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Chinese Science Bulletin

, Volume 48, Issue 10, pp 941–948 | Cite as

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

  • E’de Qin
  • Qingyu ZhuEmail author
  • Man Yu
  • Baochang Fan
  • Guohui Chang
  • Bingyin Si
  • Bao’an Yang
  • Wenming Peng
  • Tao Jiang
  • Bohua Liu
  • Yongqiang Deng
  • Hong Liu
  • Yu Zhang
  • Cui’e Wang
  • Yuquan Li
  • Yonghua Gan
  • Xiaoyu Li
  • Fushuang Lü
  • Gang Tan
  • Wuchun Cao
  • Ruifu Yang
  • Jian Wang
  • Wei Li
  • Zuyuan Xu
  • Yan Li
  • Qingfa Wu
  • Wei Lin
  • Weijun Chen
  • Lin Tang
  • Yajun Deng
  • Yujun Han
  • Changfeng Li
  • Meng Lei
  • Guoqing Li
  • Wenjie Li
  • Hong Lü
  • Jianping Shi
  • Zongzhong Tong
  • Feng Zhang
  • Songgang Li
  • Bin Liu
  • Siqi Liu
  • Wei Dong
  • Jun Wang
  • Gane K-S Wong
  • Jun Yu
  • Huanming YangEmail author
Article

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).

Keywords

Severe Acute Respiratory Syndrome (SARS) coronavirus genome phylogeny 

Abbreviations

a.a.

amino acid

CDS

coding sequences

dsRNA

double-stranded RNA

HCoV

human coronavirus

HE

hemagglutinin-esterase

kb

kilobase

kD

kilodalton

MW

molecular weight

nt

nucleotide

pI

isoelectric point

PUP

putative uncharacterized protein

ssRNA

single-stranded RNA

UTR

untranslated region

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Copyright information

© Science in China Press 2003

Authors and Affiliations

  • E’de Qin
    • 1
  • Qingyu Zhu
    • 1
    Email author
  • Man Yu
    • 1
  • Baochang Fan
    • 1
  • Guohui Chang
    • 1
  • Bingyin Si
    • 1
  • Bao’an Yang
    • 1
  • Wenming Peng
    • 1
  • Tao Jiang
    • 1
  • Bohua Liu
    • 1
  • Yongqiang Deng
    • 1
  • Hong Liu
    • 1
  • Yu Zhang
    • 1
  • Cui’e Wang
    • 1
  • Yuquan Li
    • 1
  • Yonghua Gan
    • 1
  • Xiaoyu Li
    • 1
  • Fushuang Lü
    • 1
  • Gang Tan
    • 1
  • Wuchun Cao
    • 1
  • Ruifu Yang
    • 1
  • Jian Wang
    • 2
    • 3
  • Wei Li
    • 2
    • 3
  • Zuyuan Xu
    • 2
    • 3
  • Yan Li
    • 2
    • 3
  • Qingfa Wu
    • 2
    • 3
  • Wei Lin
    • 2
    • 3
  • Weijun Chen
    • 2
    • 3
  • Lin Tang
    • 2
    • 3
  • Yajun Deng
    • 2
    • 3
  • Yujun Han
    • 2
    • 3
  • Changfeng Li
    • 2
    • 3
  • Meng Lei
    • 2
    • 3
  • Guoqing Li
    • 2
    • 3
  • Wenjie Li
    • 2
    • 3
  • Hong Lü
    • 2
    • 3
  • Jianping Shi
    • 2
    • 3
  • Zongzhong Tong
    • 2
    • 3
  • Feng Zhang
    • 2
    • 3
  • Songgang Li
    • 2
    • 3
  • Bin Liu
    • 2
    • 3
  • Siqi Liu
    • 2
    • 3
  • Wei Dong
    • 2
    • 3
  • Jun Wang
    • 2
    • 3
  • Gane K-S Wong
    • 2
    • 3
  • Jun Yu
    • 2
    • 3
  • Huanming Yang
    • 2
    • 3
    Email author
  1. 1.Institute of Microbiology and EpidemiologyChinese Academy of Military Medical SciencesBeijingChina
  2. 2.Beijing Genomics InstituteChinese Academy of SciencesBeijing
  3. 3.National Center for Genome InformationBeijingChina

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