was seen in Asia, but novel to this study, resulted in up to 100x higher abundance of circulating virus when compared to VR-2332, caused extremely exacerbated thymic atrophy such that the thymus was often difficult to discern, and the host response was assessed in comparison to animals infected with strain VR-2332 for the first time by a swine protein array including 5 innate and 5 adaptive cytokines in serum, bronchoalveolar lavage fluid and lymph nodes. It was demonstrated that infection with a highly pathogenic strain of PRRSV elicited a significant elevation of all adaptive immunity cytokines measured in BALF, as well as a majority of these cytokines in serum and TBLN homogenates of the same groups of pigs.
cord-281820-oltqsd6n	2007	A highly neurovirulent mouse hepatitis virus (MHV) JHMV strain (wt) with receptor (MHVR)-independent infection activity and its low-virulent mutant srr7 without such activity were found to attach to MHVR-negative, non-permissive BHK cells. To identify the molecule that interacts with JHMV, we focused on heparan sulfate (HS) since it works as a receptor of a mutant MHV-rec1 that infects in an MHVR-independent fashion. To evaluate the infectivity of the attached virus, 50 nM of soMHVR was added to the culture of BHK cells inoculated with wt JHMV and srr7 and those cells were further incubated for 14 h at 37°C. Binding of JHMV to HS on the cell surface HS is the major glycosaminoglycan (GAG) found on most cells and was recently reported as an entry receptor for MHV-BHK, a strain that has an extended host range and infects MHVR-negative cells (de Haan et al., 2005) .
cord-282947-3hgku2e4	2017	title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 Through the construction of recombinant IBV expressing proteins 8a, 8b and 8ab encoded by SARS-CoV ORF8, we demonstrate that expression of 8b and 8ab enables the corresponding recombinant viruses to partially overcome the inhibitory actions of IFN activation to achieve higher replication efficiencies in cells. Compared to wild type and rIBV8a/b, however, rIBV8b and rIBV8ab were observed to replicate significantly better and express higher levels of N protein in cells stimulated by poly (I:C) (Fig. 2a) . In view of the central role of IRF3 in regulating IFN activation during virus infection, 8b and 8ab with Flag epitope-tagged to their Ntermini were co-expressed with Myc-tagged IRF3 (Fig. 3a) in Cos-7 cells using the vaccinia/T7 expression system (Anderson et al., 1996; Lim and Liu, 2001) for co-immunoprecipitation assays to determine if there is any physical interaction between the proteins.
cord-283035-tpqf458q	2009	
cord-283309-ovx5fzsg	2019	
cord-283998-whwksoxt	1977	Abstract A homogeneous RNA complex with a sedimentation coefficient of 70 S and an apparent molecular weight of approximately 6.1 × 106 was released from purified 32P-labeled, mouse-brain-derived OC-43 virus after treatment with 1% sodium dodecyl sulfate (SDS) for 15 min at 23°. This suggests that (a) extensive nicking of a large RNA molecule has occurred during viral growth, due to ribonucleases which are inactivated during phenol extractions; (b) heterogeneity for OC-43 RNA is not due to internal ribonuclease activity and fragments are held together by noncovalent linkages much weaker than those present in the 70 S retroviral RNA complex, or by small proteins; or, most probably, (c) a combination of extensive nicking and weak noncovalent linkages results in the heterogeneous denaturation products. The RNA of avian infectious bronchitis virus (IBV) was first described by Tannock (1973) , who obtained from purified virions a highly heterogeneous array of RNA fragments using a phenol-sodium dodecyl sulfate (SDS) extraction procedure.
cord-284581-fl2nt4ak	2019	title: Spike proteins of novel MERS-coronavirus isolates from Northand West-African dromedary camels mediate robust viral entry into human target cells A recent study showed that MERS-CoV found in North/West(Morocco) and West-African (Burkina Faso and Nigeria) dromedary camels are genetically distinct from Arabian viruses and have reduced replicative capacity in human cells, potentially due to amino acid changes in one or more viral proteins. Here, we show that the spike (S) proteins of the prototypic Arabian MERS-CoV strain, human betacoronavirus 2c EMC/2012, and the above stated African MERS-CoV variants do not appreciably differ in expression, DPP4 binding and ability to drive entry into target cells. We employed a previously described vesicular stomatitis virus (VSV)-based pseudotyping system to study MERS-S-driven host cell entry (Kleine-Weber et al., 2018 known to adequately model key aspects of the coronavirus entry process. Host cell entry driven by the S proteins of North/West-and West-African MERS-CoV isolates from dromedary camels is robust.
cord-284646-fhruiw23	2020	Vector competence experiments showed that Ae. aegypti could transmit SPONV when 70 exposed to bloodmeal titers that approximate physiological titers, while Cx. quinquefasciatus nonpregnant, mixed sex 6-to 11-week-old mice lacking type I interferon signaling (Ifnar1 -/-) Ar94 (this is the only strain used in these studies, so it will be referred to hereafter as 86 SPONV); or 10 2 PFU of the highly pathogenic African-lineage ZIKV strain DAK AR 41524 87 (ZIKV-DAK) (Jaeger et al., 2019) . Despite significantly higher maternal 141 viremia observed at 4 dpi with ZIKV-DAK-infected dams, the fact that resorption rates did 142 not significantly differ between the two groups indicates that both ZIKV-DAK and SPONV 143 have a propensity to harm the developing fetus that is independent of the amount of 144 replication in maternal blood. In contrast, ZIKV-DAK-and SPONV-inoculated dams displayed 221 varying degrees of placental pathology with severe effects predominantly observed in the 222 the labyrinth zone, including vascular injury involving maternal and/or fetal vascular spaces, 223 infarction (obstructed blood flow), necrosis, apoptosis, and hemorrhage (Fig. 4) .
cord-284707-72vx11aq	1988	For mouse hepatitis virus (MHV), one of the most extensively studied coronaviruses, there are seven species of MHV-specific mRNA present in infected cells, the largest of which is indistinguishable from virion RNA (Leibowitz et a/., 1981; Lai et a/., 1981; Spaan et a/., 1981) . In this paper we report the characteristics of a permeabilized cell system and demonstrate that it incorporates ribonucle-otide triphosphates into RNA molecules which appear identical to the virus-specific mRNAs synthesized in MHV-infected cells. Protease inhibitors and RNase inhibitors have both been reported to increase the RNA-dependent RNA polymerase activity present in extracts of West Nile virus-infected cells (Grun and Brinton, 1986) . The kinetics of the development of the MHV-specific RNA polymerase activity over the course of infection was determined in permeabilized cells. In this work we report the development and characterization of a permeabilized cell system for assaying MHV-specific RNA polymerase activity.
cord-284968-eymvj6k3	1985	Immunoprecipitation experiments performed with VZV-infected cells, pulse labeled with [3H]glucosamine in the presence of tunicamycin, suggest that O-linked oligosaccharide is present on the glycoprotein of gp 2. In order to investigate the effect of TM on the synthesis of VZV glycoprotein, infected cell cultures were labeled with rHlglucosamine for 18 hr, and cell extracts were immunoprecipitated with three kinds of monoclonal antibodies (cl 9, cl 8, and cl 12) which react with glycoproteins gp 2, gp 3, and gp 5, respectively (Okuno et a,?., 1983) . Next, when cell extracts were reacted with antibodies of cl 8, a band at 106K was seen at pulse labeling, and additional 116K and 64K (prominent) polypeptides were detected during chase (Fig. 2, lanes e, g) . Finally, when cell extracts in the absence of TM were reacted with antibody from cl 12, 49K (major) and 43K (minor) polypeptides from cell cultures of pulse labeling and 55K (major) and 94K (minor) polypeptides were observed during chase (Fig. 2, lanes i, k) .
cord-285869-jwflooop	2008	Here, we studied the role of a putative replicase anchor, nonstructural protein 4 (nsp4), in the assembly of murine coronavirus DMVs. We used reverse genetics to generate infectious clone viruses (icv) with an alanine substitution at nsp4 glycosylation site N176 or N237, or an asparagine to threonine substitution (nsp4-N258T), which is proposed to confer a temperature sensitive phenotype. Coronaviruses, such as mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) that causes severe respiratory illness in humans (Peiris et al., 2004; Stadler et al., 2003) , generate double membrane vesicles (DMVs), which are the sites of viral RNA synthesis (Baker and Denison, 2008; Goldsmith et al., 2004; Gosert et al., 2002; Snijder et al., 2006) . However, at the non-permissive temperature, DMV assembly and mitochondria morphology are disrupted in Alb ts6 icv-infected cells and viral replicase proteins partially localize with mitochondria.
cord-286060-92lazxd7	1983	Studies on the intracellular synthesis of MHV proteins by pulse-chase experiments have shown that the nucleocapsid protein, pp60, is a primary gene product (3, 12) . In addition, two-dimensional nonequilibrium isoelectric focusing of infected cell lysates indicated that the nucleocapsid protein was composed of multiple heterogeneously charged species which are homogeneous in size (1). In examining the kinetics of the appearance of JHMV proteins in infected DBT cells, we noted that the region of the gel which contains the pp60 protein also contained another protein of slightly lower molecular weight (Fig. 1A) . When infected cells were pulse-labeled with [%]methionine for 2 min and then chased with excess unlabeled methionine (20 m&Q for various lengths of time, only ~57 was detected within the pulse interval (Fig. 1B) .
cord-286121-ltaxmp3u	2009	In this study, we demonstrate that 9b protein is translated from bicistronic mRNA9 via leaky ribosome scanning and it is incorporated into both virus-like particles (VLPs) and purified SARS-CoV virions. The expression of 9b protein in SARS-CoV infected cells was confirmed by Western blot analysis with anti-9b monoclonal antibody. To confirm that 9b protein can be translated from an mRNA corresponding to the SARS-CoV subgenomic RNA9, the sequence encoding ORFN which contains ORF9b was cloned into the eukaryotic expression vector pCAGGS and transfected into 293T cells. As 9b protein is present in virions, it is advantageous to characterize the role of other SARS-CoV structural proteins in incorporation of 9b protein into VLPs. Cultures of 293T cells were transfected with the indicated plasmids, and pCAGGS vector was added to adjust the total amount of DNA to equivalent levels. 9b protein was immunoprecipitated by anti-9b polyclonal antibody from SARS infected FRhK-4 cell lysates in RIPA buffer, the mass spectrometry analysis of the corresponding gel slices detected a specific peptide that represents 9b protein.
cord-286232-jo24ia4s	2009	Derm cells by infectious virus recovery assay after viral internalization, suggesting that EHV-1 enters E. In HeLa and receptor-expressing CHO cells, infectious entry of HSV requires trafficking of the virus to an acidic intracellular compartment, phosphatidylinositol 3-kinase activity, glycoprotein D (gD) receptors, as well as viral gB, gD, and gH-gL (Nicola et al., 2003; Nicola and Straus, 2004) . With the use of ultrastructural analysis, we have previously suggested that EHV-1 enters equine brain microvascular endothelial cells (EBMECs) via endocytosis (Hasebe et al., 2006) . Localization of EHV-1 and caveolae during viral internalization Caveolar endocytosis has emerged as a route of entry for several viruses including simian virus 40 (SV40) (Anderson et al., 1996) , mouse polyomavirus (Richterová et al., 2001; Gilbert et al., 2003; Gilbert and Benjamin, 2004) , echovirus (Marjomäki et al., 2002) , human papillomavirus type 31 (Bousarghin et al., 2003; Smith et al., 2007) , human polyomavirus BK (BKV) (Eash et al., 2004) , and species C human adenovirus (Colin et al., 2005) .
cord-287620-vuvgi8xx	2006	HCoV-OC43, harvested from a patient with an upper respiratory tract infection, was originally isolated after passage in human embryonic tracheal organ cultures; this virus caused neurological disease after only one passage in suckling mice and encephalitis within 2-4 passages (McIntosh et al., 1967) (termed HCoV-OC43 NV ). For example, Talbot and co-workers showed, using the mouse-adapted virus after passage in tissue culture cells (termed HCoV-OC43 QUE herein;) that mice infected intranasally with 10 4 -10 5 TCID 50 developed encephalitis if inoculated 8 days but not 21 days postnatally (Jacomy and Talbot, 2003) . HCoV-OC43 QUE was passaged 5-6 times in tissue culture prior to use in mice (personal communication, Dr. Pierre Talbot, INRS-Institut Armand-Frappier, Laval, Quebec) and consequently may be less virulent than virus isolated directly from infected suckling mouse brains. As shown in Fig. 5 , immunocytochemical staining for viral antigen revealed that the tissue culture-adapted virus infected hamster, pig, human, mouse, monkey and cat cells, but not FRT rat epithelium cells.
cord-287777-ogs4mq0v	2007	They include the potential recruitment of DUBs for the stabilization of β-catenin in Epstein-Barr virus (EBV)-infected B cells (Ovaa et al., 2004; Shackelford et al., 2003) , and the specific targeting of the cellular DUB ubiquitin-specific protease 7 (USP7) by the Epstein-Barr nuclear antigen 1 (EBNA1) and the herpes simplex virus type 1 (HSV-1) regulatory protein ICP0 (Everett et al., 1997; Holowaty and Frappier, 2004) . The possibility that modulation of deubiquitination is, nevertheless, a more common viral strategy has gained support by the recent in vitro demonstration of deubiquitinating activities for three viral enzymes: the adenovirus protease adenain (Balakirev et al., 2002) , the papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus (SARS-CoV) (Barretto et al., 2005; Lindner et al., 2005) , and a protease domain contained in the N-terminal fragment of the large tegument protein UL36 (UL36 USP ) from several herpesviruses, namely, HSV-1, EBV, and mouse and human cytomegalovirus (MCMV and HCMV) Schlieker et al., 2005; Wang et al., 2006) .
cord-288669-46tkedw7	2006	P129-ΔE-transfected cells however produced virion particles in the culture supernatant, and these particles contained viral genomic RNA, demonstrating that the E protein is essential for PRRSV infection but dispensable for virion assembly. Our study suggests that the PRRSV E protein may function as a viroporin in the virion envelope that facilitates uncoating of the virus in order to release the genomic RNA into the cytoplasm for subsequent replication. At 24 h postinoculation, Marc-145 cells were fixed, and virus infection was examined by immunofluorescent staining with N-specific MAb. Marc-145 cells inoculated with a culture fluid from cells cotransfected with P129-ΔE and E gene showed bright N-specific fluorescent signal, indicating that the P129-ΔE replication may be rescued by trans-complementation of the E protein (Fig. 2C ). Strand-specific RT-PCR experiments were carried out and demonstrated that PRRSV-infected Marc-145 cells produced reduced levels of positive-sense genomic RNA at 2 days post-infection in the presence of the drugs chloroquine, amantadine and verapamil (Fig. 5A, upper panel) .
cord-289045-vft163v0	2005	Cell lines from host species that are normally resistant to MHV, porcine coronavirus [transmissible gastroenteritis virus (TGEV)] or human coronavirus strain 229E (HCoV-229E) are rendered susceptible to infection by transfection with cDNA encoding the specific coronavirus receptors mCEACAM1a, porcine aminopeptidase N (pAPN) (Delmas et al., 1992; Dveksler et al., 1991; Yeager et al., 1992) . Since some of the aa substitutions in the RBD of S were chosen to reflect residues found in S330 of related rat, bovine or human coronaviruses in group II (Fig. 1A) , we examined the ability of the SA59 B, S33R A, S33G C, T62S A, T62A A, L65H C, L65A C, L79M/T82M A, L79A/ T82A B, Y162F A, K183R A and K183G A viruses to infect non-murine cells lines that are normally resistant to MHV-A59 infection.
cord-289152-w5ynbewh	2005	In porcine reproductive and respiratory syndrome virus (PRRSV)-infected cells, NF-κB activation was characterized by translocation of NF-κB from the cytoplasm to the nucleus, increased DNA binding activity, and NF-κB-regulated gene expression. Taken together, these results demonstrated that PRRSV induces nuclear translocation of NF-nB followed by increased DNA binding activity of NF-nB both in MARC-145 cells and PAM cultures. To determine if NF-nB activation by PRRSV was dependent on InBa degradation in MARC-145 cells, the NF-nB pathway was blocked by using an adenovirus vector expressing a dominant negative form of InBa (Ad-InBaDN) which lacks both constitutive (Barroga et al., 1995) and inducible (Brown et al., 1995) phosphorylation sites. This study showed that PRRSV infection resulted in increased nuclear translocation of NF-nB and increased DNA binding activity both in MARC-145 cells and PAM cultures.
cord-289248-6mx4o0eb	2018	These two mutants grew to high titer in Vero cells, were genetically stable, and were significantly more attenuated in vitro and in vivo compared to the parental rMV-Hu191 vaccine strain. We next compared the replication kinetics of the rMV-Hu191 mutants and the parental virus in Vero cells in the time course of 120 h after infection (Fig. 5 ). These data suggest that rMVs carrying mutations in the SAM binding site were more attenuated in Vero cells than the parental MV vaccine strain. In this study, we successfully generated two recombinant measles viruses with amino acid substitutions in the SAM binding site of L protein and examined the effects of these mutations on viral replication, safety, and immunogenicity. We generated two recombinant MV-Hu191 carrying mutations in the SAM binding site, which not only grew to high titer in Vero cells and were genetically stable but also were significantly more attenuated and immunogenic compared to the currently used Chinese MV vaccine strain.
cord-289712-w1y0lc5c	1984	
cord-289991-wx4rsr4g	2014	To assess whether RV modulates expression of CDK inhibitors to regulate cell cycle, whole cell lysates or total RNA of MA104 cells infected with either SA11 (3 moi) or mock infected were subjected to either immunoblotting or real time PCR with p15, p21, p27 specific antibodies or primers, respectively. This results in its inability to bind to and prevent nuclear translocation of E2F ( Fig. 2A) , since E2F in nucleus can activate transcription of several downstream genes like thymidine kinase, thymidine synthase and dihydrofolate reductase (Fig. 2C) , which promote cell cycle progression and DNA replication, nuclear accumulation of E2F by RV during early infection facilitates G 1 /S restriction point modulation in favor of RV replication. CaMKI has been shown to induce G 1 to S phase transition (Skelding et al., 2011) , concurrently activation of CaMKI (phospho CaMKI) was also observed during early RV infection (2-6 hpi) which correlated with increased CaM expression and accumulation of cells in S phase (Fig. 4A) .
cord-290231-4m9lj0uq	1992	Abstract To study the role of the precursor to the membrane protein (prM) in flavivirus maturation, we inhibited the proteolytic processing of the Murray Valley encephalitis (MVE) virus prM to membrane protein in infected cells by adding the acidotropic agent ammonium chloride late in the virus replication cycle. By using monoclonal antibodies (MAbs) and protease maps, we previously demonstrated that the E glycoprotein of tick-borne encephalitis (TBE) virus undergoes an irreversible conformational change, predominantly in the epitopes of domain A, at mildly acidic pH . To understand the role of prM protein in virus maturation and its interaction with the E glycoprotein, we investigated the effect that ammonium chloride had on MVE viruses grown in C6/36 mosquito cells. The reactivities of MAbs defining nine distinct epitopes on the MVE E glycoprotein were compared on M-and prMcontaining viruses using supernatants of ammonium chloride-treated or untreated virus-infected C6/36 cells.
cord-290282-oxyzndsj	2003	Transmissible gastroenteritis coronavirus (TGEV) contains eight overlapping genes that are expressed from a 3′-coterminal nested set of leader-containing mRNAs. To facilitate the genetic manipulation of the viral genome, genes were separated by duplication of transcription regulating sequences (TRSs) and introduction of unique restriction endonuclease sites at the 5′ end of each gene using an infectious cDNA clone. All the rTGEV viruses conserved the modifications engineered in the cDNAs (data not shown), indicating that the ORF separation and the insertion of unique endonuclease restriction sites between genes were stably maintained in the rTGEV genomes. Interestingly, analysis of viral growth in the gut of infected piglets showed a 100-to 5000-fold reduction of recombinant viruses containing one or more restriction sites in relation to the rTGEV-wt virus ( Fig. 5D and E) .
cord-290640-kh2t0kfz	2000	Abstract Gene 3b (ORF 3b) in porcine transmissible gastroenteritis coronavirus (TGEV) encodes a putative nonstructural polypeptide of 27.7 kDa with unknown function that during translation in vitro is capable of becoming a glycosylated integral membrane protein of 31 kDa. In the virulent Miller strain of TGEV, ORF 3b is 5′-terminal on mRNA 3–1 and is presumably translated following 5′ cap-dependent ribosomal entry. Here we report that, whereas mRNA 3 has a sequence predicting leaky scanning for the translation of ORF 3b by the model of Kozak (1989) , experimental results with mutant constructs suggested downstream entry of ribosomes might also be used. To test by in vitro translation whether the 27.7-and 20-kDa gene 3b products (O''Connor and Brian, 1999) are synthesized when ORF 3b is positioned downstream of ORF 3a (beginning at base 337) on synthetic transcripts, uncapped transcripts of pORF3a-3b-4 DNA linearized at the BamHI site 50 nt downstream from the stop codon of gene 4 (Fig. 1C) were translated in either wheat germ extract or rabbit reticulocyte lysate.
cord-290883-r2744fb3	1995	The antisera induced in swine by the Ad5 recombinants expressing the amino-terminal 26% of the spike protein (containing sites C and B) or the full-length spike protein, when mixed with a lethal dose of virus prior to administration to susceptible piglets, delayed or completely prevented the induction of symptoms of disease, respectively. Alternatively, S gene ces are determined rather than titers since in the first fragments were removed from the original plasmid or procedure virus-antibody mixtures are evaluated in the from pSV2X3-TS vectors without SV-40 Pr signal, or withplaque assay without further dilution of the antibody, proout both Pr and polyadenylation sequences, using the viding highly reproducible results and information about restriction endonucleases indicated in Fig. 1 . Infectious Ad-TS recombinants expressing S protein fragments were generated by cotransfecting 293 cells with pFG144K3-TS or pAB14-TS (which carry S gene sequences from TGEV and pFG173 plasmids).
cord-290993-bsnja161	2004	
cord-291192-wm2eyaam	2014	Transmissible gastroenteritis virus (TGEV) was engineered to express porcine reproductive and respiratory syndrome virus (PRRSV) small protein domains, as a strategy to improve heterologous gene stability. Recombinant TGEV (rTGEV) vectors have been engineered for dicistronic expression of heterologous genes, such as porcine reproductive and respiratory syndrome virus (PRRSV) GP5 and M proteins (Cruz et al., 2010) , or rotavirus VP2 and VP6, in which formation of rotavirus virus like particles (VLPs) in the cytoplasm of rTGEV infected cells was observed (Enjuanes et al., 2007) . Therefore, heterologous gene size reduction is a promising strategy to achieve stable expression in TGEV-derived vectors and in general in CoVs. This effect could be due to a decrease of the probability of non-homologous recombination in shorter sequences, or to the elimination of protein domains toxically affecting the host cell or rTGEV life cycle.
cord-291306-g9qmmugg	1992	It has long been known that the hemagglutinins activated by these enzymes have multiple lysine and arginine residues at theircleavage sites, and it has been shown that most of these basic amino acids are critical for cleavage activation (7). Comparison of the published hemagglutinin sequences of the pathogenic avian influenza-A-viruses of serotype H7 reveals a number of conserved amino acids upstream of the cleavage site, notably a series of arginine and lysine residues in positions -1 to -6 and two proline residues in positions -7 or -8 and in position -10 (Table 1) . To determine whether these conserved regions are important for the cleavability of the H7 hemagglutinin, we subjected a cDNA clone of the hemagglutinin of influenza virus AIFPV/Rostock/34 to site-directed mutagenesis at the cleavage site and from the panel of mutants obtained, we have selected two groups. In previous work, pathogenic variants with increased hemagglutinin cleavability could be obtained, when apathogenic avian influenza virus strains were adapted to non-permissive host cells (11, 9, 16) .
cord-291611-cfe8yujp	1991	title: Comparison of the nucleotide and deduced amino acid sequences of the S genes specified by virulent and avirulent strains of bovine coronaviruses Abstract The entire nucleotide sequences of the spike glycoprotein (S) genes of the highly virulent bovine coronavirus (BCV) strain BCV-LY138, the avirulent BCV-L9 and related Norden Vaccine (BCV-Vaccine) strains were determined using the polymerase chain reaction (PCR) to amplify cDNAs obtained by reverse transcription of viral RNA, and to produce single strand cDNAs for DNA sequencing. Substitutions of few amino acids in the putative fusogenic domains and two prolines at 507 and 567 in the antigenic domains may cause altered immunogenic and other functional properties of the S proteins specified by the virulent and avirulent BCV strains.
cord-292019-rfu0bkag	1998	We report on the immunological response elicited by two recombinant versions of the glycoprotein S from the swine-transmissible gastroenteritis coronavirus (TGEV) expressed in transgenic plants. Arabidoposis plants were genetically transformed with cDNAs constructs encoding either the N-terminal domain (amino acid residues 1–750) or the full-length glycoprotein S of TGEV, responsible for the neutralizing antibody induction against the virus, under the control of the cauliflower mosaic virus 35S (CaMV 35S) promoter. Mice immunized with leaf extracts from transgenic plants developed antibodies that reacted specifically with TGEV in ELISA, immunoprecipitated the virus-induced protein, and neutralized the virus infectivity. In this report, we show that full-length or the globular part (N-terminal domain) of TGEV spike protein (glycoprotein S) expressed in transgenic plants retained the antigenic properties and elicited neutralizing antibodies when used to immunize animals.
cord-292751-tk1oggi9	2020	Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. The previously reported viral zoonotic pathogens include SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS (Middle East respiratory syndrome coronavirus) [3, 4] , that can cause severe respiratory disease in human [5, 6] . SARS-CoV-2, a novel coronavirus (which causes COVID19) , has fast spread like a pandemic since its outbreak in Wuhan, China, in December 2019 [7] . Nowadays, Griffithsin, as an inhibitor of SARS and MERS spike, Remdesivir, favipiravir and ribavirin (nucleoside analogues), lopinavir/ritonavir (protease enzyme inhibitors) [61] , oseltamivir (neuraminidase inhibitors), anti-inflammatory drugs and EK1 peptide [62] , the clinical potential to be applied against the 2019-nCoV infection [67, 68] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan
cord-293248-8vtd9e4n	2010	Through the application of a molecular screening method targeting particle-associated nucleic acid (PAN), we recently described the detection and partial characterization of a novel enteric parvovirus in chickens. Initial analysis of this chicken-origin parvovirus (ChPV) revealed that it is a novel member of the Parvovirinae subfamily within the Parvoviridae, and led to the development of a specific molecular diagnostic test targeting the ChPV non-structural (NS) gene (Zsak et al., 2009) . Parvoviruses have been previously described in chickens based upon their morphology via electron microscopy and upon their genome size Kisary et al., 1984) , and enteric disease signs have been attributed to parvovirus-like particles detected in turkey intestinal tracts (Trampel et al., 1983) . The analysis includes comparisons to other members of the Parvovirinae that infect mammals and birds, including two novel turkey-origin parvoviruses (TuPV) recently sequenced using a similar molecular approach.
cord-293375-qcy56ui7	1992	coma-, nepo-, and potyviruses; coronaviruses; and flaviviruses (and their proposed relatives pestiviruses and hepatitis C virus.) Originally these domains were predicted to have proteolytic activity based on the presence of certain conserved amino acid residues and on the basis of protein-modeling studies (Bazan and Fletterick, 1989; Boege et a/., 1981; Gorbalenya et al., 1989; Hahn eta/., 1985) . Furthermore, we present data to show that none of the asparagine residues in the proteinase domain of Sindbis nsP2 that are conserved among alphaviruses are absolutely required for proteolytic activity, but that Trp-559, adjacent to His-558, is essential for function. We also examined the effect of changing Cys-525, one of the two remaining conserved cysteine residues in the C-terminal half of nsP2, to serine or arginine, as well as changing Ser-535, which is found in a domain of limited similarity to the active site serine of serine proteinases, to threonine.
cord-293635-36pmai6s	2004	The data shown in Fig. 2 indicate that CD4 + and CD8 + T cell infiltration into the CNS of infected CCL2 À/À and CCR2 À/À is dramatically reduced as compared to wild-type mice. In contrast to T cell trafficking, there was a similar reduction in the number of macrophages present within the brains in both CCL2 À/À and CCR2 À/À mice, indicating that both ligand and receptor are important in directing these cells into the CNS in response to MHV infection. This is consistent with an earlier study by our laboratory demonstrating that MHV infection of mice lacking CCL3 resulted in the retention of virus-specific cells in the CLN, and this was the result of impaired expression of chemokine receptors, including CXCR3 and CCR5 that greatly aids T cells in their ability to migrate to the brain (Trifilo et al., 2003) .
cord-293790-7hyelm88	2010	title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection To identify novel cellular factors that may play an essential role in HCV RNA replication, we have previously screened a human liver cDNA library for proteins interacting with the HCV NS5B RNAdependent RNA polymerase (RdRp). Here we report that ATG5, a protein required for the formation of DMV in embryonic stem cell (Mizushima et al., 2001) , specifically interacts with HCV NS5B. As a control, a panel of proteins (RAR-β, RAR-α, HCV core, and nonstructural protein: NS3 prot , NS3 hel , NS4A, and NS4B) cloned in the GAL4 DNA binding domain was tested for interaction with ATG5. A. Soluble yeast extracts containing NS5BΔ21 (N-terminal c-myc tag) and ATG5 (N-terminal HA tag) were incubated with different monoclonal antibodies and the immunoprecipitates were pulled down using protein A/G beads.
cord-294056-7e477y1x	1992	Previously, we have identified a transcription initiation site (for mRNA 2-1), which is more efficiently transcribed by viruses containing two copies of UCUAA sequence in the leader RNA than by those with three copies. To understand the mechanism of MHV mRNA transcription, we have attempted to determine whether the differential regulation of transcription initiation by leader RNA containing different UCUAA copy numbers is unique to mRNA 2-l. The analysis of several other recombinant viruses with different genome structures suggested that mRNA 3-l was synthesized only by viruses with a leader RNA containing three copies of UCUAA and gene 3 sequence derived from A59 but not JHM (10, 13). Using various primers representing sequences of different regions of gene 1 of the JHM strain of MHV (2) and a second primer representing the 5''-end of the leader RNA, we detected several PCR products which represented mRNAs initiated from various sites.
cord-294260-g410mavp	2011	Arrow, RNA3 start site at nt 2721 (Lindenbach et al., 2002) ; (D) Schematic of the RCNMV genome showing the relative positions of the in trans interacting RNA elements: the loop portion of a stem-loop in RNA2 (termed trans-activator or TA) and a complementary sequence in RNA1 (termed TA binding site or TABS) located just upstream from the initiation site for SG mRNA transcription (Guenther et al., 2004) ; (E) Representation of CLSV genome and the proposed AS2 and RS2 interaction during regulation of SG RNA2 synthesis (Xu and White, 2008) ; (F) Overview of the BYDV genome and the in cisinteraction between genomic 5′-UTR stem-loop (BCL) and the genomic 3′-BTE, and the in trans interaction between the genomic 3′ BTE and the 5′ UTR of SG RNA1 .
cord-294990-jdjbjkcp	2013	The viral nucleocapside-like particles detected in the cytoplasm (white arrows) and accumulated in the ER vesicles (Ves) of 48 h NDiV-infected C6/36 cells, appear immunoglod-labeled on ultrathin sections with anti-NDiV polyclonal antibodies, as shown in Fig. 5 . In this study, the nucleocapsid-like particle of NDiV was identified in the host cell cytoplasm as possessing a round shape and an inner core observed in several types of vesicles and in the ER and its viral nature was confirmed by immunogold labeling on thin sections. By EM analyses, we show that replication and assembly of NDiV was only detected in the cytoplasm of the host cells in which viral nucleocapsid-like particles appeared in the cytoplasm and in the endoplasmic compartments such as vacuoles, ER, and vesicles, but not in mitochondria.
cord-296075-8axbkyyz	1996	Abstract CD8+cytotoxic T lymphocytes (CTLs) isolated from the central nervous system (CNS) of C57Bl/6 mice acutely infected with mouse hepatitis virus, strain JHM (MHV-JHM), and analyzed in a directex vivocytotoxicity assay recognize two epitopes (H-2Dband H-2Kb-restricted encompassing amino acids 510–518 and 598–605, respectively) within the surface (S) glycoprotein. In this report, the preferential recognition of the H-2Db-restricted epitope is confirmed using splenocytes stimulatedin vitrowith either MHV-JHM-infected MC57 cells or with a cell line expressing the S protein and analyzed in secondary CTL assays. To determine whether these results represent a difference in epitope recognition between the spleen and CNS, secondary CTL assays were performed using spleen cells coated with peptides encompassing the CTL epitopes as stimulators. These assays using peptide-coated splenocytes as stimulators revealed comparable CTL precursor/effector frequencies for the H-2K b -(average 1/1291, range 1/927-1/1542 spleen cells) and H-2D b -restricted (average 1/987, range 1/380-1/1323 spleen cells) epitopes in these mice.
cord-296364-7rp60d2m	2005	Molecular clones of infectious bronchitis virus (IBV), derived from the Vero cell adapted Beaudette strain, were constructed, using an in vitro assembly method. Direct sequencing of RT-PCR products derived from cells infected with the plaque-purified virus, which had lost expression of EGFP, confirmed loss of the EGFP ORF. This strategy was further modified to construct an infectious cDNA clone of MHV with their bno see''mQ technology, in which restriction endonuclease sequences were incorporated into amplicons, such that upon enzyme treatment, the endonuclease sites were eliminated prior to in vitro ligation. In the current study, molecular clones of IBV were generated using the in vitro assembly of cDNA fragments as a template for transcription of full-length genomic RNA. Interestingly, the size of plaques with the 5a deletions, including a revertant that had completely lost the EGFP ORF, was comparable to plaques generated by our standard Beaudette cell-adapted Beaudette virus (Fig. 6B ).
cord-296416-q0rsfzgw	1996	In many 3-5 hr after infection, individual elements of the GA, cells the secretion blocker Brefeldin A (BFA) reversibly which are associated initially with separate microtubuleredistributes membranes and enzymes of the GA back organizing centers in perinuclear areas of fused cells, into the RER, but does not inhibit endocytosis (Doms et congregate in the center of syncytia and form an exal., 1989; Lippincott-Schwartz et al., 1989; Johnston et al., tended network of nondisrupted intact Golgi complexes 1994). In this study, we used organ-Immunohistochemistry elle-specific antibodies, immunohistochemistry, and transmission electron microscopy to examine the fate of Cells, grown on poly-D-lysine-treated coverslips, were the GA during cell fusion and syncytia formation in mouse fixed with 2% paraformaldehyde for 20 min at room tem-L-2 cells infected with MHV-A59 and fusion defective perature, washed three times in PBS, then incubated for mutants.
cord-297712-yy4g5npi	2016	Here, we demonstrate that nonstructural protein 5 (nsp5) of PDCoV, the 3C-like protease, significantly inhibits Sendai virus (SEV)-induced IFN-β production by targeting the NF-κB essential modulator (NEMO), confirmed by the diminished function of NEMO cleaved by PDCoV. A study published by our lab also demonstrated that nsp5, the 3C-like protease of porcine epidemic diarrhea virus (PEDV), which is classified into the Alphacoronavirus family, antagonizes IFN-β production by cleavage of NEMO . In this study, we reveal that nsp5 of PDCoV antagonizes the type I IFN signaling pathway through the cleavage of NEMO, a critical constituent of the IKK complex, thus representing a newly identified mechanism by which PDCoV evades the innate immune response. In contrast, TBK1induced activation of the IFN-β promoter was not affected by nsp5 (Fig. 3A) , suggesting that PDCoV nsp5 inhibits RIG-I/MDA5 signaling by targeting NEMO or other upstream proteins.
cord-298847-szezd2vb	2003	Virus inoculation of 21-day postnatal C57BL/6 and BALB/c mice led to a generalized infection of the whole CNS, demonstrating HCoV-OC43 neuroinvasiveness and neurovirulence. Moreover, mice inoculated with supernatants from cell cultures infected with brain tissue from affected mice developed the same disease, demonstrating that the virus was responsible for pathology. Cells positive for viral antigens were first observed at HCoV-OC43-infected mice gained weight normally during the first 5 days after infection, after which they all lost weight during the acute phase of the disease. (A) 100% of brains from C57BL/6 mice inoculated ic with 10 TCID 50 of HCoV-OC43 were positive for viral RNA between 3 and 11 days postinfection. However, RT-PCR analysis revealed that viral RNA could not be detected after the second week postinfection, suggesting a nonpersistent infection of HCoV-OC43 virus in 21 DPN mice. Every 2 days postinfection, five animals from two groups of infected mice of each strain were sacrificed and processed for detection of viral RNA, viral proteins, and infectious virus.
cord-298934-vtrfqozl	1988	The detection of such RNA intermediates in MHV-infected cells (Baric et a/., 1985 (Baric et a/., , 1987 suggests that coronavirus genomic RNA synthesis involves a discontinuous and nonprocessive mechanism, which may account for the high frequency of recombination via a copy choice mechanism. Since previous oligonucleotide fingerprinting analysis suggested that DlssE RNA contains the leader sequence and the 5'' end region of genomic sequence (Makino et al., 1985) cDNA clones were screened by colony hybridization using 5'' end-labeled, leader-specific 72-mer, and two cDNA clones F82 and C96, which correspond to the 5'' end of genomic RNA of MHV-JHM . Possible secondary structure at the DI RNA rearrangment sites Sequence analysis revealed that DlssE RNA consisted of three noncontiguous regions of MHV-JHM genomic RNA. Furthermore, as previously described for the standard MHV-JHM, the sequence surrounding the junction of leader RNA and the remaining 5''-end genomic sequence also contains a stable secondary structure (Soe eta/., 1987) .
cord-299122-djfj4262	2007	title: Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() Using the phage-displayed peptide library screening method and purified Fab fragments of immunoglobulin G (IgG Fab) from normal human sera and convalescent sera from SARS-CoV-infected patients as targets, 11 B cell epitopes of SARS-CoV spike glycoprotein (S protein) and membrane protein (M protein) were screened. Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice ☆ Therefore, in the present study, we screened and identified specific B cell epitopes of SARS-CoV using phagedisplayed peptide library, Fab fragments from anti-SARS-CoV immunoglobulin G (IgG) and normal human IgG as targets, and an improved biopanning procedure. Splenic lymphocytes from mice on day 42 still exhibited significant proliferative responses to specific antigen, demonstrating that the four epitope-based peptides induced long-term immune responses (data not shown).
cord-299976-36r794ow	2018	FCoVs are typically grouped into two biotypes (or pathotypes), which have been classified as feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), based on tissue tropism, disease progression, and genetic markers (reviewed in Kipar and Meli, 2014; Pedersen, 2014 Pedersen, , 2009 , although the range of disease signs and clinical outcomes are likely to extend beyond these two basic definitions. As part of this study, we characterized three feline cell lines-two from the American Type Culture Collection (ATCC) and one from Cornell University-and evaluated the replication kinetics, efficiency of plaque formation, and responsiveness of these cells to interferon (IFN) in order to identify the optimal cell culture conditions for type I FIPV Black. After observing the rapid and uniform development of CPE and release of virus into cell supernatants during infection of AK-D and Fcwf-4 CU cells, we reasoned that these cells would be employable in a standardized plaque assay to consistently determine FIPV Black titer.
cord-299994-1ksfo0pr	2019	In CavV and most other members of the genus Alphamesonivirus, the P2 position of putative 3CL pro substrates is predominantly occupied by Asn. The crystal structure of the 3CL pro /inhibitor complex shows that the Asn side chain fits perfectly into the S2 subpocket, with its carboxamide functionality acting as hydrogen bond donor and acceptor in interactions with the main chain carbonyl oxygen of Asp216 and the Oγ atom of Ser52, respectively. In the first crystal structure reported for a coronavirus 3CL pro , this Asp (Asp186 in the TGEV 3CL pro sequence) was found to form a hydrogen bond to a water molecule located in a position that, in chymotrypsin and related serine proteases, is occupied by the side chain of the third member of the catalytic triad (typically Asp) (Anand et al., 2002) .
cord-300372-h5g4z8ts	2014	Based on the central role of sPLA(2) enzymes as key initiators of inflammatory processes, we propose that activation of GX-sPLA(2) during H1N1pdm infection is an early step of pulmonary inflammation and its (Reviewer 2 Minor Comment 2) inhibition increases adaptive immunity and improves survival. Increased expression of immunoglobulin chain, lymphocyte differentiation, antigen processing genes and presence of CD3 þ T cells in the lungs of mice lacking GX-sPLA 2 after H1N1pdm infection Lack of GX-sPLA 2 resulted in decreased levels of PGD 2 , LTB 4 , cysteinyl leukotrienes, PGE 2 and Lipoxin A 4 and increased adaptive immune responses at 3 but not 6 days following H1N1pdm infection. MPO protein (neutrophil marker), CD45 protein (leukocyte marker) and GAPDH protein (loading control) expression levels were determined by immunoblot analysis from lung tissue homogenates of GX þ / þ and GX À / À mice over a 14 day time course of H1N1pdm influenza infection (Bi).
cord-300470-vgd1ol2z	2016	In both of the above reverse genetics systems, recovery of infectious AHSV-4 from plasmid DNA relies on the expression of T7 RNA polymerase within cells transfected with the AHSV-4 cDNA plasmids. The initial AHSV-4 reverse genetics system developed here consists of 10 plasmids, each containing a full-length cDNA copy of single AHSV-4 genome segments flanked by T7 RNA polymerase promoter and HDV ribozyme sequences. However, the same reassortant virus was also recovered successfully by combining the four AHSV-4 dual vectors with two single reverse genetics plasmids, which contained cDNA copies of the S5 and S6 genome segments, respectively. To this end, we have cloned a T7 RNA polymerase expression cassette onto the genetic backbone of the pJAD-S2-S6 dual reverse vector and subsequently demonstrated that AHSV-4 could be recovered in BSR and L929 cells following transfection of the cells with the modified 5-plasmid set.
cord-300810-a1skdp67	1991	title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation Abstract After intranasal instillation in the mouse, rabies virus (CVS strain) selectively infected olfactory receptor cells. On the other hand, other neuronal cells permissive for CVS, such as mitral cells or the anterior olfactory nucleus, are completely free of infection with the mutant, indicating that restriction is related to the ability of AvO1 to penetrate several categories of neurons. The G protein plays a pivotal role in the pathogenicity of the virus because of its interaction with the host cells '' Abbreviations used: AON, anterior olfactory nucleus; CNS, central nervous system; GABA, Gamma aminobutyric acid; HDB, horizontal limb of the diagonal band; HRP, horseradish peroxidase; HSVl, herpes simplex type 1; IPL, internal plexiform layer: LC, locus coeruleus; LD50, lethal dose 50%; LPA.
cord-300884-rqfxe0x1	2007	Analysis of the sequence identified 11 open reading frames which encode two replicase polyproteins, five structural proteins (hemagglutinin esterase, spike, envelope, membrane, and nucleocapsid) and four accessory proteins (NS2, p4.7, p12.7, and I). In contrast to the replicase proteins which are directly translated from the genomic RNA, coronavirus structural and accessory proteins are expressed from a nested set of 3′ coterminal subgenomic (sg) mRNAs that also possess a common 5′ leader sequence derived from the 5′ end of the genome (Pasternak et al., 2006; Sawicki et al., 2007) . Following multiple alignments with the S proteins of other group 2a coronaviruses, a potential cleavage recognition sequence (RRQRR) was identified at residues 764-768 which would predict a cleavage between amino acids 768 and 769, separating the ECoV S protein into S1 and S2 subunits (Fig. 1) .
cord-301293-jqy7lcbk	2006	In the present study, we analyzed the spectrum of immune responses of mice to three different forms of the SARS coronavirus nucleocapsid (N): (1) exogenous recombinant protein (N-GST) with Freund''s adjuvant; (2) DNA encoding unmodified N as an endogenous cytoplasmic protein (pN); and (3) DNA encoding N as a LAMP-1 chimera targeted to the lysosomal MHC II compartment (p-LAMP-N). In the present study, we have demonstrated that the dominant T-cell immune responses of mice immunized with the SARS CoV N protein plus adjuvant or with DNA encoding two different cellular trafficking forms of N are directed to the same peptide epitopes of all three immunogens. For example, in this study, the greater response to the LAMP-N chimera could be related to the quantitatively greater delivery of N to the MHC class II compartment of APCs. There can also be major differences in the repertoire or functionality of T cells responding to any given epitope, such as the differences in the IFN-g and IL-4 responses of mice immunized with DNA or with N-GST plus CFA.
cord-301755-fxfsr9bj	1992	authors: Wang, F.-I.; Fleming, John O.; Lai, Michael M.C. title: Sequence analysis of the spike protein gene of murine coronavirus variants: Study of genetic sites affecting neuropathogenicity To understand the molecular basis of MHV neuropathogenesis, we studied the spike protein gene sequences of several neutralization-resistant variants of the JHM strain of MHV, which were selected with monoclonal antibodies (MAbs) specific for the S protein. We found that variant 2.2-V-1, which was selected with MAb J.2.2 and primarily caused demyelination, had a single point mutation at nucleotide (NT) 3340, as compared to the parental JHM virus, which predominantly caused encephalitis. The viruses used in this study included several JHM variants which were selected for their resistance to neutralizing MAbs specific for the S protein (Fleming et a/., 1983) .
cord-302486-z36hcvrx	2006	Viral and prion contamination of cell cultures and "feeder" cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. The use of bovine fetal serum in stem cell cultures requires an urgent need for a risk assessment for Transmissible Spongiform Encephalopathies (TSEs) by means of a sensitive and specific test in all products derived from ruminants (U.S. Food and Drugs Administration, 1999; Directive 2004/C 24/ 03). This panel of tests should necessarily include reverse transcriptase detection as a general test for retroviruses, electron microscopy that can detect different kinds of viral particles and characterize many unknown isolates present in cell cultures and molecular techniques like PCR (conventional or real-time) and RT-PCR tests to include all the viruses that we know pose a risk to the product.
cord-302972-imtttzvr	1991	As shown in Fig. 1 B, the electrophoretic mobility of GP was slightly enhanced after incubation with endoglycosidase H (lane 4), and a distinct further increase was obtained by treatment with endoglycosidase F (lane 3) indicating that GP contains AI-glycans of the oligomannosidic, but mainly of the complex type. Glycohydrolase treatments were performed at 37" overnight after denaturing of the proteins by boiling in buffer containing 0.1% SDS, 0.5% octylglucoside, 0.5% P-mercaptoethanol, 50 mM sodium acetate, pH 7.0, and 5 mM EDTA. Growth of virus, labeling, and cross-linking were performed as described in the legend of Fig. 1 and as in A above. To further analyze the composition of the GP complexes, purified [35S]methionine-labeled virus was subjected to solubilization by nonionic detergent and sedimentation on sucrose density gradients, and the polypeptides present in the fractions obtained from the gradients were assayed by polyacrylamide gel electrophoresis under denaturing and reducing conditions. A. Virus non-cross-linked and treated with @-mercaptoethanol (5%, 10 min, 96") prior to gradient centrifugation.
cord-303238-us3dybue	2007	The papain-like protease (PLpro) encoded by the coronavirus that causes severe acute respiratory syndrome (SARS-CoV) processes three sites in the replicase polyprotein (Harcourt et al., 2004) , and has recently been shown to have de-ubiquitinating activity (Barretto et al., 2005; Lindner et al., 2005) . To extend these studies of membrane association of coronavirus replicase products, we analyzed the amino acid sequence of MHV-JHM nsp3 (from glycine-833 to glycine-2840) for probability of transmembrane helices using the five different programs designed to search for putative membrane-spanning sequences: Phobius, TMHMM, HMMTOP, SOSUI and TMpred (Fig. 2) . In contrast, when CMMs were added to the mixture, protein products that included all or part of nsp3-TM (PLP2-2485, -2390 and -2258) were detected predominantly in the pelleted fraction, consistent with membrane association (Fig. 3B ).
cord-303497-s3zs1oxf	1983	Recombinants between fowl plague virus (FPV) and these strains were obtained by double infection of chick embryo cells either with specific ts mutants of FPV or FPV wild-type and the other prototype strains, and extended plaque purifications as described by Scholtissek et aL (1976) and Rott et aL (1979) . When plaque tests were performed on chick embryo cells at 37 or 40" with recombinants between FPV and other prototype influenza virus strains it was found that the plaque morphology of most of these recombinants was similar to that of FPV. In a single-cycle multiplication experiment (infection at a multiplicity of lo-50 PFU per cell) at 33", the yield of infectious 113/Ho was very low when compared with the multiplication at 37" or with the adapted strain or FPV (Fig. 2) . These results indicate that a step before virus maturation is impeded at 33'' in 113/Ho-infected cells, since labeling of viral proteins is already slowed down at this temperature.
cord-304421-xpj6c0vx	1999	The coronavirus 3C-like proteinase (3CLpro), flanked on either side by hydrophobic, possibly membrane-spanning regions (HD1 and HD2), is believed to be the prinicipal viral proteinase responsible for the processing events leading to the formation of the viral replicase complex, with as many as 11 potential cleavage sites identified throughout pp1ab (Gorbalenya et al., 1989; Lee et al., 1991 ) (see Fig. 1 ). We therefore created several substrates of various lengths, encoding different putative cleavage sites in ORF1b, in order to investigate processing by the recombinant MBP-3CLpro. The effect of these cleavage site mutations on the autocatalytic cis release of the 29-kDa 3CLpro was assayed by the expression of the Radiolabeled, in vitro transcribed, and translated substrate from pET21-NX.3C was incubated with MBP-3CLpro (lane 2) or an equal volume of column buffer/20% glycerol (lane 1) and the processed products were separated on a 15% SDS-PAGE gel.
cord-305143-mqd4ioj4	2019	Coupled with their genome complexity and the availability of numerous complete genome sequences, this deep evolutionary history makes herpesviruses a tractable and informative model to study virus genome evolution at the levels of gene duplication and protein domain rearrangement. In addition, the gene tree for human herpesvirus uracil DNA glycosylases ( Fig. 1B ) precisely recapitulates the herpesvirus species tree (Fig. 1A) ; therefore, this protein family can be inferred to have evolved from a single common ancestor and without any gene duplications or domain rearrangements (see Table 2 for virus-specific gene names). Phylogenetic analysis of human herpesvirus DNA polymerase proteins, plus related proteins from selected mammalian herpesviruses, shows that, similar to the glycoprotein B family, DNA polymerases of the Herpesviride evolved without gene duplication.
cord-305564-dj3vj4tk	2008	All these viruses were rescued in monkey (Vero E6) cells and were also infectious for human (Huh-7, Huh7.5.1 and CaCo-2) cell lines and for transgenic (Tg) mice expressing the SARS-CoV receptor human angiotensin converting enzyme-2 (hACE-2), indicating that none of these proteins is essential for the viral cycle. These data indicate that E gene might be a virulence factor influencing replication level, tissue tropism and pathogenicity of SARS-CoV, suggesting that ΔE attenuated viruses are promising vaccine candidates. In contrast, rSARS-CoV-Δ[6-9b] virus was detected at high titers in the brains of infected hACE2 Tg mice suggesting that the E protein is important for virus replication and dissemination within this tissue. Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR
cord-307354-dkwcheu0	2015	Alpha-herpesviruses such as herpes simplex-1 (HSV-1) express a FEN1-like nuclease termed virion host shutoff protein (vhs) that is directed to mRNAs through interactions with the translation Fig. 1 . Quality control decay pathways such as NMD recognize aberrant mRNAs during translation, including the presence of premature termination codons (PTC), and induce endonucleolytic cleavage, whereupon the fragments are degraded by exonucleases. The RNAi pathway restricts gene expression by processing the long double stranded RNAs frequently generated during viral replication into short interfering RNAs (siR-NAs), which guide endonucleolytic cleavage of complementary target mRNAs. Although mammalian cells possess the RNAi machinery, in most cases RNAi does not appear to play a significant antiviral role, and has instead been supplanted by the protein-based interferon response (Cullen, 2014) . Small interfering RNAs that deplete the cellular translation factor eIF4H impede mRNA degradation by the virion host shutoff protein of herpes simplex virus
cord-307396-u6v6bxwj	2006	In a recent study, we demonstrated that the SARS-CoV E protein could obviously enhance the membrane permeability of bacterial cells to onitrophenyl-β-D-galactopyranoside and hygromycin B, suggesting that the protein may function as a viroporin (Liao et al., 2004) . Western blotting analysis of cells expressing wild type and most mutant constructs showed specific detection of three species migrating at the range of molecular masses from 14 to 18 kDa under reducing conditions and representing three isoforms of the E protein (Fig. 3a) . The E protein from coronavirus MHV and IBV was previously shown to undergo modification by palmitoylation HeLa cells expressing the Flag-tagged SARS-CoV and IBV E proteins, respectively, were harvested at 12 h posttransfection, broken by 20 stokes with a Dounce cell homogenizer, and fractionated into cytosol (C) and membrane (M) fractions after removal of cell debris and nuclei. Expression of the untagged SARS-CoV E protein in the same cell type also shows very similar Golgi localization patterns as the Flag-tagged protein (Fig. 8a , panels G-I).
cord-307904-lnagg1uw	2003	One RNA, ␥KpnI/HpaI, provided a source of the ␥a replicase protein and also contained a 350-nt deletion (from positions 2112 to 2461 on RNA␥) to remove the majority of the ␥b ORF, and a second derivative designed to assess promoter activity contained deletions engineered within the putative sgRNA␥ promoter ( Fig. 2A) . This result implies that competition between the two promoters has a major role in regulating the differential rates of synthesis of the two sgRNAs. To initially define sequences flanking the sgRNA␤2 promoter, two large deletions were generated in the ␤1Ϫ34/ ϩ14 clone that eliminated RNA␤ positions 1705 to 2109 and 2287 to 2434. Analysis of four deletions extending from position Ϫ179 to positions Ϫ110, Ϫ76, Ϫ52, and Ϫ28 relative to the transcription start site revealed that the mutant RNAs were able to replicate in protoplasts, but only mutants containing the deletions Ϫ179/Ϫ110 or Ϫ179/Ϫ76 were able to direct synthesis of sgRNA␤2 (Fig. 4A ).
cord-308835-999kewdw	1981	Abstract Seven virus-specific, polyadenylated RNA species have been identified in mouse cells infected with the murine coronaviruses MHV-A59 (A59V) or MHV-JHM (JHMV). MHV-infected 17CL·1 cells were labeled with [32P]orthophosphate in the presence of actinomycin D and the cytoplasmic RNA was extracted and analyzed by agarose gel electrophoresis. The largest intracellular RNA species is identical to RNA isolated from purified virions, as determined by agarose gel electrophoresis and oligonucleotide fingerprint studies of ribonuclease T1 digests. Oligonucleotide fingerprints of the six subgenomic RNAS show that the sequences they contain are present in virion RNA, confirming their virus-specific nature. Identification of MHV-Specific RNA Species A59V, JHMV, and mock-infected cells were labeled with [32P]orthophosphate from 4 to 8 hpi in the presence of actinomycin D. To determine if there is temporal regulation of MHV-specific RNA synthesis, replicate cultures of A59V, JHMV, or mock-infected cells were pulse labeled for 1 hr at hourly intervals and the intracellular RNA was extracted and analyzed by gel electrophoresis.
cord-309015-t5v2sjus	2005	The G2 fusion subunit of the Junín virus envelope glycoprotein GP-C contains two hydrophobic heptad-repeat regions that are postulated to form a six-helix bundle structure required for the membrane fusion activity of Class I viral fusion proteins. The mature envelope glycoprotein complex of the arenavirus consists of three noncovalently associated subunits derived from the GP-C precursor by proteolytic cleavage events: a stable myristoylated 58 amino-acid signal peptide (SSP), the receptor-binding G1 subunit and the transmembrane G2 fusion protein (Buchmeier, 2002; Eichler et al., 2003; York et al., 2004) . The molecular basis for envelope glycoprotein-mediated membrane fusion in the arenaviruses is largely unknown, however, sequence analysis of the G2 ectodomain of Lassa virus and lymphocytic choriomeningitis virus (LCMV) has revealed two heptad-repeat regions that can be represented to form amphipathic helices (Gallaher et al., 2001) .
cord-309469-2naxn580	2019	For example, polyadenylated nuclear (PAN) RNA encoded by Kaposi''s sarcoma-associated herpesvirus (Sun et al., 1996; Zhong and Ganem, 1997) , the~2-kb latency-associated transcript (LAT) expressed by Herpes simplex virus (Bloom, 2004 ), a con-served~5-kb intron expressed by Human cytomegalovirus (hCMV) (Kulesza and Shenk, 2004) , and a 7.2-kb RNA expressed by mouse CMV (Kulesza and Shenk, 2006) , U-rich RNAs (HSURs) produced by Herpesvirus saimiri (HVS), (Albrecht and Fleckenstein, 1992; Ensser and Fleckenstein, 2005) ; (3) Subgenomic ncRNAs from single-stranded RNA viruses by incomplete degradation of genomic RNA by the cellular 5-3′ exonuclease XRN1. The results confirmed previous report that IBV can synthesize sgRNA via template switch mediated by a noncanonical core sequence (Bentley et al., 2013) Notably, the mutant virus carrying four mutations (A27100U/A27111U/G27113C/G27114C) was also unable to produce ncRNA (Fig. 4) , suggesting these nucleotides are required for ncRNA production.
cord-309919-sm5o0g1c	2020	In infected cells, the MRV μ2 protein forms punctae in the enlarged region of the filamentous VFs that are co-localized with γ-tubulin and resistant to nocodazole treatment, and permitted microtubule (MT)-extension, features common to MT-organizing centers (MTOCs). Using a previously established reconstituted VF model, we addressed the functions of MT-components and MTOCs concerning their roles in the formation of filamentous VFs. Indeed, the MTOC markers γ-tubulin and centrin were redistributed within the VF-like structures (VFLS) in a μ2-dependent manner. Here, specific µ2 punctae observed in filamentous VFs are investigated concerning their 89 ability to co-localize with other reovirus proteins and host elements. Our study shows that µ2 90 punctae in VFs co-localize with γ-tubulin, are resistant to nocodazole, and permit MT 91 emergence, common features for MTOCs. Moreover, using the VFLS model, we found that 92 specific µ2/µNS ratios that support filamentous morphology relocalize γ-tubulin and centrin to 93 foci within the VFLS.
cord-310218-fky0cm5e	1991	Abstract The hemagglutinin/esterase (HE), spike precursor (S) and the S1 and S2 subunits of the spike precursor protein of bovine coronavirus were expressed in Spodoptera frugiperda (Sf9) cells, and the cell-fusing activity of each recombinant glycoprotein was examined. The hemagglutinin/esterase (HE), spike precursor (S) and the Sl and S2 subunits of the spike precursor protein of bovine coronavirus were expressed in Spodopfera frugperda (Sf9) cells, and the cell-fusing activity of each recombinant glycoprotein was examined. Thus, in order to identify the viral membrane glycoprotein which induces cell fusion by BCV, we expressed the HE, the S, and the Sl and S2 subunits of the S glycoprotein using recombinant baculoviruses, and examined the cell-fusing activity of each recombinant polypeptide. Therefore, it is clear that proteolytic cleavage is required to induce the fusion activity of both the recombinant S polypeptide in insect cells and the authentic S polypeptide produced in BCV-infected cells (14) .
cord-310748-ao29zx1u	1991	Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. To study RNA recombination in the absence of selection pressure, we developed a polymer-ase chain reaction (PCR) assay using two primers specific for the potential recombinant viruses which have a crossover site between the two primers. Only recombinant RNAs which had a crossover between the two primers and contained A59-specific sequences on the 5''-side and JHM-DL-specific sequences on the 3''-side could be detected by this PCR approach. DNA sequence analysis of 35 cloned PCR products showed that the crossover sites were almost randomly distributed throughout the nearly 1-kb region of the peplomer gene studied ( Fig. 2A) . Analysis of 53 recombinant clones revealed that, similar to the intracellular recombinants, the crossover sites in the viral recombinant RNAs were almost randomly distributed over the 1 -kb region of the peplomer gene (Fig. 2B) .
cord-310967-15mv5yx7	1989	One of these variants, ATIIf cord virus, which induced a chronic demyelinating disease in 2or 10-day-old intracerebrally inoculated Wistar Furth rats, had a deletion in the coding region of the peplomer glycoprotein mRNA. In this report, we investigated viral variants that arose in the CNS of rats with a JHM-induced demyelinating disease and studied the effect of alterations in their mRNAs. When lo-day-old rats were inoculated with ATllf brain virus or ATlIe brain virus, the rats developed a rapid encephalitis instead of the more chronic demyelinating disease that has previously been seen with wild-type parental JHM virus (Sorensen et al., 1980; Jackson et al., 1984) and was observed with ATIIf cord virus-injected rats. In contrast, when 2-day-old rats were inoculated with ATllf cord virus, the more chronic CNS disease resulted instead of the rapid encephalitis that has been reported for wild-type JHM (Sorensen et a/., 1980; Parham et a/., 1986) and was observed with the ATIIf brain virus variant.
cord-311255-zaa8i9vh	2014	Abstract The present study sought to investigate whether porcine epidemic diarrhea virus (PEDV) induces apoptosis and to elucidate the mechanisms associated with apoptotic cell death after PEDV infection. Interestingly, mitochondrial apoptosis-inducing factor (AIF) was found to translocate to the nucleus during PEDV infection, and AIF relocalization was completely abrogated by the presence of cyclosporin A (CsA), an inhibitor of cyclophilin D (CypD) that is an essential component of the mitochondrial permeabilization transition pore (mPTP) complex. Altogether, our results indicate that a caspase-independent mitochondrial AIF-mediated pathway plays a central role in PEDV-induced apoptosis to facilitate viral replication and pathogenesis. Therefore, in this study, we aimed to determine if PEDV induces apoptosis following infection in vitro and in vivo and to define the specific pathways involved in apoptotic death of virus-infected cells.
cord-311774-fhdvcvi0	2011	
cord-312210-3x9s3g8n	2019	title: The use of cells from ANPEP knockout pigs to evaluate the role of aminopeptidase N (APN) as a receptor for porcine deltacoronavirus (PDCoV) However, lung fibroblast-like cells, derived from the ANPEP KO PAM cultures, supported PDCoV infection to high levels. In this study, we investigated the role of pAPN as a receptor for PDCoV by evaluating the permissiveness of different cell populations derived from the lungs of ANPEP KO and wild-type (WT) pigs. Porcine alveolar macrophages (PAMs) from ANPEP KO and WT pigs were used to evaluate the permissiveness of cells for infection with PDCoV and TGEV. The results showed that PAMs from pigs lacking a functional ANPEP gene are resistant to TGEV and PDCoV infection. The results from this study showed no PDCoV infection of PAMs obtained from ANPEP KO pigs (see Fig. 1A ), which supports the observations of Wang et al.
cord-313091-ksrxsdpp	2017	Studies using the ATCC isolate suggest that HCoV-229E enters cells via the late endosome using cathepsin L to cleave S protein, although it can enter cells via the cell surface or early endosome in the presence of transmembrane protease serine 2 (TMPRSS2) or trypsin (Bertram et al., 2013; Kawase et al., 2009) . In the present study, we found that field isolates of HCoV-OC43 and HCoV-HKU1 could be isolated using HBTE-ALI cell culture, and we then used these clinical isolates to assess whether the mode of virus entry found in HCoV-229E was also in play in other HCoVs. For isolation of HCoVs, nasal swabs were collected from outpatients who showed respiratory infection as a cardinal symptom when assessed at a hospital in Tokyo, Japan. To evaluate the entry routes of clinical isolates of HCoVs, viruses were inoculated onto HBTE-ALI in the presence of EST or camostat (10 μM) and the amounts virus that entered were estimated by detecting subgenomic mRNAs using real-time RT-PCR (Fig. 2) .
cord-313906-fh85fzq9	2016	We found that VSVs pseudotyped with BatIV HAs and NAs efficiently infected particular bat cell lines but not those derived from primates, and that proteolytic cleavage with a trypsin-like protease was necessary for HA-mediated virus entry. Treatment of the susceptible bat cells with some enzymes and inhibitors revealed that BatIV HAs might recognize some cellular glycoproteins as receptors rather than the sialic acids used for the other known influenza viruses. To obtain information on the biological characteristics of cellular receptors for BatIVs, IndFSPT1 cells were pretreated with tunicamycin, pronase, or neuraminidase (i.e., an N-linked glycosylation inhibitor, mixture of proteases, and sialidase, respectively), and then infected with pseudotyped VSVs (Fig. 4B-D) . IndFSPT1 should also have such molecules since it showed the highest susceptibility to BatIV HA-pseudotyped VSVs. It was noted that VSVΔG*-H17N10 and -H18N11 also infected MDCK cells, although less efficiently than these bat cell lines.
cord-315069-xo4mbxei	1991	Abstract Defective interfering (DI) RNAs were generated de novo in each of 12 independent isolates of tomato bushy stunt virus (TBSV) upon serial passage at high multiplicities of infection (m.o.i.) in plants, but not in any of 4 additional isolates after 11 serial passages at low m.o.i. The DI RNAs were detected in RNA isolated from virus particles and in 2.3 M LiCl-soluble RNA fractions isolated from inoculated leaves. On each host species, six isolates were passed at high m.o.i. and two control isolates were passed at low m.o.i. In these hosts, DI-free TBSV induces lethal necrosis within 7-l 0 days postinoculation (d.p.i.), except in the presence of DI RNAs which are associated with attenuation and the establishment of persistent infections (Hillman et a/., 1987) . The small RNAs which developed in each of the high m.o.i. isolates hybridized to both 5''-and 3''-proximal TBSV genomic sequences, but generally were larger (-600 bases) than the previously characterized DI 1 RNA species (-400 bases).
cord-315158-f6msh8od	1989	Abstract We have examined six different JHMV variants, sp-4 (recloned wt JHMV), cl-2, CNSV, DL, DS, and JHM-X, in terms of the sizes of the mRNA3 and E2 glycoprotein as well as their reactivity to a panel of monoclonal antibodies to the E2 glycoprotein. Recently, we have shown that the highly virulent variant viruses with larger E2 glycoproteins were preferentially isolated from rat brain (19) and cultured astrocytes (20) after infection by wild-type (wt) JHMV which contains a small mRNA3 and E2 glycoprotein. E2 glycoproteins produced by sp-4 and JHM-X, both of which synthesized a small mRNA3, were shown to be approximately 15,000 Da smaller than those produced by the other variant viruses with larger mRNA3.s. No significant differences were observed in the sizes of N proteins produced by the variants. As shown in Fig. 3 , the monoclonal antibodies uniformly had excellent binding to all the viruses tested, with the exception of sp-4 and JHM-X, the two variants with small mRNA3s and E2 proteins.
cord-316134-lkd2mj27	2020	Investigation of possible molecular interactions between components of PEDV, PDCoV and TGEV and their influence on replication of each virus would provide a crucial insight into comprehensive understanding of these CoVs. Of all viral proteins, we have chosen to start with the N protein, as it is among the most abundant and ubiquitous structural proteins in infected cells. For viral infection in the transient CoV N expression experiment, VeroE6 cells were transfected with 1 or 2 μg of pCAGGS-PEDV N-Myc, pCAGGS-PDCoV N-HA, pCAGGS-TGEV N-FLAG, or the empty pCAGGS vector and were incubated for 24 h to allow for protein expression. To investigate how this protein-protein interaction might affect PEDV replication, we transiently transfected VeroE6 cells with varying amounts of the pCAGGS plasmid expressing N proteins from either PDCoV or TGEV for 24 h before infection with PEDV-mCherry (MOI = 0.0001) and followed the course of viral replication for each condition.
cord-316460-ibprgdh4	2014	To assess whether muNS cleavage is promoted by avian reovirus proteins and/or by changes induced in the host during infection, we compared muNS-to-muNSC conversion in ARV-infected cells with that in transfected cells and in insect cells infected with a muNSexpressing recombinant baculovirus (Fig. 1A ). To verify that this putative caspase recognition sequence is a bona fide cleavage site we first examined whether the electrophoretic mobility of muNS, muNSC and muNSN matched with that of transiently expressed polypeptides comprising muNS residues 1-635, The resulting extracts were immunoprecipitated with polyclonal anti-muNS serum and the imunoprecipitated proteins were resolved on an electrophoresis gel system (8% tricine-SDS-PAGE gel) specifically designed to resolve small peptides (Schägger, 2006) . In the absence of an established reverse genetics system for ARV that would allow us to generate a recombinant virus that expresses an uncleavable muNS protein, like D154A, we examined the effect of Q-VD-OPh on ARV replication in CEF cells, since this compound had been shown to block both apoptosis and muNS processing.
cord-317333-unrd76bo	2011	Evaluation of gene expression patterns in PBMCs and lung necropsies of SARS-CoV-infected ferrets led us to the identification of 7 upregulated IRGs that also were upregulated in response to IFN-α2b injection. Since STAT1 was phosphorylated following SARS-CoV infection and IFN-α2b injection, we investigated select IRG expression by qRT-PCR following in vitro stimulation of ferret peripheral whole blood with IFN-α2b. These gene expression and STAT1 phosphorylation findings suggested that robust IFN responses were activated following SARS-CoV infection 2 days post-infection. The comparison of microarray results between the lung tissue of IFN-α2b and SARS-CoV ferrets at day 1 revealed commonalities in the expression patterns of most IRGs. STAT1, MX1, OAS1, OAS2, ISG15, IFI44, IFI44L and EIF2AK2 were among the overlapping genes (Fig. 3B ). Analysis of the IFN signaling canonical pathway showed the upregulation of STAT1, MX1, OAS1, OAS2, ISG15 and IFI44 in lung necropsies of IFN-α2b injected and SARS-CoV infected ferrets (Fig. 4) .
cord-317537-wgu5cd0y	2009	All constructs were replication competent in protoplasts as assayed by northern blot hybridization (Fig. 4I) , and statistics analysis (ANOVA) of real-time RT-PCR quantification of average relative percentage (from 3 independent experiments) of CymMV RNA from CymMV clone-infected protoplasts at 24 h postinoculation revealed no significant difference in percentage between these clones (P = 0.91). All constructs were replication competent in protoplasts as assayed by northern blot hybridization (Fig. 6J) , and statistics analysis (ANOVA) of realtime RT-PCR quantification of average relative percentage (from 3 independent experiments) of CymMV RNA from CymMV cloneinfected protoplasts at 24 h post-inoculation revealed no significant difference in percentage between these clones (P = 0.83). Our results indicated that the important amino acids of the CP that allowed for the CymMV systemic infection are located within the previously predicted RNA binding domain ( Fig. 7A; 1) .
cord-318400-l9kwxsq7	2016	To establish a characteristic host response to predict the pathogenicity and tissue tropism of infectious bronchitis viruses (IBV), we investigated innate immune responses (IIR) and apoptosis in chicken embryo kidney cells (CEKC) and tracheal organ cultures (TOC) infected with three IBV strains. In contrast, M41 infection caused greater expression of these genes than 885 or QX in TOCs. In summary, greater levels of apoptosis and elevated levels of TLR3, MDA5 and IFN-β expression are associated with increased pathogenicity of IBV strains in renal and tracheal tissues. In order to establish the characteristic host response to predict the tissue tropism and pathogenicity of IBVs, we investigated apoptosis and innate immune responses in chicken embryo kidney (CEK) cells and tracheal organ cultures (TOCs) following infection with IS/885/00-like, QX-like and M41 IBV strains. Nephropathogenic IBV strains 885 and QX resulted in significantly greater up-regulation of innate immune sensing genes namely TLR3 and MDA5 along with greater IFN-β mRNA levels in CEK cells at 9 h of infection when compared to M41 infection.
cord-319179-gqaxf7mz	1987	When infected cells and isolated virions were assayed for this protein by two-dimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. When infected cells and isolated virions were assayed for this protein by twodimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. To determine if p28 was a minor protein actually present in virions, infected 17CL-1 cells were labeled with [35S] methionine and virus was purified as described in Fig. 4 . A portion of the labeled virus preparation was analyzed directly by two-dimensional gel electrophoresis whereas a second part was mixed with the [35S] methionine-labeled cell-free products prior to analysis (Fig. 4) .
cord-319403-5qyc0wsz	2007	Type I cells were productively infected with SDAV and RCoV-P, and both live virus and UV-inactivated virus induced mRNA and protein expression of three CXC chemokines: CINC-2, CINC-3, and LIX, which are neutrophil chemoattractants. Bronchial epithelial cells and alveolar type II cells express and secrete proinflammatory cytokines and chemokines in response to infection with respiratory viruses including respiratory syncytial virus, influenza A virus, and the SARS-associated coronavirus (SARS-CoV) Yen et al., 2006; Zhang et al., 2001) . In this study, cultures of rat alveolar type I cells were evaluated for susceptibility to RCoV infection, and for expression and secretion of proinflammatory cytokines and chemokines in response to RCoV inoculation. To determine whether the CXC chemokine response to infectious or UV-inactivated RCoV-P or SDAV was specific for the rat coronaviruses, we inoculated rat alveolar type I cells with a related group 2a coronavirus, mouse hepatitis virus (MHV) strain A59 that had been purified by sucrose density gradient centrifugation.
cord-320590-irybhp4j	2019	
cord-321162-pgd34ewv	1981	Abstract Tunicamycin has different effects on the glycosylation of the two envelope glycoproteins of mouse hepatitis virus (MHV), a coronavirus. The coronavirus envelope envelope glycoprotein E1 appears to be a novel type of viral glycoprotein which is post-translationally glycosylated by a tunicamycin-resistant process that yields oligosaccharide side chains different from those of N-linked glycoproteins. of the synthesis, glycosylation, and intracellular transport of glycoproteins is essential to understanding the structure and function of cell membranes and the role of oligosaccharides in glycoprotein processing and secretion. Labeling with monospecific fluorescent antibody against isolated El or E2 (Sturman et cd, 1980) showed that El remains restricted to the perinuclear area of the cell while E2, like most other viral glycoproteins, migrates rapidly via intracellular membranes to the plasma membrane (Doller and Holmes, 1980) .
cord-321265-il9vbbgk	1995	In general, MHV transcription was extremely sensitive to translation inhibition, whereas EAV genomic RNA synthesis became independent ofde novoprotein synthesis late in infection. The replication of SIN involves the synthesis of a EAV-infected BHK-21 cells were UV-irradiated at 6 1 2 hr single 4.1-kb sg RNA (26S) from a well-defined internal promoter on the genome-sized minus-strand template p.i., when RNA synthesis approaches its maximum (van RNA (Ou et al., 1982; Levis et al., 1990) . The UV transcription mapping data showed that the Third, the overall MHV transcription was significantly EAV sg RNAs were not produced by processing of a more dependent on de novo protein synthesis than that genome-length precursor RNA. Protein synthesis was inhibited by the addition of cycloheximide to EAV-infected BHK-21 cells at fully independent transcription system the slopes of the curves in Fig. 2B , which reflect the UV target sizes, should different time points after infection.
cord-322062-nnefbeo6	1991	We now report on the molecular cloning and sequencing of the complete HEV (Burma; B) viral genome together with the deduced amino acid sequences of viral-encoded proteins General perspectives on the genetic organization of the virus, as deduced from sequence and open reading frame analyses, indicate that HEV bears some similarity to the caliciviridae but may represent a new class of nonenveloped RNA virus. Bife was chosen as the RNA source for cDNA synthesis because it contained relatively large numbers of virus particles when HEV cDNA clones were identified from libraries made from randomly primed cyno bile (solid square), or from cyno liver after priming by oligo-dT (solid circle), random sequence hexamers (open circle) and HEV-sequence specific oligonucleotides (open square). The presence of HEV-specific subgenomic RNAs localized to the 3'' one-third of the genome suggests that these may be the transcripts from which these 3'' end ORFs are expressed and is indicative of a unique expression strategy among nonenveloped positive-sense RNA viruses infecting humans.
cord-322084-gkg1059v	1996	Abstract In our studies of murine coronavirus transcription, we continue to use defective interfering (DI) RNAs of mouse hepatitis virus (MHV) in which we insert a transcription consensus sequence in order to mimic subgenomic RNA synthesis from the nondefective genome. By using PCR-based sequences flanking the same intergenic region between site-directed mutagenesis, a 12-nucleotide-long segenes 6 and 7 do not affect the efficiency of subgenomic quence, TCTAATCTAAAC, was inserted into DI cDNA DI RNA transcription (Makino and Joo, 1993) . For all of the constructs used in Deletion analysis of those MHV DI RNAs that contain this study we sequenced the inserts that were derived the intergenic sequence from gene 6-7 with its naturally from PCR products to confirm the presence of specific occurring flanking sequences showed that reducing the mutations and the absence of extraneous mutations.
cord-322904-9mta0aem	2009	
cord-324054-d71rj29o	1992	Abstract The complete nucleotide sequences of the hemagglutinin/esterase (HE) genes of human coronavirus (HCV) strain OC43 and bovine respiratory coronavirus (BRCV) strain G95 were determined from single-stranded cDNA fragments generated by reverse transcription of virus-specific mRNAs and amplified by polymerase chain reaction. Phylogenetic analysis suggests that the HE genes of coronaviruses and influenza C virus have a common ancestral origin, and that bovine coronaviruses and HCV-OC43 are closely related. We report here the complete nucleotide sequence of the HE genes of HCV-OC43 and BRCV-G95, and their phylogenetic relatedness to BCVs, MHV, and ICV. The predicted amino acid sequences of the HE genes from HCV-OC43 and BRCV-G95 (Fig. l) , BCVMost importantly, the putative acetylesterase active site (F-G-D-S) (at amino acids 72 to 75 in Fig. 2) is conserved in all HE proteins of human, bovine, and murine coronaviruses and ICV.
cord-324321-y96x8x3h	2003	Furthermore, treatment of cells with chloroquine, which blocks the acidification of endosomes, significantly inhibited the repression of the BNip3 promoter activity induced by the acidic pH-dependent MHV mutant OBLV60, which enters cells via endocytosis, indicating that the down-regulation of BNip3 expression is mediated by fusion between viral envelope and cell membranes during entry. To establish further the specificity of the down-regulation of BNip3 gene expression, we used vesicular stomatitis virus (VSV) in a parallel experiment, because VSV is also an enveloped RNA virus whose infection has a broad host cell range and is mediated by the interaction between the envelope G protein and cell membranes (Riedel et al., 1984) . By extrapolating the data from the mutant virus, we can envision that fusion between viral envelope and plasma/endosomal membranes during wild-type MHV infection is involved in the down-regulation of BNip3 gene expression.
cord-325179-gsf8ad65	1985	In some experiments, SV40-infected cells were labeled with pS]methionine or 3H-monosaccharides in the presence of excess unlabeled amino acids, excess unlabeled sugars, or TM. Infected cells were starved in glucose-free E-MEM from 20.5 to 21 hr p.i., then labeled for 3 hr using 25 &i/ml [?S]methionine or 100 &i/ml rH]galactose in E-MEM containing different sugar concentrations. A polypeptide of about 88,000 (88K) in apparent MW was detected by immunoprecipitation of pS]methionine-labeled, SV40-infected cell extracts with HAF (Fig. lA, lane 3) . Coomassie blue staining revealed that both large T-ag -and small t-ag were also immunoprecipitated from galactose-labeled infected cell extracts (data not shown). To determine the effect of TM treatment, SV40-infected cells were treated with E-MEM or various concentrations of TM starting at 15 hr pi., then were glucose-starved and labeled with pS]methionine or THlglucosamine from 21 to 24 hr p.i. After extraction, T-ag was immunoprecipitated and analyzed by SDS-PAGE (Fig. 8A) .
cord-325423-d212h4bp	2011	
cord-325481-uzch2hwd	2011	For instance, the majority of strains of the murine coronavirus mouse hepatitis virus (MHV) contain Sproteins that are cleaved by furin in infected cells, and these viruses are believed to enter target cells by receptor-dependent, pH-independent fusion with the plasma membrane (de Haan et al., 2004; Nash and Buchmeier, 1997; Qiu et al., 2006) , although some of these findings are controversial (Eifart et al., 2007) . Treatment of cell-bound virus with trypsin was shown to allow infectious SARS-S-driven entry into ammonium chloride-treated cells (Simmons et al., 2005) , indicating that trypsin can functionally replace cathepsin L as a SARS-S-activating protease under these conditions ("trypsin bypass"). The fusion efficiency is then quantified by the addition of virions to leupeptin-treated (to exclude an impact of host cell proteases on SARS-S activation) HeLa cells, which express the EnvA receptor TvA, and which are not susceptible to SARS-S-driven infection (Simmons et al., 2005) .
cord-326027-58whwspe	2006	title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). To determine that protein p54, a major component of the external envelope of ASFV, fused to EGFP protein remains incorporated to the viral particle, BA71V and B54GFP-2 virions were Percoll purified and analyzed by SDS-PAGE and Western blotting using specific antibodies (Fig. 2a) . This new role for p54 in morphogenesis supports the selection of p54 as viral fusion protein and suggests that studies about p54-EGFP trafficking during infection in live cells would be helpful to analyze the acquisition of ASFV envelopes from ER during virus assembly.
cord-326688-a1djgqpa	1982	The replication of three different MHV strains was studied in mouse dissociated spinal cord cultures containing differentiated neurons and nonneuronal cells (NN) (including astrocytes). Cell tropism and maturation of each virus strain was analyzed by immunolabeling methods using antisera to the virion or to purified membrane glycoproteins (E1 and E2) and by electron microscopy (EM). In conclusion, in primary CNS cultures consisting of neurons and NN cells: (1) wt-JHM replicates in both neurons and NN cells but has different effects on these cells; (2) Ts8-JHM exhibits no productive infection of neurons, and in NN cells appears to be defective in assembly and to stimulate membrane synthesis; (3) A59 also shows tropism restricted to NN cells which produce many viruses and display differential distribution of the two virion glycoproteins. DISCUSSION The present study describes how three different MHV strains interact in vitro with cultured neurons and NN cells, including astrocytes, isolated from mouse spinal cords.
cord-328046-5us4se5o	2001	In cells infected with avian coronavirus infectious bronchitis virus (IBV), three proteins of 100, 39, and 35 kDa, respectively, were previously identified as mature cleavage products released from the 1b region of the 1a/1b polyprotein by the 3C-like proteinase. Immunofluorescent staining of IBV-infected cells and cells expressing individual cleavage products showed that the 100-, 68-, and 58-kDa proteins were associated with the membranes of the endoplasmic reticulum, and the 39and 35-kDa proteins displayed diffuse distribution patterns. Taken together with the Q 3928 -S 2929 dipeptide bond (encoded by nucleotides 12310-12315) identified as the N-terminal cleavage site of the 100-kDa protein, cleavage at these positions would result in the release of five mature products with molecular masses of approximately 100, 68, 58, 39, and 35 kDa. Among them, the 100-, 39-, and 35-kDa proteins were specifically identified in IBV-infected cells (Liu et al., 1994 .
cord-329245-6tj2k1yn	2003	Indeed, it has been shown that both the MHV E and the infectious bronchitis virus (IBV) E proteins are sufficient for formation of the virus-like particles (VLPs) described above (Corse and Machamer, 2000; Maeda et al., 1999) , although the efficiency probably varies with cell type and protein expression system. (B) IBV-infected Vero cells were labeled with [ 35 S]methionine-cysteine at 45 h postinfection, treated with DSP as indicated, lysed, and immunoprecipitated with anti-E or anti-M antibodies as described under Materials and methods. The E and M proteins of several coronaviruses are released from cotransfected cells in membrane-bound particles that are morphologically similar to virions (VLPs), suggesting that interactions between these proteins are an integral part of coronavirus assembly (Baudoux et al., 1998; Corse and Machamer, 2000; Godeke et al., 2000; Vennema et al., 1996) .
cord-329625-hx2rsi91	2008	title: A model for the dynamic nuclear/nucleolar/cytoplasmic trafficking of the porcine reproductive and respiratory syndrome virus (PRRSV) nucleocapsid protein based on live cell imaging Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus, in common with many other positive strand RNA viruses, encodes a nucleocapsid (N) protein which can localise not only to the cytoplasm but also to the nucleolus in virus-infected cells and cells over-expressing N protein. To investigate whether the trafficking of N protein between the cytoplasm and the nucleus/nucleolus was associated with microtubules or energy dependent, the mobility of EGFP-PRRSV-N protein was compared in 3D4/31 cells incubated at 37°C in the presence and absence of nocodazole (60ng/ml nocodazole (Sigma) for 16h), a microtubule inhibitor, or incubated at 10°C. In approximately 10% of cells expressing EGFP-PRRSV-N protein fluorescence was observed in the cytoplasm, but only if imaging was adjusted so that the fluorescent signal in the nucleus/nucleolus was above the linear range (for example Fig. 8C, lower panels) .
cord-329794-msxrdhb3	2004	Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Here, we provide the evidence that RNAi targeting at coronavirus RDRP using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Design of specific shRNA expression plasmids targeting at coronavirus RDRP Coronavirus isolated from SARS patients has a large genomic RNA (approximately 30 kb). After transfecton, about 40-90% of RDRP gene expression was inhibited, depending on the sequence of the shRNA inserts, based on RT-PCR analysis in both HeLa and 293 cells transfected with RDRP (data not shown). shRNA reduced the expression of SARS RDRP mRNA in 293 and HeLa cells As shown in Fig. 1A , based on the RT-PCR analysis, the expression of extraneous RDRP gene was observed peaking at 48 h after the transfection.
cord-329819-dpgexphf	2018	IPEC-J2 cells were infected with TGEV (MOI = 2) and cultured for 30 min, then stained for fluorescence microscopy using mouse anti-APN pAb, followed by DyLight 488-conjugated goat anti-mouse IgG and rabbit anti-p-EGFR mAb, followed by DyLight 594-conjugated goat anti-rabbit IgG. Plaque formation in ST cells by the intracellular of infected IPEC-J2 cells showed that APN + EGFR-targeting shRNAs inhibited TGEV entry more significantly (Fig. 3G) . To explore the role of caveolin and clathrin in EGFR internalization early in TGEV infection, we reduced clathrin or caveolin down in normal IPEC-J2 cells through targeting shRNAs, and investigated cell membrane EGFR expression levels during TGEV invasion. We can get to the conclusion that in the early infection stage of TGEV, TGEV particles bound with APN and EGFR, the virus-receptors complex are subsequently internalized by clathrin.
cord-330847-a84pcc9z	1992	Northern and Southern hybridization with oligonucleotide probes specific for either α or γ leader sequences indicated that CV17 γ cDNA clones are representative of native CV17 γ RNAs. Furthermore, bioassays indicated that in vitro transcripts derived from these γ cDNA clones were infectious when coinoculated with in vitro transcripts of full-length α and β cDNA clones. A "bandaid" cloning strategy, which exploits the conservation of the 3'' terminal sequence, as well as the unique nature of the 5'' ends of the BSMV RNAs, has been used previously to obtain full-length cDNA clones from which infectious in vitro transcripts can be produced (3, 7). Analysis of the resulting cDNA clones suggested that CV17 RNA y is a naturally occurring chimeric recombinant, composed of a 70nucleotide (nt) a-specific leader sequence preceding a r-specific coding region. 3. ldentrfrcatron of barley stripe mosaic virus strarn CV17 LY and Type strain y-specific leader sequences In 15 putative CV17 y cDNA clones and native RNAs of strains CV17, CV42, and ND1 8.
cord-330907-srb8ac7l	1997	We have previously shown that C12 has two amino acid substitutions relative to wild type virus in the spike protein, Q159L (within a region of S1 shown to bind to viral receptor in anin vitroassay) and H716D (in the proteolytic cleavage recognition site). for the altered pathogenic properties of the mutant viruses, we compared the sequence of the spike (S) genes The murine coronavirus, mouse hepatitis virus strain of wild type and mutant viruses isolated from persistently A59 (MHV-A59), produces both hepatitis and neurologiinfected glial cells cultures. We have shown previously that the spike (S) protein from the supernatant of either the ''''C'''' culture of persisencoded by the C12 mutant has two amino acid substitutently infected glial cells at 1 week (C3), 6 weeks (C5), tions as compared with the wild type S protein.
cord-331807-ooym5eh3	2020	title: A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) The current outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China firstly. Here, we established a real-time reverse-transcription recombinase-aided amplification assay (RT-RAA) to detect SARS-CoV-2 rapidly. These results indicated that this real-time RT-RAA assay may be a valuable tool for detecting SARS-CoV-2. The minimum detection limit of real-time RAA assay was 10 copies / reaction. Use of a rapid 207 reverse-transcription recombinase aided amplification assay for respiratory syncytial virus detection Detection of 2019 novel coronavirus (2019-nCoV) by real-time 214 RT-PCR A rapid 235 and sensitive recombinase aided amplification assay to detect hepatitis B virus without DNA 236 extraction Development of a reverse 248 transcription recombinase-aided amplification assay for the detection of coxsackievirus A10 and 249 coxsackievirus A6 RNA
cord-331916-n744pymd	2006	Specific inhibition of endogenous or pathogen mRNA by RNAi can be triggered by the introduction of 21 -23 nucleotide (nt) duplexes of RNA (siRNA) or by transcription of DNA precursor into short hairpin RNAs (shRNA) homologous to target sequences (Brummelkamp et al., 2002; Elbashir et al., 2001a; Paddison et al., 2002) , opening up possibilities for controlling replicative processes of pathogens. To further examine the ability of ORF1 shRNA to suppress viral gene expression in PCV2-infected PK15 cells, single nucleotide mutations were introduced into pSIR3 sequence as shown in Fig. 4A . As shown in Fig. 4B , a mutant with one nucleotide mutation in the 5V-end of the sense strand (pSIR3-m1) still had an effective reduction in the synthesis of ORF1 and ORF2 proteins, whereas with a nucleotide substitution at the center (pSIR3-m2) or 3V-end (pSIR3-m3) of the sense sequence, the resultant shRNAs failed to significantly suppress expression of PCV2 ORF1 and ORF2 in the transfected cells, further verifying the specificity of RNAi as demonstrated (Amarzguioui et al., 2003; Harborth et al., 2003) .
cord-332356-au7s3dmp	2011	The results indicate that the binding ability of Gn-CT towards nucleic acids is rather unspecific since in addition to genomic RNA, also unrelated RNA as well as single-stranded DNA was able to interact with Gn-CTs of PUUV and TULV. Purified, lysed and micrococcal nuclease (MNase)-treated virus preparation and in vitro transcribed and radiolabeled genomic PUUV S segment were allowed to form RNA-protein complexes prior to UV cross-linking. The capability of structural proteins to bind RNA was analyzed by incubating purified, lysed and micrococcal nuclease (MNase)-treated virus preparations with radioactive PUUV S segment RNA in the case of PUUV ( The samples were immunoprecipitated with MAbs or PAbs specific to N, Gn or Gc and retained radioactivity on protein G beads after washing was measured by scintillation counting. The mapping indicated that the same peptides that were previously shown to interact with RNP and N protein (Hepojoki et al., 2010b) were capable of binding also nucleic acids (Fig. 5A ).
cord-333525-67bbmo4m	2013	In the current study, we analyzed the effects of the Endo charge-rich motif on virion incorporation of MHV S protein through substitutions of the homologous regions from the alphacoronavirus porcine transmissible gastroenteritis virus (TGEV), the betacoronaviruses bovine coronavirus (BCoV) and SARS-CoV, or the gammacoronavirus avian infectious bronchitis virus (IBV). Although the S2 portions of coronavirus S proteins show some degree of conservation, the Tm and Endo domains are highly divergent, with the exception of a conserved cluster of seven hydrophobic residues (WPWYVWL) at the start of Tm. To evaluate the functionality of different C-terminal sequence motifs in the MHV S protein, we constructed two sets of mutants in which the ectodomain of either S protein or HK protein was fused to the Tm and Endo domains from TGEV (an alphacoronavirus), BCoV (a betacoronavirus), SARS-CoV (a betacoronavirus), or IBV (a gammacoronavirus) ( Fig. 2A) . Reverting mutations in TGEV chimeras improved S assembly by eliminating positively charged residues in the endodomain MHV S protein mutants containing the entire carboxy terminus or just the charge-rich motif of TGEV S (Mut-TGEV and Mut-MMT) produced irregular plaques (Figs.
cord-334133-61om170g	2005	For example, the GL envelope protein of equine arteritis virus is proposed to have 1 or 3 MSDs (Snijder and Meulenberg, 1998) , the M protein of transmissible gastroenteritis coronavirus and equine arteritis virus, and the S antigen of hepatitis B virus are proposed to have three or four MSDs (Prange and Streeck, 1995; Risco et al., 1995; Snijder and Meulenberg, 1998) , and the herpes simplex virus glycoprotein B (Pellett et al., 1985) , and the Epstein -Barr virus 58 kDa latent protein Hennessy et al., 1984) both have multiple MSDs. Based on an analysis of their sequence and structure, we propose that the gp41 transmembrane region and C-terminal tail of all HIV-1 clades A to D can exist in two conformations, with either 1 MSD (the conventional structure) or with 3 MSDs. We suggest that these are, respectively, the majority and minority forms of intracellular Env. In the 3-MSD form, MSD 1 and MSD 2 are separated by a highly conserved beta turn, while the MSD 2 and MSD 3 support an unstructured hydrophilic loop/minor ectodomain of 41 residues that in clade B strains is highly antibody-reactive and involved in fusion.
cord-335482-nx7odchj	1984	We have observed marked reduction of infectivity in the course od serial undiluted passages of JHM virus in DBT cell culture. To avoid contamination of the standard virus stock with DI particles, plaque purified MHV (JHM strain) (Hirano et aL, 1981; Makino et al, 1983) was propagated on DBT cells at a multiplicity of infection (m.o.i.) of 0.0002 and at 15 hr postinfection (p.i.) culture fluid was harvested and clarified by low speed centrifugation. Preparation of the Standard JHM Virus for Interference Assay JHM virus was propagated on DBT cells after infection at an m.o.i. of 1.0 and was harvested at 14 hr p.i. The culture fluid was clarified by centrifugation at 8000 rpm for 30 min. To determine if the reduction in the yield of infectious virus was due to the presence of DI particles, a''n interference analysis was performed with several culture fluid samples at different passage levels.
cord-337976-c2auspti	1983	A cDNA probe representing the genome of mouse hepatitis virus (MHV) strain A59 (MHV-A59) was used to measure nucleotide sequence homologies among murine and human coronaviruses and the SD and SK coronaviruses isolated by Burks et al. Since SD and SK were isolated by inoculation of multiple sclerosis (MS) central nervous system (CNS) tissue into mice or cultured mouse cells, it is important to determine their relationships to other murine and human coronavirus isolates. Some strains of HCV such as 0C43, are antigenically related to murine coronaviruses such as MHV strain JHM (McIntosh, 1974; Gerdes et al., 1981a, b) and may be grown in the brains of suckling mice (McIntosh et al., 1967) . We have further compared murine and human coronaviruses and SD and SK by using molecular hybridization of virus-specific RNA with cDNA probes. RNA extracted either from brain homogenates of OC43-infected suckling mice or from HRT cells infected with OC43 shows homology with A59 cDNA when assayed by blot hybridization.
cord-340983-w219g6qs	2006	Using the rabies virus (RV) envelope protein as a carrier molecule we show here that inactivated RV particles can be utilized to present Bacillus anthracis protective antigen (PA) domain-4 in the viral membrane. Rabies virus is a promising vaccine vector able to induce humoral and cellular immune responses efficiently to foreign antigens (McGettigan et al., 2001a (McGettigan et al., , 2001b Schnell et al., 2000) . To evaluate the cell surface expression of the recombinant RV G-D4 fusion proteins, BSR cells were infected with recombinant vaccinia virus expressing T7 RNA polymerase for one h, transfected with 5 μg of each of the five plasmids and 24 h later fixed in paraformaldehyde, permeabilized, and immunostained with anti-PA monoclonal antibody. In contrast, PA expressed on the surface of virus particles induced potent humoral responses with either live or killed SPBN-D4-E51 particles stimulating antibody production after only a single dose.
cord-342901-ca2xxkb2	2015	Though PTB was the first, a wide spectrum of factors, largely nuclear RBPs, have also been proposed as poliovirus ITAFs, including Lupus autoantigen (La) (Meerovitch et al., 1993 (Meerovitch et al., , 1989 , poly(rC)binding proteins (PCBPs) (Blyn et al., 1996; Gamarnik and Andino, 1997) , upstream of N-ras (UNR) (Anderson et al., 2007; Boussadia et al., 2003; Hunt et al., 1999) , SRp20 (Bedard et al., 2007) and glycyl-tRNA synthetase (GARS) (Andreev et al., 2012) (Table 1 ). In addition, certain ITAFs play crucial roles in regulating the conversion of translation-competent genomic RNAs into replicationcompetent RNAs. PTB was known as a nuclear splicing factor when its role as an ITAF of poliovirus and EMCV was discovered; a classic hijacked nuclear protein pressed into a new role required for the virus.
cord-344515-e0g911le	2014	title: Inhibition of host extracellular signal-regulated kinase (ERK) activation decreases new world alphavirus multiplication in infected cells Our previous studies have indicated that host kinases including IKK-β and GSK-3β were modulated in VEEV-infected cells and that inhibition of these kinases with small molecule inhibitors resulted in decreased viral multiplication (Amaya et al., 2014; Kehn-Hall et al., 2012) . Cumulatively, the data included in Fig. 1 suggest that infection of U87MGs with the attenuated TC-83 strain of VEEV results in an activation of the ERK signaling cascade and phosphorylation of ERK1/2 at early time points after infection. Therefore, to confirm that Ag-126 treatment indeed resulted in decreased phosphorylation of ERK1/2 in U87MG cells, we investigated the intracellular p-ERK1/2 localization during VEEV infection in the presence or absence of Ag-126 at different time points using confocal microscopy as described previously (Amaya et al., 2014) .
cord-345088-krb1eidw	2004	title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature Here, we report the emergence and isolation of two temperature sensitive (ts) mutants and a revertant in the process of cold-adaptation of coronavirus infectious bronchitis virus (IBV) to a monkey kidney cell line. Evidence presented demonstrated that the Q(294)-to-L(294) mutation, located at a highly conserved domain of the S1 subunit, might hamper processing of the S protein to a matured 180-kDa, endo-glycosidase H-resistant glycoprotein and the translocation of the protein to the cell surface. In virus-infected cells, the Endo-H sensitive, 155-kDa form of ts291602 was abundant at the nonpermissive temperature, clearly indicating that the mutant S protein was trimmed in the ER and cis-Golgi but was not transported to the trans-Golgi.
cord-345630-bam3pa70	1991	authors: Lee, Han-Jung; Shieh, Chien-Kou; Gorbalenya, Alexander E.; Koonin, Eugene V.; La Monica, Nicola; Tuler, Jeremy; Bagdzhadzhyan, Anush; Lai, Michael M.C. title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase Third, the 3''-half of the gene 1 sequences of IBV and MHV-A59 contains the sequence motifs for RNA polymerase and helicase, which are the activities expected to be involved in RNA synthesis Gorbalenya et a/., 198913; Bredenbeek et a/., 1990) . The alignment of amino acids in ORF la of MHV-JHM and IBV showed that there are four possible stretches of moderate homology which are separated by highly diverged sequences (Fig. 8) . Although ORF la is highly diverged between MHV-JHM and IBV, common functional domains could be identified in this ORF of both viruses by detailed amino acid sequence analysis (see Materials and Methods) (Fig. 9 ).
cord-346514-vyo8l14p	2013	The polyadenylation signal in the 3′ UTR of BaMV was shown to be involved in the synthesis of minus-strand viral RNA and regulating the length of the poly(A) tail (Chen et al., 2005) . To test whether the replicase preparation could polyadenylate exogenous plus-strand RNA templates, 5′ end-labeled radioactive BaMV plus-strand RNA substrate containing the entire 3′-UTR and 7, 15, or 40 adenylates (r138/7A, r138/15A, or r138/40A, respectively), were subjected to the polyadenylation activity assay. BaMV minigenomes were demonstrated to be suitable templates for an in vitro replication assays (Huang et al., 2009) ; therefore, the exogenous plus-strand or minus-strand BaMV minigenome was added to the reaction to help determine whether the poly(A) tail could be added to the 3′ end of preformed or newly transcribed plus-strand RNA, respectively.
cord-351197-xv6ymc4l	2020	From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. A detailed taxonomic 136 classification, including the numbers of reads for each Eukarya-related viral contig 137 recovered is this study, is provided in Supplementary gives them the ability to persist and spread in the environment. A detailed taxonomic classification, including the numbers of 245 J o u r n a l P r e -p r o o f sequenced reads of each Eukarya-related viral contig recovered in this study, is 246 provided in Supplementary Table 1 . including numbers of sequenced reads of each Eukarya-related viral contig recovered in 334 this study, is provided in Supplementary Table 1 . Cressdnaviricota: a virus phylum unifying 7 families of Rep-encoding 519 viruses with single-stranded, circular DNA genomes
cord-353467-wbtzvm4i	2004	In the late stages of an HBV infection, progeny virions are formed by budding of the pre-assembled cytosolic nucleocapsids, enclosing the partially double-stranded DNA genome 3.2 kb in length and the viral polymerase through intracellular membranes accommodating the viral envelope proteins (for review, see Nassal, 1996) . To determine whether the co-secreted GFP.S and SHA proteins resembled authentic subviral HBV envelope particles, the culture supernatant of transfected cells was fractionated by isopycnic CsCl gradient centrifugation and fractions were analyzed by an S-specific ELISA. According to current models for the transmembrane structure of S, its N-terminus and hence the GFP fusion site are located to the lumenal side of intracellular membranes that is topologically equivalent to the virion surface ( Fig. 4A ) (Berting et al., 1995; Stirk et al., 1992) . Here we applied this approach to hepatitis B virus and obtained fluorescent subviral and viral particles by incorporation of the viral S envelope protein, tagged with GFP, in trans, thereby preserving all the functions necessary for the viral life cycle.
cord-353748-y1a52z8e	2021	title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 Nisin, a food-grade antimicrobial peptide produced by lactic acid bacteria has been examined for its probable interaction with the human ACE2 (hACE2) receptor, the site where spike protein of SARS-CoV-2 binds. Among the eight nisin variants examined, nisin H, nisin Z, nisin U and nisin A showed a significant binding affinity towards hACE2, higher than that of the RBD (receptor binding domain) of the SARS-CoV-2 spike protein. The present study attempts to investigate the ability of food-grade nisin A and its natural variants to block the interaction between hACE2 and the spike protein of SARS-CoV-2, a key step of COVID-19 disease initiation. The binding affinity of docked structures of all eight variants of nisin in complex with hACE2 was calculated as ΔG derived from analysis with Prodigy for each complex in comparison with the RBD of spike protein of SARS-CoV-2.