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      A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01)

      research-article
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      Chinese Science Bulletin = Kexue Tongbao
      Science in China Press
      Severe Acute Respiratory Syndrome (SARS), coronavirus, genome, phylogeny

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          Abstract

          The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS-associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to be involved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the M protein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides no evidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of other possible SARS-related pathogen(s).

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          The Spike but Not the Hemagglutinin/Esterase Protein of Bovine Coronavirus Is Necessary and Sufficient for Viral Infection

          The spike (S) and hemagglutinin/esterase (HE) of bovine coronavirus (BCV) are the two envelope proteins that recognize the same receptor-determinant of 9-O-acetylneuraminic acid on host cells. However, the precise and relative roles of the two proteins in BCV infectivity remain elusive. To unequivocally determine their roles in viral cytopathogenicity, we developed a system in which phenotypically chimeric viruses were generated by infecting a closely related mouse hepatitis virus (MHV) in cells that stably express an individual BCV protein (S or HE). The chimeric viruses were then used to infect human rectal tumor (HRT)-18 cells that are permissive to BCV but are nonsusceptible to MHV. Using this approach, we found that the chimeric virus containing the BCV S protein on the virion surface entered and replicated in HRT-18 cells; this was specifically blocked by prior treatment of the virus with a neutralizing antibody specific to the BCV S protein, indicating that the BCV S protein is responsible for initiating chimeric virus infection. In contrast, chimeric viruses that contain biologically active and functional BCV HE protein on the surface failed to enter HRT-18 cells, indicating that the BCV HE protein alone is not sufficient for BCV infection. Taken together, these results demonstrate that the S protein but not the HE protein of BCV is necessary and sufficient for infection of the chimeric viruses in HRT-18 cells, suggesting that BCV likely uses the S protein as a primary vehicle to infect permissive cells.
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            Characterization of RNA synthesis, replication mechanism, and in vitro RNA-dependent RNA polymerase activity of Japanese encephalitis virus.

            In vitro RNA-dependent RNA polymerase assays revealed that the JEV replication complex (RC) synthesized viral RNA utilizing a semiconservative and asymmetric mechanism. Peak viral replicase activity and levels of viral RNA observed 15-18 h postinfection (h p.i.) preceded maximum viral titers in the culture medium seen 21 h p.i. Among divalent cations, Mg(2+) was essential and exhibited cooperative binding for its two replicase-binding sites. Mn(2+), despite sixfold higher affinity for the replicase, elicited only 70% of the maximum Mg(2+)-dependent activity, and deficit of either cation led to synthesis of incomplete RNA products. We also determined as a first instance for a flavivirus RC, kinetic parameters using cytoplasmic "virus-induced heavy membranes" after depleting endogenous nucleotides. Exhaustive trypsin treatment, which degraded the bulk of NS3 and NS5, had no effect on replicase activity, suggesting that the active flaviviral RC resides behind a membrane barrier and recruits minuscule proportions of the replicase proteins.
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              Programmed ribosomal frameshifting: much ado about knotting!

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                Author and article information

                Contributors
                zhuqy@nic.bmi.ac.cn
                yanghm@genomics.org.cn
                Journal
                Chin Sci Bull
                Chin. Sci. Bull
                Chinese Science Bulletin = Kexue Tongbao
                Science in China Press (Beijing )
                1001-6538
                1861-9541
                2003
                : 48
                : 10
                : 941-948
                Affiliations
                [1 ]GRID grid.410740.6, ISNI 0000000418034911, Institute of Microbiology and Epidemiology, , Chinese Academy of Military Medical Sciences, ; 100071 Beijing, China
                [2 ]GRID grid.9227.e, ISNI 0000000119573309, Beijing Genomics Institute, , Chinese Academy of Sciences, ; 101300 Beijing,
                [3 ]National Center for Genome Information, 101300 Beijing, China
                Article
                BF03184203
                10.1007/BF03184203
                7088533
                fd202736-feb9-404b-86b7-dae5fa55f25c
                © Science in China Press 2003

                This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

                History
                : 29 April 2003
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                © Science in China Press 2003

                severe acute respiratory syndrome (sars),coronavirus,genome,phylogeny

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