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

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 (RIOI ) 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 SARSassociated 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).

A Genome Sequence of Novel SARS-CoV Isolates: the Genotype, GD-Ins29, Leads to a Hypothesis of Viral Transmission in South China

“…Sixteen complete or partial genome sequences of SARS-CoV isolates have been available since March 14 this year (ref. 2., 3., 4., 5.; http://www.ncbi.nlm.nih.gov/; Table 1). In the process of surveying all available genomic sequences of the SARS-CoV, we have obtained the complete genomic sequence of an isolate, named Isolate GZ01 originally.…”

The Structural Characterization and Antigenicity of the S Protein of SARS-CoV

“… 11 ). The total size, together with its defined 5’ transcription regulation sequence (TRS, 10 nt), is 3,778 nt and accounts for 12.7% of the total genome (29,725 nt).…”

“…We report, in this paper, the results of the comparative analyses on the S protein of BJ Group (BJ01-BJ04) and 13 other reported SARS-CoV genome sequences 9., 10., 11., 12. as well as 13 out of 17 members of Coronaviridae with the data of the S protein available.…”

The reporting of the risks from severe acute respiratory syndrome (SARS) in the news media, 2003–2004

“…They discovered first, that it was caused by a coronavirus (Peiris et al 2003) and second, the genetic sequence of the virus (Marra et al 2003, Qin et al 2003, Ruan et al 2003. There were 652 papers in 2003 on the disease in peer-reviewed journals covered by the Science Citation Index, of which 222 were research articles or reviews.…”