Molecular Evolution of the SARS Coronavirus During the Course of the SARS Epidemic in China

Sixty-one SARS coronavirus genomic sequences derived from the early, middle, and late phases of the severe acute respiratory syndrome (SARS) epidemic were analyzed together with two viral sequences from palm civets. Genotypes characteristic of each phase were discovered, and the earliest genotypes were similar to the animal SARS-like coronaviruses. Major deletions were observed in the Orf8 region of the genome, both at the start and the end of the epidemic. The neutral mutation rate of the viral genome was constant but the amino acid substitution rate of the coding sequences slowed during the course of the epidemic. The spike protein showed the strongest initial responses to positive selection pressures, followed by subsequent purifying selection and eventual stabilization.

[1]  H. Laude,et al.  Porcine respiratory coronavirus differs from transmissible gastroenteritis virus by a few genomic deletions. , 1990, The Journal of general virology.

[2]  P. Sharp,et al.  Rates and dates of divergence between AIDS virus nucleotide sequences. , 1988, Molecular biology and evolution.

[3]  X. L. Liu,et al.  Isolation and Characterization of Viruses Related to the SARS Coronavirus from Animals in Southern China , 2003, Science.

[4]  Flood of Sequence Data Yields Clues But Few Answers , 2003, Science.

[5]  K. Yuen,et al.  Genomic characterisation of the severe acute respiratory syndrome coronavirus of Amoy Gardens outbreak in Hong Kong , 2003, The Lancet.

[6]  S. Baird,et al.  Pattern of mutation in the genome of influenza A virus on adaptation to increased virulence in the mouse lung: Identification of functional themes , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[7]  M. Chan-yeung,et al.  A cluster of cases of severe acute respiratory syndrome in Hong Kong. , 2003, The New England journal of medicine.

[8]  J. Peiris,et al.  Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People's Republic of China, in February, 2003 , 2003, The Lancet.

[9]  Christian Drosten,et al.  Identification of a novel coronavirus in patients with severe acute respiratory syndrome. , 2003, The New England journal of medicine.

[10]  Y. Guan,et al.  Unique and Conserved Features of Genome and Proteome of SARS-coronavirus, an Early Split-off From the Coronavirus Group 2 Lineage , 2003, Journal of Molecular Biology.

[11]  D. Mindell,et al.  SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting , 2003, Infection, Genetics and Evolution.

[12]  R. Webster,et al.  Lethal H5N1 influenza viruses escape host anti-viral cytokine responses , 2002, Nature Medicine.

[13]  P. Ewald.  The evolution of virulence and emerging diseases , 1988, Journal of Urban Health.

[14]  Peter Cameron,et al.  A major outbreak of severe acute respiratory syndrome in Hong Kong. , 2003, The New England journal of medicine.

[15]  S. Weiss,et al.  Amino Acid Substitutions within the Leucine Zipper Domain of the Murine Coronavirus Spike Protein Cause Defects in Oligomerization and the Ability To Induce Cell-to-Cell Fusion , 1999, Journal of Virology.

[16]  R. Chiu,et al.  Molecular epidemiology of SARS--from Amoy Gardens to Taiwan. , 2003, The New England journal of medicine.

[17]  S. Tsui,et al.  Coronavirus genomic-sequence variations and the epidemiology of the severe acute respiratory syndrome. , 2003, The New England journal of medicine.

[18]  S. Twu,et al.  Update: outbreak of severe acute respiratory syndrome--worldwide, 2003. , 2003, MMWR. Morbidity and mortality weekly report.

[19]  Philip M. Long,et al.  Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection , 2003, The Lancet.

[20]  J. Drake,et al.  Mutation rates among RNA viruses. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[21]  W. Fitch,et al.  Effects of passage history and sampling bias on phylogenetic reconstruction of human influenza A evolution. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Christian Drosten,et al.  Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome , 2003, Science.

[23]  Malik Peiris,et al.  Aetiology: Koch's postulates fulfilled for SARS virus , 2003, Nature.

[24]  Obi L. Griffith,et al.  The Genome Sequence of the SARS-Associated Coronavirus , 2003, Science.

[25]  J. A. Comer,et al.  A novel coronavirus associated with severe acute respiratory syndrome. , 2003, The New England journal of medicine.