# bib

id: cord-300884-rqfxe0x1
title: Genomic characterization of equine coronavirus
author: Zhang, Jianqiang
date: 2007-12-05
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url: https://www.sciencedirect.com/science/article/pii/S0042682207004655
doi: 10.1016/j.virol.2007.06.035
summary:
  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) .

abstract:
  The complete genome sequence of the first equine coronavirus (ECoV) isolate, NC99 strain was accomplished by directly sequencing 11 overlapping fragments which were RT–PCR amplified from viral RNA. The ECoV genome is 30,992 nucleotides in length, excluding the polyA tail. 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). The two replicase polyproteins are predicted to be proteolytically processed by three virus-encoded proteases into 16 non-structural proteins (nsp1–16). The ECoV nsp3 protein had considerable amino acid deletions and insertions compared to the nsp3 proteins of bovine coronavirus, human coronavirus OC43, and porcine hemagglutinating encephalomyelitis virus, three group 2 coronaviruses phylogenetically most closely related to ECoV. The structure of subgenomic mRNAs was analyzed by Northern blot analysis and sequencing of the leader–body junction in each sg mRNA.


id: cord-301293-jqy7lcbk
author: Gupta, Vandana
date: 2006-03-30
txt: ./txt/cord-301293-jqy7lcbk.txt
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url: https://www.sciencedirect.com/science/article/pii/S004268220500783X
doi: 10.1016/j.virol.2005.11.042
summary:
  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.

title:
  SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens

abstract:
  Correspondence between the T-cell epitope responses of vaccine immunogens and those of pathogen antigens is critical to vaccine efficacy. 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). Lysosomal trafficking of the LAMP/N chimera in transfected cells was documented by both confocal and immunoelectron microscopy. The responses of the immunized mice differed markedly. The strongest T-cell IFN-γ and CTL responses were to the LAMP-N chimera followed by the pN immunogen. In contrast, N-GST elicited strong T cell IL-4 but minimal IFN-γ responses and a much greater antibody response. Despite these differences, however, the immunodominant T-cell ELISpot responses to each of the three immunogens were elicited by the same N peptides, with the greatest responses being generated by a cluster of five overlapping peptides, N(76–114), each of which contained nonameric H2(d) binding domains with high binding scores for both class I and, except for N(76–93), class II alleles. These results demonstrate that processing and presentation of N, whether exogenously or endogenously derived, resulted in common immunodominant epitopes, supporting the usefulness of modified antigen delivery and trafficking forms and, in particular, LAMP chimeras as vaccine candidates. Nevertheless, the profiles of T-cell responses were distinctly different. The pronounced Th-2 and humoral response to N protein plus adjuvant are in contrast to the balanced IFN-γ and IL-4 responses and strong memory CTL responses to the LAMP-N chimera.


id: cord-301755-fxfsr9bj
author: Wang, F.-I.
date: 1992-02-29
txt: ./txt/cord-301755-fxfsr9bj.txt
cache: ./cache/cord-301755-fxfsr9bj.txt
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url: https://api.elsevier.com/content/article/pii/004268229290041M
doi: 10.1016/0042-6822(92)90041-m
summary:
  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) .

title:
  Sequence analysis of the spike protein gene of murine coronavirus variants: Study of genetic sites affecting neuropathogenicity

abstract:
  Abstract Mouse hepatitis virus (MHV), a coronavirus, causes encephalitis and demyelination in susceptible rodents. Previous investigations have shown that the MHV spike (S) protein is a critical determinant of viral tropism and pathogenicity in mice and rats. 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. This site was in the S2 subunit of the S protein. In contrast, variant 7.2-V-1, which was selected with MAb J.7.2 and primarily caused encephalitis, had two point mutations at NT 1766 and 1950, which were in the S1 subunit. Finally, the double mutant 2.2/7.2-V-2, which was selected with both MAbs J.2.2 and J.7.2, and was attenuated with respect to both virulence and the ability to cause demyelination, had a deletion spanning from NT 1523 to 1624 in the S1 and a point mutation at NT 3340 in the S2. We conclude that at least two regions of the S protein contribute to neuropathogenicity of MHV. We have also isolated a partial revertant of 2.2-V-1, which was partially resistant to MAb 1.2.2 but retained the same neuropathogenicity as the variant 2.2-V-1. This revenant retained the mutation at NT 3340, but had a second-site mutation at NT 1994, further confirming that NT 3340 contributed to the pathogenic phenotype of MHV. By comparing these results with MHV variants isolated in other laboratories, which had mutations in other sites on the S gene and yet retained the demyelinating ability, we suggest that the ability of JHM viruses to induce demyelination is determined by the interaction of multiple sites on the S gene, rather than the characteristics of a single, unique site. Our study also revealed the possible presence of microheterogeneity of S gene sequence, particularly in the S1 region, in these viruses. The sequence microheterogeneity may also contribute to the differences in their biological properties.


id: cord-302486-z36hcvrx
title: Diagnostic approaches for viruses and prions in stem cell banks
author: Cobo, Fernando
date: 2006-03-30
txt: ./txt/cord-302486-z36hcvrx.txt
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mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682205007725
doi: 10.1016/j.virol.2005.11.026
summary:
  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.

abstract:
  Some stem cell lines may contain an endogenous virus or can be contaminated with exogenous viruses (even of animal origin) and may secrete viral particles or express viral antigens on their surface. Moreover, certain biotechnological products (e.g. bovine fetal serum, murine feeder cells) may contain prion particles. 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. Stem cell banks should introduce adequate quality assurance programs like the microbiological control program and can provide researchers with valuable support in the standardization and safety of procedures and protocols used for the viral and prion testing and in validation programs to assure the quality and safety of the cells.


id: cord-302972-imtttzvr
title: Glycosylation and oligomerization of the spike protein of marburg virus
author: Feldmann, H.
date: 1991-05-31
txt: ./txt/cord-302972-imtttzvr.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/2024471/
doi: 10.1016/0042-6822(91)90680-a
summary:
  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.

abstract:
  Abstract The oligosaccharide side chains of the glycoprotein of Marburg virus (MW 170,000) have been analyzed by determining their sensitivity to enzymatic degradation and their reactivity with lectins. It was found that they consist of N- and O-glycans. Studies employing chemical cross-linking showed that the glycoprotein is present as a homotrimer in the viral envelope.


id: cord-303238-us3dybue
title: Membrane Topology of Murine Coronavirus Replicase Nonstructural Protein 3
author: Kanjanahaluethai, Amornrat
date: 2007-05-01
txt: ./txt/cord-303238-us3dybue.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17222884/
doi: 10.1016/j.virol.2006.12.009
summary:
  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 ).

abstract:
  Mouse hepatitis virus (MHV) is a member of the family Coronaviridae. These positive strand RNA viruses encode a replicase polyprotein that is processed into 16 nonstructural proteins (nsps). The nsps assemble with membranes to generate double membrane vesicles, which are the sites of viral RNA synthesis. MHV nsp3 contains multiple domains including two papain-like protease domains, PLP1 and PLP2, and a predicted transmembrane (TM) domain. In this study, we determined the membrane topology of nsp3-TM and showed that TM-mediated tethering of PLP2 is important for processing at cleavage site 3. Biochemical analysis revealed that nsp3 is an integral membrane protein that is inserted into endoplasmic reticulum (ER) membranes co-translationally and glycosylated at asparagine-2357. Proteinase K digestion experiments indicate that the TM domain of nsp3 has 4 membrane-spanning helices. We show that nsp3-TM is sufficient to mediate ER membrane association of a cytosolic protein. This study is the first detailed analysis of the topology and function of the coronavirus nsp3 TM domain.


id: cord-303497-s3zs1oxf
title: Characterization of a cold-sensitive (cs) recombinant between two influenza a strains
author: Breuning, Astrid
date: 1983-10-15
txt: ./txt/cord-303497-s3zs1oxf.txt
cache: ./cache/cord-303497-s3zs1oxf.txt
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mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/0042682283901174
doi: 10.1016/0042-6822(83)90117-4
summary:
  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.

abstract:
  Abstract Recombinants between fowl plague virus (FPV, H7N1) and the Hong Kong (H3N2) or Singapore (H2N2) influenza virus strains carrying the hemagglutinin of FPV and the neuraminidase of the human strains form only very tiny plaques at 33°, but normal plaques at 37°. One recombinant (113/Ho) has been studied in more detail. It multiplies only very slowly at 33°, the nonpermissive temperature. Adsorption and penetration are normal at 33°, but synthesis of protein is impeded. Temperature-shift experiments suggest that the synthesis of viral mRNA is slowed at 33°. 113/Ho does not agglutinate chicken erythrocytes at 40°, as the parent viruses do. 113/Ho can be adapted to grow normally at 33°. The frequency of adaptation is comparable to reversion of a single point mutation (ca. 10−5). Recombinants which grow well at 37° but not at 33° are called cold-sensitive (cs) recombinants.


id: cord-304421-xpj6c0vx
author: Piñón, Josefina D.
date: 1999-10-25
txt: ./txt/cord-304421-xpj6c0vx.txt
cache: ./cache/cord-304421-xpj6c0vx.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682299999543
doi: 10.1006/viro.1999.9954
summary:
  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.

title:
  Further Requirements for Cleavage by the Murine Coronavirus 3C-like Proteinase: Identification of a Cleavage Site within ORF1b

abstract:
  Abstract The coronavirus mouse hepatitis virus strain A59 (MHV-A59) encodes a 3C-like proteinase (3CLpro) that is proposed to be responsible for the majority of the processing events that take place within the replicase polyproteins pp1a and pp1ab. In this study we demonstrate that the Q939↓S940 peptide bond, located between the polymerase and Zn-finger regions of pp1ab (the POL↓Zn site), is processed by the 3CLpro, albeit inefficiently. Mutagenesis of the POL↓Zn site, as well as the previously identified HD1↓3C site in the 1a region of pp1a and pp1ab, demonstrated that the amino acid residues at the P2 and P1 positions of the cleavage site, occupied by L and Q, respectively, were important determinants of 3CLpro substrate specificity. Finally, a direct comparison of the 3CLpro-mediated cleavages at the HD1↓3C and POL↓Zn sites was made by determining the rate constants using synthetic peptides. The results show that while a larger polypeptide substrate carrying the HD1↓3C site was processed more efficiently than a polypeptide substrate carrying the POL↓Zn site, cleavage of the synthetic peptide substrates containing these two cleavage sites occurred at similar efficiencies. This indicates that the overall conformation of a large polyprotein substrate is important in the accessibility of the cleavage site to the proteinase.


id: cord-305143-mqd4ioj4
author: Zmasek, Christian M.
date: 2019-01-06
txt: ./txt/cord-305143-mqd4ioj4.txt
cache: ./cache/cord-305143-mqd4ioj4.txt
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mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682219300054
doi: 10.1016/j.virol.2019.01.005
summary:
  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.

title:
  Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO)

abstract:
  We developed a computational approach called Domain-architecture Aware Inference of Orthologs (DAIO) for the analysis of protein orthology by combining phylogenetic and protein domain-architecture information. Using DAIO, we performed a systematic study of the proteomes of all human Herpesviridae species to define Strict Ortholog Groups (SOGs). In addition to assessing the taxonomic distribution for each protein based on sequence similarity, we performed a protein domain-architecture analysis for every protein family and computationally inferred gene duplication events. While many herpesvirus proteins have evolved without any detectable gene duplications or domain rearrangements, numerous herpesvirus protein families do exhibit complex evolutionary histories. Some proteins acquired additional domains (e.g., DNA polymerase), whereas others show a combination of domain acquisition and gene duplication (e.g., betaherpesvirus US22 family), with possible functional implications. This novel classification system of SOGs for human Herpesviridae proteins is available through the Virus Pathogen Resource (ViPR, www.viprbrc.org).


id: cord-305564-dj3vj4tk
title: PATHOGENICITY OF SEVERE ACUTE RESPIRATORY CORONAVIRUS DELETION MUTANTS IN hACE-2 TRANSGENIC MICE
author: DeDiego, Marta L.
date: 2008-07-01
txt: ./txt/cord-305564-dj3vj4tk.txt
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mime: text/plain
url: https://doi.org/10.1016/j.virol.2008.03.005
doi: 10.1016/j.virol.2008.03.005
summary:
  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

abstract:
  Recombinant severe acute respiratory virus (SARS-CoV) variants lacking the group specific genes 6, 7a, 7b, 8a, 8b and 9b (rSARS-CoV-Δ[6-9b]), the structural gene E (rSARS-CoV-ΔE), and a combination of both sets of genes (rSARS-CoV-Δ[E,6-9b]) have been generated. 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. Furthermore, in Vero E6 cells, all the viruses showed the formation of particles with the same morphology as the wt virus, indicating that these proteins do not have a high impact in the final morphology of the virions. Nevertheless, in the absence of E protein, release of virus particles efficacy was reduced. Viruses lacking E protein grew about 100-fold lower than the wt virus in lungs of Tg infected mice but did not grow in the brains of the same animals, in contrast to the rSARS-CoV-Δ[6-9b] virus, which grew almost as well as the wt in both tissues. Viruses lacking E protein were highly attenuated in the highly sensitive hACE-2 Tg mice, in contrast to the minimal rSARS-CoV-Δ[6-9b] and wt viruses. 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.


id: cord-307354-dkwcheu0
title: Emerging roles for RNA degradation in viral replication and antiviral defense
author: Abernathy, Emma
date: 2015-05-31
txt: ./txt/cord-307354-dkwcheu0.txt
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mime: text/plain
url: https://doi.org/10.1016/j.virol.2015.02.007
doi: 10.1016/j.virol.2015.02.007
summary:
  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

abstract:
  Abstract Viral replication significantly alters the gene expression landscape of infected cells. Many of these changes are driven by viral manipulation of host transcription or translation machinery. Several mammalian viruses encode factors that broadly dampen gene expression by directly targeting messenger RNA (mRNA). Here, we highlight how these factors promote mRNA degradation to globally regulate both host and viral gene expression. Although these viral factors are not homologous and use distinct mechanisms to target mRNA, many of them display striking parallels in their strategies for executing RNA degradation and invoke key features of cellular RNA quality control pathways. In some cases, there is a lack of selectivity for degradation of host versus viral mRNA, indicating that the purposes of virus-induced mRNA degradation extend beyond redirecting cellular resources towards viral gene expression. In addition, several antiviral pathways use RNA degradation as a viral restriction mechanism, and we will summarize new findings related to how these host-encoded ribonucleases target and destroy viral RNA.


id: cord-307396-u6v6bxwj
author: Liao, Y.
date: 2006-06-05
txt: ./txt/cord-307396-u6v6bxwj.txt
cache: ./cache/cord-307396-u6v6bxwj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16507314/
doi: 10.1016/j.virol.2006.01.028
summary:
  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).

title:
  Biochemical and functional characterization of the membrane association and membrane permeabilizing activity of the severe acute respiratory syndrome coronavirus envelope protein

abstract:
  A diverse group of cytolytic animal viruses encodes small, hydrophobic proteins to modify host cell membrane permeability to ions and small molecules during their infection cycles. In this study, we show that expression of the SARS-CoV E protein in mammalian cells alters the membrane permeability of these cells. Immunofluorescent staining and cell fractionation studies demonstrate that this protein is an integral membrane protein. It is mainly localized to the ER and the Golgi apparatus. The protein can be translocated to the cell surface and is partially associated with lipid rafts. Further biochemical characterization of the protein reveals that it is posttranslationally modified by palmitoylation on all three cysteine residues. Systematic mutagenesis studies confirm that the membrane permeabilizing activity of the SARS-CoV E protein is associated with its transmembrane domain.


id: cord-307904-lnagg1uw
title: Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo
author: Johnson, Jennifer A
date: 2003-08-15
txt: ./txt/cord-307904-lnagg1uw.txt
cache: ./cache/cord-307904-lnagg1uw.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S004268220300285X
doi: 10.1016/s0042-6822(03)00285-x
summary:
  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 ).

abstract:
  Barley stripe mosaic virus (BSMV) contains three positive-sense, single-stranded genomic RNAs, designated α, β, and γ, that encode seven major proteins and one minor translational readthrough protein. Three proteins (αa, βa, and γa) are translated directly from the genomic RNAs and the remaining proteins encoded on RNAβ and RNAγ are expressed via three subgenomic messenger RNAs (sgRNAs). sgRNAβ1 directs synthesis of the triple gene block 1 (TGB1) protein. The TGB2 protein, the TGB2′ minor translational readthrough protein, and the TGB3 protein are expressed from sgRNAβ2, which is present in considerably lower abundance than sgRNAβ1. A third sgRNA, sgRNAγ, is required for expression of the γb protein. We have used deletion analyses and site-specific mutations to define the boundaries of promoter regions that are critical for expression of the BSMV sgRNAs in infected protoplasts. The results reveal that the sgRNAβ1 promoter encompasses positions −29 to −2 relative to its transcription start site and is adjacent to a cis-acting element required for RNAβ replication that maps from −107 to −74 relative to the sgRNAβ1 start site. The core sgRNAβ2 promoter includes residues −32 to −17 relative to the sgRNAβ2 transcriptional start site, although maximal activity requires an upstream hexanucleotide sequence residing from positions −64 to −59. The sgRNAγ promoter maps from −21 to +2 relative to its transcription start site and therefore partially overlaps the γa gene. The sgRNAβ1, β2, and γ promoters also differ substantially in sequence, but have similarities to the putative homologous promoters of other Hordeiviruses. These differences are postulated to affect competition for the viral polymerase, coordination of the temporal expression and abundance of the TGB proteins, and constitutive expression of the γb protein.


id: cord-308835-999kewdw
title: The virus-specific intracellular RNA species of two murine coronaviruses: MHV-A59 and MHV-JHM
author: Leibowitz, Julian L.
date: 1981-10-15
txt: ./txt/cord-308835-999kewdw.txt
cache: ./cache/cord-308835-999kewdw.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/0042682281902506
doi: 10.1016/0042-6822(81)90250-6
summary:
  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.

abstract:
  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. These RNA species range in size from 6.3 × 105 to 6.1 × 106 daltons. The A59V and JHMV-specific RNAs have identical molecular weights and comigrate in agarose gels. 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. The fingerprinting studies also demonstrate that the six subgenomic RNA species make up a nested set. The sequences present in each RNA species are also present in all larger RNA species. These larger RNAs also contain additional sequences consistent with their greater size. The subgenomic RNAs fulfull many of the criteria for mRNAs. Possible mechanisms for generating these RNAs are discussed.


id: cord-309015-t5v2sjus
author: York, Joanne
date: 2005-12-20
txt: ./txt/cord-309015-t5v2sjus.txt
cache: ./cache/cord-309015-t5v2sjus.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682205005209
doi: 10.1016/j.virol.2005.08.030
summary:
  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) .

title:
  Genetic analysis of heptad-repeat regions in the G2 fusion subunit of the Junín arenavirus envelope glycoprotein

abstract:
  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. We have investigated the role of these heptad-repeat regions and, specifically, the importance of the putative interhelical a and d position sidechains by using alanine-scanning mutagenesis. All the mutant glycoproteins were expressed and transported to the cell surface. Proteolytic maturation at the subtilisin kexin isozyme-1/site-1-protease (SKI-1/S1P) cleavage site was observed in all but two of the mutants. Among the adequately cleaved mutant glycoproteins, four positions in the N-terminal region (I333, L336, L347 and L350) and two positions in the C-terminal region (R392 and W395) were shown to be important determinants of cell–cell fusion. Taken together, our results indicate that α-helical coiled-coil structures are likely critical in promoting arenavirus membrane fusion. These findings support the inclusion of the arenavirus GP-C among the Class I viral fusion proteins and suggest pharmacologic and immunologic strategies for targeting arenavirus infection and hemorrhagic fever.


id: cord-309469-2naxn580
author: An, Hongliu
date: 2019-01-05
txt: ./txt/cord-309469-2naxn580.txt
cache: ./cache/cord-309469-2naxn580.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2018.12.019
doi: 10.1016/j.virol.2018.12.019
summary:
  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.

title:
  Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus

abstract:
  Viral noncoding (nc) RNAs have been shown to play important roles in viral life cycle. Many viruses employ different mechanism to produce ncRNAs. Here, we report that coronavirus infectious bronchitis virus (IBV) produces a novel ncRNA in virus-infected cells. This ncRNA consists of 563 nucleotides excluding a poly(A) tail, is mainly derived from the 3′-untranslated region of IBV genome, and contains a 63-nt-long of terminal leader sequence derived from the 5′ end of the viral genome. Using mutagenesis and reverse genetics, we reveal that this ncRNA is a subgenomic RNA generated by discontinuous transcription mechanism.


id: cord-309919-sm5o0g1c
title: Mammalian orthoreovirus core protein μ2 reorganizes host microtubule-organizing center components.
author: Eichwald, Catherine
date: 2020-08-04
txt: ./txt/cord-309919-sm5o0g1c.txt
cache: ./cache/cord-309919-sm5o0g1c.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682220301355?v=s5
doi: 10.1016/j.virol.2020.07.008
summary:
  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.

abstract:
  Filamentous mammalian orthoreovirus (MRV) viral factories (VFs) are membrane-less cytosolic inclusions in which virus transcription, replication of dsRNA genome segments, and packaging of virus progeny into newly synthesized virus cores take place. 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. Moreover, the MT-nucleation centers significantly increased in numbers, and γ-tubulin was pulled-down in a binding assay when co-expressed with histidine-tagged-μ2 and μNS. Thus, μ2, by interaction with γ-tubulin, can modulate MTOCs localization and function according to viral needs.


id: cord-310218-fky0cm5e
author: Yoo, Dongwan
date: 1991-01-31
txt: ./txt/cord-310218-fky0cm5e.txt
cache: ./cache/cord-310218-fky0cm5e.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/004268229190045D
doi: 10.1016/0042-6822(91)90045-d
summary:
  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) .

title:
  The S2 subunit of the spike glycoprotein of bovine coronavirus mediates membrane fusion in insect cells

abstract:
  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. Extensive syncytia formation was observed in cells infected with the S2 recombinant but not with the HE or S1 recombinant baculoviruses. Fusion of Sf9 cells expressing the intact S protein precursor was evident after trypsin treatment. These results demonstrate that proteolytic cleavage of the S spike precursor is required for fusion induction and that the fusion is mediated by the S2 subunit. These observations may reflect the biological role of the S2 subunit in fusion-penetration during bovine coronavirus infection.


id: cord-310748-ao29zx1u
title: Random nature of coronavirus RNA recombination in the absence of selection pressure
author: Banner, Lisa R.
date: 1991-11-30
txt: ./txt/cord-310748-ao29zx1u.txt
cache: ./cache/cord-310748-ao29zx1u.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/004268229190795D
doi: 10.1016/0042-6822(91)90795-d
summary:
  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) .

abstract:
  Abstract RNA-RNA recombination is thought to occur preferentially at certain selected sites and in only a few RNA viruses; the mechanism for these restrictions is unknown. In this paper we report the development of a recombination assay for coronavirus, using polymerase chain reaction, in the absence of selection pressure. Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. Thus, coronavirus RNA recombination appears to be more random than previously realized. However, after serial passages of the recombinant viruses in tissue culture, the recombination sites among the progeny viruses became clustered in the region which contains the previously reported “hot spot” for coronavirus recombination. These results suggest that RNA recombination is common and random in nature, but only certain recombinants can be selected. Thus, the presence of recombinational “hot spots” for coronavirus or other RNA viruses most likely resulted from selection of certain recombinant viruses and not restriction on the occurrence of RNA recombination. The failure to detect recombinants in other RNA viruses may therefore be due to unfavorable properties of recombinant viruses. This approach can be used to detect recombinants in these viruses.


id: cord-310967-15mv5yx7
author: Morris, Vincent L.
date: 1989-03-31
txt: ./txt/cord-310967-15mv5yx7.txt
cache: ./cache/cord-310967-15mv5yx7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/2538027/
doi: 10.1016/0042-6822(89)90048-2
summary:
  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.

title:
  Characterization of coronavirus JHM variants isolated from wistar furth rats with a viral-induced demyelinating disease

abstract:
  Abstract Murine hepatitis virus (MHV) can cause neurological disease when inoculated intracerebrally (ic) into mice and rats. Specifically the JHM strain of MHV (MHV-JHM) generally causes an acute encephalitis when inoculated is into 2-day-old Wistar Furth rats. In contrast, JHM generally produces a chronic demyelinating disease with resulting posterior paralysis when inoculated is into 10-day-old Wistar Furth rats. In addition, while JHM readily produces a productive infection in a mouse fibroblast cell line (L-2), it does not form syncytia or replicate well in a tissue cell line of glial origin (G26-24). We have isolated and characterized three MHV-JHM viral variants from the central nervous system of two Wistar Furth rats with a MHV-JHM-induced demyelinating disease. The pattern of viral-specific mRNA for all three of these variants differed from what was observed for the wild-type parental MHV-JHM that had been passaged only in tissue culture. One of these variants, ATIIf cord virus, which induced a chronic demyelinating disease in 2- or 10-day-old intracerebrally inoculated Wistar Furth rats, had a deletion in the coding region of the peplomer glycoprotein mRNA. In addition, this variant formed massive syncytia and replicated well in G26-24 cells. We have not detected this deletion in the other two JHM variants, ATIIf brain virus and ATIIe brain virus. ATIIf brain virus and ATIIe brain virus primarily produced an acute encephalitis when reinoculated into 2-or 10-day-old Wistar Furth rats. In addition, these two variants did not form syncytia and had a reduced ability to replicate in G26-24 cells.


id: cord-311255-zaa8i9vh
author: Kim, Youngnam
date: 2014-07-31
txt: ./txt/cord-311255-zaa8i9vh.txt
cache: ./cache/cord-311255-zaa8i9vh.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2014.04.040
doi: 10.1016/j.virol.2014.04.040
summary:
  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.

title:
  Porcine epidemic diarrhea virus induces caspase-independent apoptosis through activation of mitochondrial apoptosis-inducing factor

abstract:
  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. PEDV-infected cells showed evidence of apoptosis in vitro and in vivo. However, experimental data indicated that the caspase cascade is not involved in PEDV-induced apoptotic cell death. 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. CsA treatment resulted in significant inhibition of PEDV-triggered apoptosis and suppressed PEDV replication. Furthermore, direct inhibition of AIF strongly impaired PEDV infection and virus-induced apoptosis. 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.


id: cord-311774-fhdvcvi0
title: Foot-and-mouth disease virus utilizes an autophagic pathway during viral replication
author: O'Donnell, Vivian
date: 2011-02-05
url: https://api.elsevier.com/content/article/pii/S004268221000704X
doi: 10.1016/j.virol.2010.10.042
abstract:
  Foot-and-mouth disease virus (FMDV) is the type species of the Aphthovirus genus within the Picornaviridae family. Infection of cells with positive-strand RNA viruses results in a rearrangement of intracellular membranes into viral replication complexes. The origin of these membranes remains unknown; however induction of the cellular process of autophagy is beneficial for the replication of poliovirus, suggesting that it might be advantageous for other picornaviruses. By using confocal microscopy we showed in FMDV-infected cells co-localization of non-structural viral proteins 2B, 2C and 3A with LC3 (an autophagosome marker) and viral structural protein VP1 with Atg5 (autophagy-related protein), and LC3 with LAMP-1. Importantly, treatment of FMDV-infected cell with autophagy inducer rapamycin, increased viral yield, and inhibition of autophagosomal pathway by 3-methyladenine or small-interfering RNAs, decreased viral replication. Altogether, these studies strongly suggest that autophagy may play an important role during the replication of FMDV.


id: cord-312210-3x9s3g8n
author: Stoian, Ana
date: 2019-12-24
txt: ./txt/cord-312210-3x9s3g8n.txt
cache: ./cache/cord-312210-3x9s3g8n.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682219303496
doi: 10.1016/j.virol.2019.12.007
summary:
  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.

title:
  The use of cells from ANPEP knockout pigs to evaluate the role of aminopeptidase N (APN) as a receptor for porcine deltacoronavirus (PDCoV)

abstract:
  The coronaviruses, porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV) represent important sources of neonatal diarrhea on pig farms. The requirement for aminopeptidase N (APN) as a receptor for TGEV, but not for PEDV, is well established. In this study, the biological relevance of APN as a receptor for PDCoV was tested by using CRISPR/Cas9 to knockout the APN gene, ANPEP, in pigs. Porcine alveolar macrophages (PAMs) from ANPEP knockout (KO) pigs showed resistance to PDCoV infection. However, lung fibroblast-like cells, derived from the ANPEP KO PAM cultures, supported PDCoV infection to high levels. The results suggest that APN is a receptor for PDCoV in PAMs but is not necessary for infection of lung-derived fibroblast cells. The infection of the ANPEP KO pigs with PDCoV further confirmed that APN is dispensable as a receptor for PDCoV.


id: cord-313091-ksrxsdpp
title: Wild-type human coronaviruses prefer cell-surface TMPRSS2 to endosomal cathepsins for cell entry
author: Shirato, Kazuya
date: 2017-12-06
txt: ./txt/cord-313091-ksrxsdpp.txt
cache: ./cache/cord-313091-ksrxsdpp.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2017.11.012
doi: 10.1016/j.virol.2017.11.012
summary:
  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) .

abstract:
  Human coronaviruses (HCoVs) enter cells via two distinct pathways: the endosomal pathway using cathepsins to activate spike protein and the cell-surface or early endosome pathway using extracellular proteases such as transmembrane protease serine 2 (TMPRSS2). We previously reported that clinical isolates of HCoV-229E preferred cell-surface TMPRSS2 to endosomal cathepsin for cell entry, and that they acquired the ability to use cathepsin L by repeated passage in cultured cells and were then able to enter cells via the endosomal pathway. Here, we show that clinical isolates of HCoV-OC43 and -HKU1 preferred the cell-surface TMRRSS2 to endosomal cathepsins for cell entry, similar to HCoV-229E. In addition, the cell-culture-adapted HCoV-OC43 lost the ability to infect and replicate in air-liquid interface cultures of human bronchial tracheal epithelial cells. These results suggest that circulating HCoVs in the field generally use cell-surface TMPRSS2 for cell entry, not endosomal cathepsins, in human airway epithelial cells.


id: cord-313906-fh85fzq9
title: Characterization of the glycoproteins of bat-derived influenza viruses
author: Maruyama, Junki
date: 2016-01-15
txt: ./txt/cord-313906-fh85fzq9.txt
cache: ./cache/cord-313906-fh85fzq9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26605499/
doi: 10.1016/j.virol.2015.11.002
summary:
  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.

abstract:
  Recently found bat-derived influenza viruses (BatIVs) have hemagglutinin (HA) and neuraminidase (NA) gene segments distinct from those of previously known influenza A viruses. However, pathogenicities of these BatIVs remain unknown since infectious virus strains have not been isolated yet. To gain insight into the biological properties of BatIVs, we generated vesicular stomatitis viruses (VSVs) pseudotyped with the BatIV HA and NA. 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. These data provide fundamental information on the mechanisms underlying the cellular entry and host restriction of BatIVs.


id: cord-315069-xo4mbxei
author: Knorr, D. A.
date: 1991-03-31
txt: ./txt/cord-315069-xo4mbxei.txt
cache: ./cache/cord-315069-xo4mbxei.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/004268229190484S
doi: 10.1016/0042-6822(91)90484-s
summary:
  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).

title:
  De novo generation of defective interfering RNAs of tomato bushy stunt virus by high multiplicity passage

abstract:
  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. Symptom attenuation leading to persistent infections was closely correlated with the passage in which DIs first developed. Comparisons of nucleotide sequences of 10 cDNA clones from 2 DI RNA populations and with a previously characterized TBSV DI RNA revealed the same four regions of sequence from the TBSV genome were strictly conserved in each of the DI RNAs: the virus 5′ leader sequence of 168 bases; a region of approximately 200–250 bases from the viral polymerase gene; approximately 70 bases from the 3′ terminus of the viral pl9 and p22 genes; and approximately 130 bases from the 3′terminal noncoding region. Conservation of the sequence motif present in all of the DIs suggests that there might be a common mechanism of DI formation as well as selection pressure to maintain sequences essential for replication and encapsidation.


id: cord-315158-f6msh8od
author: Taguchi, Fumihiro
date: 1989-03-31
txt: ./txt/cord-315158-f6msh8od.txt
cache: ./cache/cord-315158-f6msh8od.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682289900615
doi: 10.1016/0042-6822(89)90061-5
summary:
  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.

title:
  Comparison of six different murine coronavirus jhm variants by monoclonal antibodies against the e2 glycoprotein

abstract:
  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. Two of these variants, sp-4 and JHM-X, were found to have smaller mRNA3 and E2 glycoprotein species compared with those of the other four variants. In addition, sp-4 and JHM-X were distinguished from the other four variants by their inability to bind to monoclonal antibodies recognizing two antigenic domains of the E2 molecule. Thus, six JHMV variants could clearly be divided into two groups with respect to the size and antigenicity of their E2 glycoproteins.


id: cord-316134-lkd2mj27
author: Sungsuwan, Suttipun
date: 2020-01-15
txt: ./txt/cord-316134-lkd2mj27.txt
cache: ./cache/cord-316134-lkd2mj27.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682219303150
doi: 10.1016/j.virol.2019.11.007
summary:
  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.

title:
  Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication

abstract:
  Porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV) and porcine deltacoronavirus (PDCoV) share tropism for swine intestinal epithelial cells. Whether mixing of viral components during co-infection alters pathogenic outcomes or viral replication is not known. In this study, we investigated how different coronavirus nucleocapsid (CoV N) proteins interact and affect PEDV replication. We found that PDCoV N and TGEV N can competitively interact with PEDV N. However, the presence of PDCoV or TGEV N led to very different outcomes on PEDV replication. While PDCoV N significantly suppresses PEDV replication, overexpression of TGEV N, like that of PEDV N, increases production of PEDV RNA and virions. Despite partial interchangeability in nucleocapsid oligomerization and viral RNA synthesis, endogenous PEDV N cannot be replaced in the production of infectious PEDV particles. Results from this study give insights into functional compatibilities and evolutionary relationship between CoV viral proteins during viral co-infection and co-evolution.


id: cord-316460-ibprgdh4
author: Rodríguez-Grille, Javier
date: 2014-06-17
txt: ./txt/cord-316460-ibprgdh4.txt
cache: ./cache/cord-316460-ibprgdh4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2014.04.039
doi: 10.1016/j.virol.2014.04.039
summary:
  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.

title:
  Avian reovirus-triggered apoptosis enhances both virus spread and the processing of the viral nonstructural muNS protein

abstract:
  Avian reovirus non-structural protein muNS is partially cleaved in infected chicken embryo fibroblast cells to produce a 55-kDa carboxyterminal protein, termed muNSC, and a 17-kDa aminoterminal polypeptide, designated muNSN. In this study we demonstrate that muNS processing is catalyzed by a caspase 3-like protease activated during the course of avian reovirus infection. The cleavage site was mapped by site directed mutagenesis between residues Asp-154 and Ala-155 of the muNS sequence. Although muNS and muNSC, but not muNSN, are able to form inclusions when expressed individually in transfected cells, only muNS is able to recruit specific ARV proteins to these structures. Furthermore, muNSC associates with ARV factories more weakly than muNS, sigmaNS and lambdaA. Finally, the inhibition of caspase activity in ARV-infected cells does not diminish ARV gene expression and replication, but drastically reduces muNS processing and the release and dissemination of progeny viral particles.


id: cord-317333-unrd76bo
author: Danesh, Ali
date: 2011-01-05
txt: ./txt/cord-317333-unrd76bo.txt
cache: ./cache/cord-317333-unrd76bo.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682210006380
doi: 10.1016/j.virol.2010.10.002
summary:
  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) .

title:
  Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation

abstract:
  Type I interferons (IFNs) are essential to the clearance of viral diseases, however, a clear distinction between genes upregulated by direct virus–cell interactions and genes upregulated by secondary IFN production has not been made. Here, we investigated differential gene regulation in ferrets upon subcutaneous administration of IFN-α2b and during SARS-CoV infection. In vivo experiments revealed that IFN-α2b causes STAT1 phosphorylation and upregulation of abundant IFN response genes (IRGs), chemokine receptors, and other genes that participate in phagocytosis and leukocyte transendothelial migration. During infection with SARS-CoV not only a variety of IRGs were upregulated, but also a significantly broader range of genes involved in cell migration and inflammation. This work allowed dissection of several molecular signatures present during SARS-CoV which are part of a robust IFN antiviral response. These signatures can be useful markers to evaluate the status of IFN responses during a viral infection and specific features of different viruses.


id: cord-317537-wgu5cd0y
author: Lu, Hsiang-Chia
date: 2009-05-25
txt: ./txt/cord-317537-wgu5cd0y.txt
cache: ./cache/cord-317537-wgu5cd0y.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S004268220900172X
doi: 10.1016/j.virol.2009.02.049
summary:
  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) .

title:
  Cymbidium mosaic potexvirus isolate-dependent host movement systems reveal two movement control determinants and the coat protein is the dominant

abstract:
  Little is known about how plant viruses of a single species exhibit different movement behavior in different host species. Two Cymbidium mosaic potexvirus (CymMV) isolates, M1 and M2, were studied. Both can infect Phalaenopsis orchids, but only M1 can systemically infect Nicotiana benthamiana plants. Protoplast inoculation and whole-mount in situ hybridization revealed that both isolates can replicate in N. benthamiana; however, M2 was restricted to the initially infected cells. Genome shuffling between M1 and M2 revealed that two control modes are involved in CymMV host dependent movement. The M1 coat protein (CP) plays a dominant role in controlling CymMV movement between cells, because all chimeric CymMV viruses containing the M1 CP systemically infected N. benthamiana plants. Without the M1 CP, one chimeric virus containing the combination of the M1 triple gene block proteins (TGBps), the M2 5′ RNA (1–4333), and the M2 CP effectively moved in N. benthamiana plants. Further complementation analysis revealed that M1 TGBp1 and TGBp3 are co-required to complement the movement of the chimeric viruses in N. benthamiana. The amino acids within the CP, TGBp1 and TGBp3 which are required or important for CymMV M2 movement in N. benthamiana plants were mapped. The required amino acids within the CP map to the predicted RNA binding domain. RNA–protein binding assays revealed that M1 CP has higher RNA binding affinity than does M2 CP. Yeast two-hybrid assays to detect all possible interactions of M1 TGBps and CP, and only TGBp1 and CP self-interactions were observed.


id: cord-318400-l9kwxsq7
author: Chhabra, Rajesh
date: 2016-01-15
txt: ./txt/cord-318400-l9kwxsq7.txt
cache: ./cache/cord-318400-l9kwxsq7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26655241/
doi: 10.1016/j.virol.2015.11.011
summary:
  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.

title:
  Pathogenicity and tissue tropism of infectious bronchitis virus is associated with elevated apoptosis and innate immune responses

abstract:
  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. Results showed nephropathogenic IBV strains 885 and QX induced greater apoptosis in CEKC than M41, which induced greater apoptosis in TOCs compared to 885 and QX. Elevated IIR is associated with tissue tropism of different IBV strains. Compared to M41, 885 and QX caused greater induction of toll like receptor 3 (TLR3), melanoma differentiation associated protein 5 (MDA5) and interferon beta (IFN-β) in CEKC. 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.


id: cord-319179-gqaxf7mz
title: Identification of putative polymerase gene product in cells infected with murine coronavirus A59
author: Denison, M.
date: 1987-04-30
txt: ./txt/cord-319179-gqaxf7mz.txt
cache: ./cache/cord-319179-gqaxf7mz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/3029990/
doi: 10.1016/0042-6822(87)90303-5
summary:
  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) .

abstract:
  Abstract The virion RNA of mouse hepatitis virus, strain A59 (MHV-A59) is believed to be the mRNA for the viral RNA-dependent RNA polymerase. The cell-free translation of virion RNA results in the synthesis of two predominant products p220 and p28 (M. R. Denison and S. Perlman, 1986, J. Virol. 60, 12–18). p28 is a basic protein and is readily detected by two-dimensional gel electrophoresis. 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. p28 represents the first protein product of the putative coronavirus polymerase gene to be identified in infected cells.


id: cord-319403-5qyc0wsz
author: Miura, Tanya A.
date: 2007-12-01
txt: ./txt/cord-319403-5qyc0wsz.txt
cache: ./cache/cord-319403-5qyc0wsz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17804032/
doi: 10.1016/j.virol.2007.07.030
summary:
  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.

title:
  Rat coronaviruses infect rat alveolar type I epithelial cells and induce expression of CXC chemokines

abstract:
  We analyzed the ability of two rat coronavirus (RCoV) strains, sialodacryoadenitis virus (SDAV) and Parker’s RCoV (RCoV-P), to infect rat alveolar type I cells and induce chemokine expression. Primary rat alveolar type II cells were transdifferentiated into the type I cell phenotype. 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. Dual immunolabeling of type I cells for viral antigen and CXC chemokines showed that chemokines were expressed primarily by uninfected cells. Virus-induced chemokine expression was reduced by the IL-1 receptor antagonist, suggesting that IL-1 produced by infected cells induces uninfected cells to express chemokines. Primary cultures of alveolar epithelial cells are an important model for the early events in viral infection that lead to pulmonary inflammation.


id: cord-320590-irybhp4j
author: Wang, Zhitao
date: 2019-08-13
url: https://doi.org/10.1016/j.virol.2019.08.011
doi: 10.1016/j.virol.2019.08.011
title:
  Host Src controls gallid alpha herpesvirus 1 intercellular spread in a cellular fatty acid metabolism-dependent manner

abstract:
  Viral spread is considered a promising target for antiviral therapeutics, but the associated mechanisms remain unclear for gallid alpha herpesvirus 1 (ILTV). We previously identified proto-oncogene tyrosine-protein kinase Src (Src) as a crucial host determinant of ILTV infection. The present study revealed accelerated spread of ILTV upon Src inhibition. This phenomenon was independent of either viral replication or the proliferation of infected cells and could not be compromised by neutralizing antibody. Neither extracellular vesicles nor the direct cytosol-to-cytosol connections between adjacent cells contributed to the enhanced spread of ILTV upon Src inhibition. Further genome-wide transcriptional profile analyses in combination with functional validation identified fatty acid metabolism as an essential molecular event during modulation of the intercellular spread and subsequent cytopathic effect of ILTV by Src. Overall, these data suggest that Src controls the cell-to-cell spread of ILTV in a cellular fatty acid metabolism-dependent manner, which determines the virus's cytopathic effect.


id: cord-321162-pgd34ewv
author: Holmes, Kathryn V.
date: 1981-12-31
txt: ./txt/cord-321162-pgd34ewv.txt
cache: ./cache/cord-321162-pgd34ewv.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/7314449/
doi: 10.1016/0042-6822(81)90115-x
summary:
  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) .

title:
  Tunicamycin resistant glycosylation of a coronavirus glycoprotein: Demonstration of a novel type of viral glycoprotein

abstract:
  Abstract Tunicamycin has different effects on the glycosylation of the two envelope glycoproteins of mouse hepatitis virus (MHV), a coronavirus. Unlike envelope glycoproteins of other viruses, the transmembrane glycoprotein El is glycosylated normally in the presence of tunicamycin. This suggests that glycosylation of El does not involve transfer of core oligosaccharides from dolichol pyrophosphate intermediates to asparagine residues, but may occur by 0-linked glycosylation of serine or threonine residues. Synthesis of the peplomeric glycoprotein E2 is not readily detectable in the presence of tunicamycin. Inhibition of N-linked glycosylation of E2 by tunicamycin either prevents synthesis or facilitates degradation of the protein moiety of E2. Radiolabeling with carbohydrate precursors and borate gel electrophoresis of glycopeptides show that different oligcsaccharide side chains are attached to El and E2. The two coronavirus envelope glycoproteins thus appear to be glycosylated by different mechanisms. In tunicamycin-treated cells, noninfectious virions lacking peplomers are formed at intracytoplasmic membranes and released from the cells. These virions contain normal amounts of nucleocapsid protein and glycosylated El, but lack E2. Thus the transmembrane glycoprotein El is the only viral glycoprotein required for the formation of the viral envelope or for virus maturation and release. The peplomeric glycoprotein E2 appears to be required for attachment to virus receptors on the plasma membrane. 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. These findings suggest that El may be particularly useful as a model for studying the biosynthesis, glycosylation, and intracellular transport of 0-linked glycoproteins.


id: cord-321265-il9vbbgk
author: DEN BOON, JOHAN A.
date: 1995-11-30
txt: ./txt/cord-321265-il9vbbgk.txt
cache: ./cache/cord-321265-il9vbbgk.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682285700098
doi: 10.1006/viro.1995.0009
summary:
  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.

title:
  Equine Arteritis Virus Subgenomic RNA Transcription: UV Inactivation and Translation Inhibition Studies

abstract:
  Abstract The expression of the genetic information of equine arteritis virus (EAV), an arterivirus, involves the synthesis of six subgenomic (sg) mRNAs. These are 5′ and 3′ coterminal since they are composed of a leader and a body sequence, which are identical to the 5′ and 3′ ends of the genome, respectively. Previously, it has been suggested thatcis-splicing of a genome-length precursor RNA is involved in their synthesis. This was reevaluated in a comparative analysis of the sg RNA synthesis of EAV, the coronavirus mouse hepatitis virus (MHV), and the alphavirus Sindbis virus. UV transcription mapping showed that the majority of the EAV sg RNAs made at later stages of infection is not derived from a genome-length precursor. However, complete independence of sg RNA synthesis from that of genomic RNA was never observed during the course of infection. The possibility that this resulted from UV irradiation-induced effects on the synthesis of the viral replicase was investigated by inhibiting translation using cycloheximide. For EAV, ongoing protein synthesis was found to be more important for the synthesis of sg RNA than for that of genomic RNA. In general, MHV transcription was extremely sensitive to translation inhibition, whereas EAV genomic RNA synthesis became independent ofde novoprotein synthesis late in infection.


id: cord-322062-nnefbeo6
title: Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome
author: Tam, Albert W.
date: 1991-11-30
txt: ./txt/cord-322062-nnefbeo6.txt
cache: ./cache/cord-322062-nnefbeo6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1926770/
doi: 10.1016/0042-6822(91)90760-9
summary:
  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.

abstract:
  Abstract We have recently described the cloning of a portion of the hepatitis E virus (HEV) and confirmed its etiologic association with enterically transmitted (waterborne, epidemic) non-A, non-B hepatitis. The virus consists of a single-stranded, positive-sense RNA genome of approximately 7.5 kb, with a polyadenylated 3' end. We now report on the cloning and nucleotide sequencing of an overlapping, contiguous set of cDNA clones representing the entire genome of the HEV Burma strain [HEV(B)]. The largest open reading frame extends approximately 5 kb from the Fend and contains the RNA-directed RNA polymerase and nucleoside triphosphate binding motifs. The second major open reading frame (ORF2) begins 37 by downstream of the first and extends approximately 2 kb to the termination codon present 65 by from the 3' terminal stretch of poly(A) residues. ORF2 contains a consensus signal peptide sequence at its amino terminus and a capsid-like region with a high content of basic amino acids similar to that seen with other virus capsid proteins. A third open reading frame partially overlaps the first and second and encompasses only 369 bp. In addition to the 7.5-kb full-length genomic transcript, two subgenomic polyadenylated messages of approximately 3.7 and 2.0 kb were detected in infected liver using a probe from the 3' third of the genome. The genomic organization of the virus is consistent with the Fend encoding nonstructural and the 3' end encoding the viral structural gene(s). The expression strategy of the virus involves the use of three different open reading frames and at least three different transcripts. HEV was previously determined to be a nonenveloped particle with a diameter of 27–34 nm. These findings on the genetic organization and expression strategy of HEV suggest that it is the prototype human pathogen for a new class of RNA virus or perhaps a separate genus within the Caliciviridae family


id: cord-322084-gkg1059v
title: Coronavirus Transcription Mediated by Sequences Flanking the Transcription Consensus Sequence
author: JEONG, YONG SEOK
date: 1996-03-01
txt: ./txt/cord-322084-gkg1059v.txt
cache: ./cache/cord-322084-gkg1059v.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S004268229690118X
doi: 10.1006/viro.1996.0118
summary:
  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.

abstract:
  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. Using our subgenomic DI system, we have studied the effects of sequences flanking the MHV transcription consensus sequence on subgenomic RNA transcription. We obtained the following results. (i) Insertion of a 12-nucleotide-long sequence including the UCUAAAC transcription consensus sequence at different locations of the DI RNA resulted in different efficiencies of subgenomic DI RNA synthesis. (ii) Differences in the amount of subgenomic DI RNA were defined by the sequences that flanked the 12-nucleotide-long sequence and were not affected by the location of the 12-nucleotide-long sequence on the DI RNA. (iii) Naturally occurring flanking sequences of intergenic sequences at gene 6–7, but not at genes 1–2 and 2–3, contained a transcription suppressive element(s). (iv) Each of three naturally occurring flanking sequences of an MHV genomic cryptic transcription consensus sequence from MHV gene 1 also contained a transcription suppressive element(s). These data showed that sequences flanking the transcription consensus sequence affected MHV transcription.


id: cord-322904-9mta0aem
author: Neu, Ursula
date: 2009-02-01
url: https://doi.org/10.1016/j.virol.2008.12.021
doi: 10.1016/j.virol.2008.12.021
title:
  The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry

abstract:
  This review summarizes the fields major findings related to the characterization of polyomavirus structures and to the characterization of virus receptors and mechanisms of host cell invasion. Four members of the family that have received the most attention in this regard are the mouse polyomavirus (mPyV), the monkey polyomavirus SV40, and the two human polyomaviruses, JCV and BKV. The structures of both the mPyV and SV40 alone and in complex with receptor fragments have been solved to high resolution. The majority of polyomaviruses recognize terminal sialic acid in either an α 2,3 linkage or an α 2,6 linkage to the underlying galactose. Studies on virus structure, receptor utilization and mechanisms of entry have led to new insights into how these viruses interact in an active way with cells to ensure the nuclear delivery and expression of their genomes. Critical work on virus entry has led to the discovery of a pH neutral endocytic compartment that accepts cargo from caveolae and to novel roles for endoplasmic reticulum (ER) associated factors in virus uncoating and penetration of ER membranes. This review will summarize the major findings and compare and contrast the mechanisms used by these viruses to infect cells.


id: cord-324054-d71rj29o
author: Zhang, Xuming
date: 1992-01-31
txt: ./txt/cord-324054-d71rj29o.txt
cache: ./cache/cord-324054-d71rj29o.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682292900898
doi: 10.1016/0042-6822(92)90089-8
summary:
  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.

title:
  The hemagglutinin/esterase gene of human coronavirus strain OC43: Phylogenetic relationships to bovine and murine coronaviruses and influenza C virus

abstract:
  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. An open reading frame of 1272 nucleotides was identified as the putative HE gene by homology to the bovine coronavirus HE gene. This open reading frame encodes a protein of 424 amino acids with an estimated molecular weight of 47.7 kDa. Ten potential N-linked glycosylation sites were predicted in the HE protein of HCV-OC43 while nine of them were present in BRCV-G95. Fourteen cysteine residues were conserved in the HE proteins of both viruses. Two hydrophobic sequences at the N-terminus and the C-terminus may serve as signal peptide and transmembrane anchoring domain, respectively. The predicted HE protein of HCV-OC43 was 95% identical to the HEs of BRCV-G95 and other bovine coronaviruses, and 60% identical to the HEs of mouse hepatitis viruses. 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.


id: cord-324321-y96x8x3h
author: Cai, Yingyun
date: 2003-11-10
txt: ./txt/cord-324321-y96x8x3h.txt
cache: ./cache/cord-324321-y96x8x3h.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/14599795/
doi: 10.1016/j.virol.2003.07.007
summary:
  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.

title:
  Down-regulation of transcription of the proapoptotic gene BNip3 in cultured astrocytes by murine coronavirus infection

abstract:
  Murine coronavirus mouse hepatitis virus (MHV) causes encephalitis and demyelination in the central nervous system of susceptible rodents. Astrocytes are the major target for MHV persistence. However, the mechanisms by which astrocytes survive MHV infection and permit viral persistence are not known. Here we performed DNA microarray analysis on differential gene expression in astrocyte DBT cells by MHV infection and found that the mRNA of the proapoptotic gene BNip3 was significantly decreased following MHV infection. This finding was further confirmed by quantitative reverse transcription–polymerase chain reaction, Western blot analysis, and BNip3-promoter-luciferase reporter system. Interestingly, infection with live and ultraviolet light-inactivated viruses equally repressed BNip3 expression, indicating that the down-regulation of BNip3 expression does not require virus replication and is mediated during cell entry. 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. Deletion analysis showed that the sequence between nucleotides 262 and 550 of the 588-base-pair BNip3 promoter is necessary and sufficient for driving the BNip3 expression and that it contains signals that are responsible for MHV-induced down-regulation of BNip3 expression in DBT cells. These results may provide insights into the mechanisms by which MHV evades host antiviral defense and promotes cell survival, thereby allowing its persistence in the host astrocytes.


id: cord-325179-gsf8ad65
title: Modification of simian virus 40 large tumor antigen by glycosylation
author: Jarvis, Donald L.
date: 1985-03-31
txt: ./txt/cord-325179-gsf8ad65.txt
cache: ./cache/cord-325179-gsf8ad65.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/0042682285902508
doi: 10.1016/0042-6822(85)90250-8
summary:
  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) .

abstract:
  Abstract The SV40-encoded transforming protein, large tumor antigen (T-ag), is multifunctional. Chemical modifications of the T-ag polypeptide may be important for its multifunctional capacity. T-ag is additionally modified by glycosylation. T-ag was metabolically labeled in SV40-infected cells with tritiated galactose or glucosamine, but not with mannose or fucose. The identity of glycosylated T-ag was established by immunoprecipitation with a variety of T-ag-specific antisera, including monoclonal antibodies. Incorporation of labeled sugar into T-ag was inhibited in the presence of excess unlabeled sugars, but not in the presence of excess unlabeled amino acids. Labeled monosaccharides could be preferentially removed from T-ag with a mixture of glycosidic enzymes. In addition, galactose was removed from purified T-ag by acid hydrolysis and identified as such by thin-layer chromatography. T-ag oligosaccharides were resistant to treatment with EndoH, and glycosylation was not inhibited by tunicamycin. Together, these data strongly suggest that T-ag is glycosylated. Several characteristics, including lack of mannose labeling, EndoH resistance, and tunicamycin resistance, suggest that T-ag is not an N-linked glycoprotein. Rather, these properties are more consistent with the identification of T-ag as an O-linked glycoprotein.


id: cord-325423-d212h4bp
title: A small nonhuman primate model for filovirus-induced disease
author: Carrion, Ricardo
date: 2011-11-01
url: https://www.sciencedirect.com/science/article/pii/S0042682211003965
doi: 10.1016/j.virol.2011.08.022
abstract:
  Ebolavirus and Marburgvirus are members of the filovirus family and induce a fatal hemorrhagic disease in humans and nonhuman primates with 90% case fatality. To develop a small nonhuman primate model for filovirus disease, common marmosets (Callithrix jacchus) were intramuscularly inoculated with wild type Marburgvirus Musoke or Ebolavirus Zaire. The infection resulted in a systemic fatal disease with clinical and morphological features closely resembling human infection. Animals experienced weight loss, fever, high virus titers in tissue, thrombocytopenia, neutrophilia, high liver transaminases and phosphatases and disseminated intravascular coagulation. Evidence of a severe disseminated viral infection characterized principally by multifocal to coalescing hepatic necrosis was seen in EBOV animals. MARV-infected animals displayed only moderate fibrin deposition in the spleen. Lymphoid necrosis and lymphocytic depletion observed in spleen. These findings provide support for the use of the common marmoset as a small nonhuman primate model for filovirus induced hemorrhagic fever.


id: cord-325481-uzch2hwd
author: Simmons, Graham
date: 2011-05-01
txt: ./txt/cord-325481-uzch2hwd.txt
cache: ./cache/cord-325481-uzch2hwd.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682211000924
doi: 10.1016/j.virol.2011.02.020
summary:
  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) .

title:
  Different host cell proteases activate the SARS-coronavirus spike-protein for cell-cell and virus-cell fusion

abstract:
  Severe acute respiratory syndrome coronavirus (SARS-CoV) poses a considerable threat to human health. Activation of the viral spike (S)-protein by host cell proteases is essential for viral infectivity. However, the cleavage sites in SARS-S and the protease(s) activating SARS-S are incompletely defined. We found that R667 was dispensable for SARS-S-driven virus-cell fusion and for SARS-S-activation by trypsin and cathepsin L in a virus-virus fusion assay. Mutation T760R, which optimizes the minimal furin consensus motif 758-RXXR-762, and furin overexpression augmented SARS-S-activity, but did not result in detectable SARS-S cleavage. Finally, SARS-S-driven cell-cell fusion was independent of cathepsin L, a protease essential for virus-cell fusion. Instead, a so far unknown leupeptin-sensitive host cell protease activated cellular SARS-S for fusion with target cells expressing high levels of ACE2. Thus, different host cell proteases activate SARS-S for virus-cell and cell-cell fusion and SARS-S cleavage at R667 and 758-RXXR-762 can be dispensable for SARS-S activation.


id: cord-326027-58whwspe
author: Hernaez, Bruno
date: 2006-06-20
txt: ./txt/cord-326027-58whwspe.txt
cache: ./cache/cord-326027-58whwspe.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682206000353
doi: 10.1016/j.virol.2006.01.021
summary:
  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.

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

abstract:
  Many stages of African swine fever virus infection have not yet been studied in detail. 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). The incorporation of the fusion protein into the virus particle was confirmed immunologically and it was determined that p54-EGFP was fully functional by confirmation that the recombinant virus made normal-sized plaques and presented similar growth curves to the wild-type virus. The tagged virus was visualized as individual fluorescent particles during the first stages of infection and allowed to visualize the infection progression in living cells through the viral life cycle by confocal microscopy. In this work, diverse potential applications of B54GFP-2 to study different aspects of ASFV infection are shown. By using this recombinant virus it was possible to determine the trajectory and speed of intracellular virus movement. Additionally, we have been able to visualize for first time the ASFV factory formation dynamics and the cytophatic effect of the virus in live infected cells. Finally, we have analyzed virus progression along the infection cycle and infected cell death as time-lapse animations.


id: cord-326688-a1djgqpa
title: Cell tropism and expression of mouse hepatitis viruses (MHV) in mouse spinal cord cultures
author: Dubois-Dalcq, Monique E.
date: 1982-06-30
txt: ./txt/cord-326688-a1djgqpa.txt
cache: ./cache/cord-326688-a1djgqpa.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/6281976/
doi: 10.1016/0042-6822(82)90092-7
summary:
  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.

abstract:
  Abstract Mouse hepatitis viruses (MHV) are coronaviruses which cause various infections in mice affecting lung, intestine, liver, and other organs as well as the central nervous system. 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). Wt-JHM, which causes acute encephalitis in mice, produces acute cytopathic changes in both neurons and NN cells. In neurons, virions mature in smooth ER cisternae closely associated to the Golgi apparatus. As judged by EM, fewer virions are produced by neurons than NN cells and neurons do not fuse or stain for E2 as do NN cells. NN cells contain large inclusions made of nucleocapsid strands. A temperature-sensitive mutant of JHM, Ts8-JHM, which causes demyelination in mice, infects NN cells but not neurons. Infected NN cells synthesize E1 and E2, and contain large inclusions but few mature virions, even at permissive temperatures. These inclusions appear granular and rarely contain nucleocapsid strands in contrast to wt-JHM infection. NN cells infected with this mutant also display numerous membrane whorls. The hepatotropic strain A59 lacks tropism for neurons and primarily infects NN cells, thus resembling ts8-JHM. Infected NN cells become loaded with intracytoplasmic virions which are secreted from the cells. E1 can only be detected in the perinuclear area of these cells while E2 rapidly spreads throughout the cytoplasm. The cytoplasm of A59 infected NN cells frequently contains large tubular structures often in the lumen of the RER. 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. Thus, in the absence of the immune system, the MHV strains assayed exhibit differences in viral tropism, cytopathic changes, and viral assembly in CNS cells, and these differences may account for the different disease patterns.


id: cord-328046-5us4se5o
author: Xu, H. Y.
date: 2001-09-30
txt: ./txt/cord-328046-5us4se5o.txt
cache: ./cache/cord-328046-5us4se5o.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682201910980
doi: 10.1006/viro.2001.1098
summary:
  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 .

title:
  Further Identification and Characterization of Novel Intermediate and Mature Cleavage Products Released from the ORF 1b Region of the Avian Coronavirus Infectious Bronchitis Virus 1a/1b Polyprotein

abstract:
  Abstract The coronavirus 3C-like proteinase is one of the viral proteinases responsible for processing of the 1a and 1a/1b polyproteins to multiple mature products. 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. In this report, we show the identification of two more cleavage products of 68 and 58 kDa released from the same region of the polyprotein. In addition, two stable intermediate cleavage products with molecular masses of 160 and 132 kDa, respectively, were identified in IBV-infected cells. The 160-kDa protein was shown to be an intermediate cleavage product covering the 100- and 68-kDa proteins, and the 132-kDa protein to be an intermediate cleavage product covering the 58-, 39-, and 35-kDa proteins. 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 39- and 35-kDa proteins displayed diffuse distribution patterns.


id: cord-329245-6tj2k1yn
title: The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction
author: Corse, Emily
date: 2003-07-20
txt: ./txt/cord-329245-6tj2k1yn.txt
cache: ./cache/cord-329245-6tj2k1yn.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682203001752
doi: 10.1016/s0042-6822(03)00175-2
summary:
  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) .

abstract:
  Abstract Virus-like particle (VLP) formation by the coronavirus E and M proteins suggests that interactions between these proteins play a critical role in coronavirus assembly. We studied interactions between the infectious bronchitis virus (IBV) E and M proteins using in vivo crosslinking and VLP assembly assays. We show that IBV E and M can be crosslinked to each other in IBV-infected and transfected cells, indicating that they interact. The cytoplasmic tails of both proteins are important for this interaction. We also examined the ability of the mutant and chimeric E and M proteins to form VLPs. IBV M proteins that are missing portions of their cytoplasmic tails or transmembrane regions were not able to support VLP formation, regardless of their ability to be crosslinked to IBV E. Interactions between the E and M proteins and the membrane bilayer are likely to play an important role in VLP formation and virus budding.


id: cord-329625-hx2rsi91
author: You, Jae-Hwan
date: 2008-08-15
txt: ./txt/cord-329625-hx2rsi91.txt
cache: ./cache/cord-329625-hx2rsi91.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18550142/
doi: 10.1016/j.virol.2008.04.037
summary:
  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) .

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

abstract:
  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. The dynamic trafficking of positive strand RNA virus nucleocapsid proteins and PRRSV N protein in particular between the cytoplasm and nucleolus is unknown. In this study live imaging of permissive and non-permissive cell lines, in conjunction with photo-bleaching (FRAP and FLIP), was used to investigate the trafficking of fluorescent labeled (EGFP) PRRSV-N protein. The data indicated that EGFP-PRRSV-N protein was not permanently sequestered to the nucleolus and had equivalent mobility to cellular nucleolar proteins. Further the nuclear import of N protein appeared to occur faster than nuclear export, which may account for the observed relative distribution of N protein between the cytoplasm and the nucleolus.


id: cord-329794-msxrdhb3
author: Lu, Aili
date: 2004-06-20
txt: ./txt/cord-329794-msxrdhb3.txt
cache: ./cache/cord-329794-msxrdhb3.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682204002181
doi: 10.1016/j.virol.2004.03.031
summary:
  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.

title:
  Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase

abstract:
  Abstract Severe acute respiratory syndrome (SARS) is a highly contagious and sometimes a lethal disease, which spread over five continents in 2002–2003. Laboratory analysis showed that the etiologic agent for SARS is a new type of coronavirus. Currently, there is no specific treatment for this disease. RNA interference (RNAi) is a recently discovered antiviral mechanism in plant and animal cells that induces a specific degradation of double-stranded RNA. 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. Moreover, this construct significantly reduced the plaque formation of SARS coronaviruses in Vero-E6 cells. The data may suggest a new approach for treatment of SARS patients.


id: cord-329819-dpgexphf
title: Epidermal growth factor receptor is a co-factor for transmissible gastroenteritis virus entry
author: Hu, Weiwei
date: 2018-06-04
txt: ./txt/cord-329819-dpgexphf.txt
cache: ./cache/cord-329819-dpgexphf.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682218301508
doi: 10.1016/j.virol.2018.05.009
summary:
  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.

abstract:
  Transmissible gastroenteritis virus (TGEV) causes severe diarrhea and high mortality in newborn piglets. It is well established that porcine intestinal epithelium is the target of the TGEV infection, however the mechanism that TGEV invades the host epithelium remains largely unknown. Aminopeptidase N (APN) is a known receptor of TGEV. This study discovered that the extracellular receptor binding domain 1 pertaining to epidermal growth receptor (EGFR) interact with TGEV spike protein. APN and EGFR synergistically promote TGEV invasion. TGEV promotes APN and EGFR clustering early in infection. Furthermore APN and EGFR synergistically stimulate PI3K/AKT as well as MEK/ERK1/2 endocytosis signaling pathways. TGEV entry is via clathrin and caveolin mediated endocytosis in IPEC-J2 cells. TGEV binds with EGFR, and subsequently promotes EGFR internalization by a clathrin-mediated endocytosis pathway. These results show that EGFR is a co-factor of TGEV, and that it plays a synergistic role with APN early in TGEV infection.


id: cord-330847-a84pcc9z
title: RNA recombination in the genome of Barley stripe mosaic virus
author: Edwards, M. C.
date: 1992-07-31
txt: ./txt/cord-330847-a84pcc9z.txt
cache: ./cache/cord-330847-a84pcc9z.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1604824/
doi: 10.1016/0042-6822(92)90722-2
summary:
  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.

abstract:
  Abstract Barley stripe mosaic Hordeivirus (BSMV) is a positive-strand RNA virus requiring three single-stranded RNAs (α, β, and γ) for infectivity. A terminal-sequence-dependent cloning strategy was used to clone the entire genome of the CV17 strain. Full-length γ cDNA clones were obtained when oligonucleotides specific for the 5′-terminal sequence of RNA α were used in the cloning procedure, but not when RNA γ-specific oligonucleotides were used. Sequence analysis of six putative γ cDNA clones revealed that nucleotides 1–70 possess 89% homology with the first 70 nucleotides of RNA α. This leader region is separated from the γ-specific coding region by an eight-base intervening sequence common to both CV17 RNAs α and γ. 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. Thus, the evidence suggests that RNA γ of BSMV strain CV17 is a recombinant molecule which may have arisen as a result of natural recombination between RNAs α and γ.


id: cord-330907-srb8ac7l
author: Leparc-Goffart, Isabelle
date: 1997-12-08
txt: ./txt/cord-330907-srb8ac7l.txt
cache: ./cache/cord-330907-srb8ac7l.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/9426441/
doi: 10.1006/viro.1997.8877
summary:
  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.

title:
  Altered Pathogenesis of a Mutant of the Murine Coronavirus MHV-A59 Is Associated with a Q159L Amino Acid Substitution in the Spike Protein

abstract:
  Abstract C12, an attenuated, fusion delayed, very weakly hepatotropic mutant of mouse hepatitis virus strain A59 (MHV-A59) has been further characterized. 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). We have sequenced the rest of the 31-kb genome of C12 and compared it to wild type virus. Only three additional amino acids substitutions were found, all encoded within the replicase gene. Analysis of C12in vivoin C57Bl/6 mice has shown that despite the fact that this virus replicates in the brain to titers at least as high as wild type and causes acute encephalitis similar to wild type, this virus causes a minimal level of demyelination and only at very high levels of virus inoculation. Thus acute encephalitis is not sufficient for the induction of demyelination by MHV-A59. Analysis of mutants isolated at earlier times from the same persistently infected glial cell culture as C12, as well as mutants isolated from a second independent culture of persistently infected glial cells, suggests that both the weakly demyelinating and the weakly hepatotropic phenotypes of C12 are associated with the Q159L amino acid substitution.


id: cord-331807-ooym5eh3
author: Wu, Tao
date: 2020-07-29
txt: ./txt/cord-331807-ooym5eh3.txt
cache: ./cache/cord-331807-ooym5eh3.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682220301331
doi: 10.1016/j.virol.2020.07.006
summary:
  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

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)

abstract:
  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. A rapid, highly sensitive, specific, and simple operational method was needed for the detection of SARS-CoV-2. Here, we established a real-time reverse-transcription recombinase-aided amplification assay (RT-RAA) to detect SARS-CoV-2 rapidly. The primers and probe were designed based on the nucleocapsid protein gene (N gene) sequence of SARS-CoV-2. The detection limit was 10 copies per reaction in this assay, which could be conducted within 15 min at a constant temperature (39 °C), without any cross-reactions with other respiratory tract pathogens, such as other coronaviruses. Furthermore, compared with commercial real-time RT-PCR assay, it showed a kappa value of 0.959 (p < 0.001) from 150 clinical specimens. These results indicated that this real-time RT-RAA assay may be a valuable tool for detecting SARS-CoV-2.


id: cord-331916-n744pymd
title: Inhibition of porcine circovirus type 2 replication in mice by RNA interference
author: Liu, Jue
date: 2006-04-10
txt: ./txt/cord-331916-n744pymd.txt
cache: ./cache/cord-331916-n744pymd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16427679/
doi: 10.1016/j.virol.2005.12.006
summary:
  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) .

abstract:
  Porcine circovirus type 2 (PCV2) is the primary causative agent of an emerging swine disease, postweaning multisystemic wasting syndrome (PMWS) for which no antiviral treatment is available. To exploit the possibility of using RNA interference (RNAi) as a therapeutic approach against the disease, plasmid-borne short hairpin RNAs (shRNAs) were generated to target the PCV2 genome. Transfection of these shRNAs into cultured PK15 cells caused a significant reduction in viral RNA production that was accompanied by inhibiting viral DNA replication and protein synthesis in infected cells. The effect was further tested in vivo in a mouse model that has been developed for PCV2 infection. Mice injected with shRNA before PCV2 infection showed substantially decreased microscopic lesions in inguinal lymph nodes compared to controls. In situ hybridization and immunohistochemical analyses showed that shRNA caused a significant inhibition in the level of viral DNA and protein synthesis detected in the lymph nodes of the treated mice relative to the controls. Taken together, these results indicate that shRNAs are capable of inhibiting PCV2 infection in vitro as well as in vivo and thus may constitute an effective therapeutic strategy for PCV2 infection.


id: cord-332356-au7s3dmp
title: The cytoplasmic tail of hantavirus Gn glycoprotein interacts with RNA
author: Strandin, Tomas
date: 2011-09-15
txt: ./txt/cord-332356-au7s3dmp.txt
cache: ./cache/cord-332356-au7s3dmp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21807393/
doi: 10.1016/j.virol.2011.06.030
summary:
  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 ).

abstract:
  We recently characterized the interaction between the intraviral domains of envelope glycoproteins (Gn and Gc) and ribonucleoprotein (RNP) of Puumala and Tula hantaviruses (genus Hantavirus, family Bunyaviridae). Herein we report a direct interaction between spike-forming glycoprotein and nucleic acid. We show that the envelope glycoprotein Gn of hantaviruses binds genomic RNA through its cytoplasmic tail (CT). The nucleic acid binding of Gn-CT is unspecific, as demonstrated by interactions with unrelated RNA and with single-stranded DNA. Peptide scan and protein deletions of Gn-CT mapped the nucleic acid binding to regions that overlap with the previously characterized N protein binding sites and demonstrated the carboxyl-terminal part of Gn-CT to be the most potent nucleic acid-binding site. We conclude that recognition of the RNP complex by the Gn-CT could be mediated by interactions with both genomic RNA and the N protein. This would provide the required selectivity for the genome packaging of hantaviruses.


id: cord-333525-67bbmo4m
author: Yao, Qianqian
date: 2013-07-01
txt: ./txt/cord-333525-67bbmo4m.txt
cache: ./cache/cord-333525-67bbmo4m.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682213001955
doi: 10.1016/j.virol.2013.04.001
summary:
  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.

title:
  Negatively charged residues in the endodomain are critical for specific assembly of spike protein into murine coronavirus

abstract:
  Coronavirus spike (S) protein assembles into virions via its carboxy-terminus, which is composed of a transmembrane domain and an endodomain. Here, the carboxy-terminal charge-rich motif in the endodomain was verified to be critical for the specificity of S assembly into mouse hepatitis virus (MHV). Recombinant MHVs exhibited a range of abilities to accommodate the homologous S endodomains from the betacoronaviruses bovine coronavirus and human SARS-associated coronavirus, the alphacoronavirus porcine transmissible gastroenteritis virus (TGEV), and the gammacoronavirus avian infectious bronchitis virus respectively. Interestingly, in TGEV endodomain chimeras the reverting mutations resulted in stronger S incorporation into virions, and a net gain of negatively charged residues in the charge-rich motif accounted for the improvement. Additionally, MHV S assembly could also be rescued by the acidic carboxy-terminal domain of the nucleocapsid protein. These results indicate an important role for negatively charged endodomain residues in the incorporation of MHV S protein into assembled virions.


id: cord-334133-61om170g
author: Hollier, Mark J.
date: 2005-07-05
txt: ./txt/cord-334133-61om170g.txt
cache: ./cache/cord-334133-61om170g.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15913700/
doi: 10.1016/j.virol.2005.04.015
summary:
  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.

title:
  The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function

abstract:
  In addition to the major ectodomain, the gp41 transmembrane glycoprotein of HIV-1 is now known to have a minor ectodomain that is part of the long C-terminal tail. Both ectodomains are highly antigenic, carry neutralizing and non-neutralizing epitopes, and are involved in virus-mediated fusion activity. However, data have so far been biologically based, and derived solely from T cell line-adapted (TCLA), B clade viruses. Here we have carried out sequence and theoretically based structural analyses of 357 gp41 C-terminal sequences of mainly primary isolates of HIV-1 clades A, B, C, and D. Data show that all these viruses have the potential to form a tail loop structure (the minor ectodomain) supported by three, β-sheet, membrane-spanning domains (MSDs). This means that the first (N-terminal) tyrosine-based sorting signal of the gp41 tail is situated outside the cell membrane and is non-functional, and that gp41 that reaches the cell surface may be recycled back into the cytoplasm through the activity of the second tyrosine-sorting signal. However, we suggest that only a minority of cell-associated gp41 molecules – those destined for incorporation into virions – has 3 MSDs and the minor ectodomain. Most intracellular gp41 has the conventional single MSD, no minor ectodomain, a functional first tyrosine-based sorting signal, and in line with current thinking is degraded intracellularly. The gp41 structural diversity suggested here can be viewed as an evolutionary strategy to minimize HIV-1 envelope glycoprotein expression on the cell surface, and hence possible cytotoxicity and immune attack on the infected cell.


id: cord-335482-nx7odchj
title: Defective interfering particles of mouse hepatitis virus
author: Makino, Shinji
date: 1984-02-29
txt: ./txt/cord-335482-nx7odchj.txt
cache: ./cache/cord-335482-nx7odchj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/6322437/
doi: 10.1016/0042-6822(84)90420-3
summary:
  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.

abstract:
  Abstract After six to eight serial undiluted passages of mouse hepatitis virus (JHM strain) in DBT cell culture, a decrease in the yield of infectious virus occurred, and with further passages fluctuating yields of infectious virus were observed. The serially passaged virus interfered with the multiplication of the standard JHM virus, but not with vesicular stomatitis virus. After sucrose equilibrium centrifugation of high passage virus, a single peak contained both infectious virus and interfering activity. This virus population resembled the original JHM virus in its structural proteins, but it contained an increased proportion of a protein with a molecular weight of 65 × 103. Genomic RNA from standard JHM virus contained a single species of RNA with a molecular weight of 5.4 × 106. After five undiluted passages, however, the virion population contained two RNA species with molecular weights of 5.4 × 106 and 5.2 × 106. RNase T1 resistant oligonucleotide finger-printing of these RNAs showed that the lower molecular weight RNA had lost several oligonucleotide spots that were present in the genomic RNA of the standard JHM virus. After several serial diluted passages of passage 10 virus, a single virus population was obtained which again had only standard virus RNA with a molecular weight of 5.4 × 106 and lacked interfering activity. These results indicated that defective interfering particles were generated by serial undiluted passages of JHM virus.


id: cord-337976-c2auspti
author: Weiss, Susan R.
date: 1983-04-30
txt: ./txt/cord-337976-c2auspti.txt
cache: ./cache/cord-337976-c2auspti.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682283800221
doi: 10.1016/s0042-6822(83)80022-1
summary:
  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.

title:
  Coronaviruses SD and SK share extensive nucleotide homology with murine coronavirus MHV-A59, more than that shared between human and murine coronaviruses

abstract:
  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. Our results indicate that SD and SK share almost complete nucleotide homology (approximately 90%) with MHV-A59 and generate subgenomic RNAs of the same sizes as MHV-A59. The human coronavirus (HCV) strains tested show less homology with MHV-A59. The immunologically unrelated HCV-229 E shows no nucleotide homology with MHV-A59. The immunologically crossreactive HCV-OC43 shows nucleotide homology with MHV-A59 by blot hybridization but not when hybridized in solution and assayed by S1 nuclease digestion.


id: cord-340983-w219g6qs
title: Rabies Virus Glycoprotein as a Carrier for Anthrax Protective Antigen
author: Smith, Mary Ellen
date: 2006-09-01
txt: ./txt/cord-340983-w219g6qs.txt
cache: ./cache/cord-340983-w219g6qs.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16820183/
doi: 10.1016/j.virol.2006.05.010
summary:
  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.

abstract:
  Live viral vectors expressing foreign antigens have shown great promise as vaccines against viral diseases. However, safety concerns remain a major problem regarding the use of even highly attenuated viral vectors. 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. In addition to the RV glycoprotein (G) transmembrane and cytoplasmic domains, a portion of the RV G ectodomain was required to express the chimeric RV G anthrax PA on the cell surface. The novel antigen was also efficiently incorporated into RV virions. Mice immunized with the inactivated recombinant RV virions exhibited seroconversion against both RV G and anthrax PA, and a second inoculation greatly increased these responses. These data demonstrate that a viral envelope protein can carry a bacterial protein and that a viral carrier can display whole polypeptides compared to the limited epitope presentation of previous viral systems.


id: cord-342901-ca2xxkb2
title: Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses
author: Lloyd, Richard E.
date: 2015-05-31
txt: ./txt/cord-342901-ca2xxkb2.txt
cache: ./cache/cord-342901-ca2xxkb2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25818028/
doi: 10.1016/j.virol.2015.03.001
summary:
  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.

abstract:
  Abstract Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups.


id: cord-344515-e0g911le
author: Voss, Kelsey
date: 2014-11-30
txt: ./txt/cord-344515-e0g911le.txt
cache: ./cache/cord-344515-e0g911le.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2014.09.005
doi: 10.1016/j.virol.2014.09.005
summary:
  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) .

title:
  Inhibition of host extracellular signal-regulated kinase (ERK) activation decreases new world alphavirus multiplication in infected cells

abstract:
  Abstract New World alphaviruses belonging to the family Togaviridae are classified as emerging infectious agents and Category B select agents. Our study is focused on the role of the host extracellular signal-regulated kinase (ERK) in the infectious process of New World alphaviruses. Infection of human cells by Venezuelan equine encephalitis virus (VEEV) results in the activation of the ERK-signaling cascade. Inhibition of ERK1/2 by the small molecule inhibitor Ag-126 results in inhibition of viral multiplication. Ag-126-mediated inhibition of VEEV was due to potential effects on early and late stages of the infectious process. While expression of viral proteins was down-regulated in Ag-126 treated cells, we did not observe any influence of Ag-126 on the nuclear distribution of capsid. Finally, Ag-126 exerted a broad-spectrum inhibitory effect on New World alphavirus multiplication, thus indicating that the host kinase, ERK, is a broad-spectrum candidate for development of novel therapeutics against New World alphaviruses.


id: cord-345088-krb1eidw
author: Shen, S
date: 2004-09-01
txt: ./txt/cord-345088-krb1eidw.txt
cache: ./cache/cord-345088-krb1eidw.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682204003988
doi: 10.1016/j.virol.2004.06.016
summary:
  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.

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

abstract:
  The spike (S) glycoprotein of coronavirus is responsible for receptor binding and membrane fusion. A number of variants with deletions and mutations in the S protein have been isolated from naturally and persistently infected animals and tissue cultures. 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. The complete sequences of wild type (wt) virus, two ts mutants, and the revertant were compared and variations linked to phenotypes were mapped. A single amino acid reversion (L(294)-to-Q) in the S protein is sufficient to abrogate the ts phenotype. Interestingly, unlike wt virus, the revertant grows well at and below 32 °C, the permissive temperature, as it carries other mutations in multiple genes that might be associated with the cold-adaptation phenotype. If the two ts mutants were allowed to enter cells at 32 °C, the S protein was synthesized, core-glycosylated and at least partially modified at 40 °C. However, compared with wt virus and the revertant, no infectious particles of these ts mutants were assembled and released from the ts mutant-infected cells at 40 °C. 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. Consequently, some essential functions of the S protein, including mediation of cell-to-cell fusion and its incorporation into virions, were completely abolished.


id: cord-345630-bam3pa70
author: Lee, Han-Jung
date: 1991-02-28
txt: ./txt/cord-345630-bam3pa70.txt
cache: ./cache/cord-345630-bam3pa70.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/004268229190071I
doi: 10.1016/0042-6822(91)90071-i
summary:
  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 ).

title:
  The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase

abstract:
  Abstract The 5′-most gene, gene 1, of the genome of murine coronavirus, mouse hepatitis virus (MHV), is presumed to encode the viral RNA-dependent RNA polymerase. We have determined the complete sequence of this gene of the JHM strain by cDNA cloning and sequencing. The total length of this gene is 21,798 nucleotides long, which includes two overlapping, large open reading frames. The first open reading frame, ORF 1 a, is 4488 amino acids long. The second open reading frame, ORF 1 b, overlaps ORF 1 a for 75 nucleotides, and is 2731 amino acids long. The overlapping region may fold into a pseudoknot RNA structure, similar to the corresponding region of the RNA of avian coronavirus, infectious bronchitis virus (IBV). The in vitro transcription and translation studies of this region indicated that these two ORFs were most likely translated into one polyprotein by a ribosomal frameshifting mechanism. Thus, the predicted molecular weight of the gene 1 product is more than 800,000 Da. The sequence of ORF 1 b is very similar to the corresponding ORF of IBV. In contrast, the ORF 1 a of these two viruses differ in size and have a high degree of divergence. The amino acid sequence analysis suggested that ORF 1 a contains several functional domains, including two hydrophobic, membrane-anchoring domains, and three cysteine-rich domains. It also contains a picornaviral 3C-like protease domain and two papain-like protease domains. The presence of these protease domains suggests that the polyprotein is most likely processed into multiple protein products. In contrast, the ORF 1b contains polymerase, helicase, and zinc-finger motifs. These sequence studies suggested that the MHV gene 1 product is involved in RNA synthesis, and that this product is processed autoproteolytically after translation. This study completes the sequence of the MHV genome, which is 31 kb long, and constitutes the largest viral RNA known.


id: cord-346514-vyo8l14p
author: Chen, I-Hsuan
date: 2013-06-13
txt: ./txt/cord-346514-vyo8l14p.txt
cache: ./cache/cord-346514-vyo8l14p.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682213003139
doi: 10.1016/j.virol.2013.05.032
summary:
  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.

title:
  Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants

abstract:
  Bamboo mosaic virus (BaMV) has a positive-sense single-stranded RNA genome with a 5′ cap and a 3′ poly(A) tail. To characterize polyadenylation activity in the BaMV replicase complex, we performed the in vitro polyadenylation with various BaMV templates. We conducted a polyadenylation activity assay for BaMV RNA by using a partially purified BaMV replicase complex. The results showed that approximately 200 adenylates at the 3′ end of the RNA were generated on the endogenous RNA templates. Specific fractions derived from uninfected Nicotiana benthamiana plants enhanced the polyadenylation activity, implying that host factors are involved in polyadenylation. Furthermore, polyadenylation can be detected in newly synthesized plus-strand RNA in vitro when using the exogenous BaMV minus-strand minigenome. For polyadenylation on the exogenous plus-strand minigenome, the 3′ end requires at least 4A to reach 22% polyadenylation activity. The results indicate that the BaMV replicase complex recognizes the 3′ end of BaMV for polyadenylation.


id: cord-351197-xv6ymc4l
title: A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil
author: Cibulski, Samuel
date: 2020-09-28
txt: ./txt/cord-351197-xv6ymc4l.txt
cache: ./cache/cord-351197-xv6ymc4l.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33032031/
doi: 10.1016/j.virol.2020.09.005
summary:
  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

abstract:
  A viral metagenomics study was conducted in beef, pork, and chicken sold in supermarkets from Southern Brazil. 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. From pork, genomes of numerous anelloviruses, porcine parvovirus 5 (PPV5) and 6 (PPV6), two new genomoviruses and two new CRESS-DNA viruses were found. Finally, two new CRESS-DNA genomes were recovered from beef. Although none of these viruses have history of transmission to humans, the findings reported here reveal that such agents are inevitably consumed in diets that include these types of meat.


id: cord-353467-wbtzvm4i
title: Functional incorporation of green fluorescent protein into hepatitis B virus envelope particles
author: Lambert, Carsten
date: 2004-12-05
txt: ./txt/cord-353467-wbtzvm4i.txt
cache: ./cache/cord-353467-wbtzvm4i.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15527842/
doi: 10.1016/j.virol.2004.09.031
summary:
  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.

abstract:
  The envelope of hepatitis B virus (HBV), containing the L, M, and S proteins, is essential for virus entry and maturation. For direct visualization of HBV, we determined whether envelope assembly could accommodate the green fluorescent protein (GFP). While the C-terminal addition of GFP to S trans-dominant negatively inhibited empty envelope particle secretion, the N-terminal GFP fusion to S (GFP.S) was co-integrated into the envelope, giving rise to fluorescent particles. Microscopy and topogenesis analyses demonstrated that the proper intracellular distribution and folding of GFP.S, required for particle export were rescued by interprotein interactions with wild-type S. Thereby, a dual location of GFP, inside and outside the envelope, was observed. GFP.S was also efficiently packaged into the viral envelope, and these GFP-tagged virions retained the capacity for attachment to HBV receptor-positive cells in vitro. Together, GFP-tagged virions should be suitable to monitor HBV uptake and egress in live hepatocytes.


id: cord-353748-y1a52z8e
author: Bhattacharya, Rajarshi
date: 2021-01-02
txt: ./txt/cord-353748-y1a52z8e.txt
cache: ./cache/cord-353748-y1a52z8e.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S004268222030204X
doi: 10.1016/j.virol.2020.10.002
summary:
  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.

title:
  A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2

abstract:
  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 molecular interaction of nisin with hACE2 was investigated by homology modeling and docking studies. Further, binding efficiency of the most potent nisin H was evaluated through the interaction of hACE2:nisin H complex with RBD (receptor-binding domain) of SARS-CoV-2 and that of hACE2:RBD complex with nisin H. Here, nisin H acted as a potential competitor of RBD to access the hACE2 receptor. The study unravels for the first time that a globally used food preservative, nisin has the potential to bind to hACE2.


