Phylogenetic analysis and sequence comparisons of structural and non-structural SARS coronavirus proteins in Taiwan.
Taiwan experienced a large number of severe acute respiratory syndrome (SARS) viral infections between March and July 2003; by September of that year, 346 SARS cases were confirmed by RT-PCR or serological tests. In order to better understand evolutionary relationships among SARS coronaviruses (SCoVs) from different international regions, we performed phylogenetic comparisons of full-length genomic and protein sequences from 45 human SCoVs (including 12 from Taiwan) and two civet SCoVs. All the Taiwanese SARS-CoV strains which associated with nosocomial infection formed a monophyletic clade within the late phase of the SARS epidemic. This Taiwanese clade could be further divided into two epidemic waves. Taiwan SCoVs in the first wave clustered with three isolates from the Amoy Gardens housing complex in Hong Kong indicating their possible origin. Of the 45 human SCoVs, one isolate from Guangdong province, China, exhibited an extra 29-nucleotide fragment between Orf 10 and Orf 11--similar to the civet SCoV genome. Nucleotide and protein sequence comparisons suggested that all SCoVs of late epidemic came from human-to-human transmission, while certain SCoVs of early epidemic might have originated in animals.
Lan
Yu-Ching
YC
AIDS Prevention and Research Center, Institute of Public Health, National Yang-Ming University, Taipei 112, Taiwan.
Liu
Hsin-Fu
HF
Shih
Yi-Ping
YP
Yang
Jyh-Yuan
JY
Chen
Hour-Young
HY
Chen
Yi-Ming Arthur
YM
D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D010802:Phylogeny; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics* / Q000502:physiology*; D017386:Sequence Homology, Amino Acid; D045169:Severe Acute Respiratory Syndrome / Q000235:genetics / Q000821:virology*; D013624:Taiwan; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D015678:Viral Structural Proteins / Q000235:genetics*
D017361:Viral Nonstructural Proteins; D015678:Viral Structural Proteins
Cell. 1987 Sep 11;50(6):975-85
2441877
Science. 2003 Oct 10;302(5643):276-8
12958366
Nature. 2003 Nov 27;426(6965):450-4
14647384
Biochem Biophys Res Commun. 2003 Dec 26;312(4):1159-64
14651994
N Engl J Med. 2003 May 15;348(20):1967-76
12690091
N Engl J Med. 2003 May 15;348(20):1995-2005
12671061
MMWR Morb Mortal Wkly Rep. 2003 May 23;52(20):461-6
12807078
Biochem Biophys Res Commun. 2003 Oct 10;310(1):78-83
14511651
Lancet. 2003 Oct 25;362(9393):1353-8
14585636
Nature. 2003 May 15;423(6937):240
12748632
J Virol. 1998 Dec;72(12):9628-36
9811696
Bioinformatics. 2001 Dec;17(12):1244-5
11751241
Emerg Infect Dis. 2003 Sep;9(9):1163-7
14519257
J Mol Evol. 1980 Dec;16(2):111-20
7463489
J Virol. 2003 Feb;77(4):2530-8
12551991
N Engl J Med. 2003 May 15;348(20):1953-66
12690092
Lancet. 2003 May 24;361(9371):1767-72
12781535
Lancet. 2003 Nov 29;362(9398):1807-8
14654320
Science. 2003 May 30;300(5624):1394-9
12730500
J Virol. 1999 Sep;73(9):7607-18
10438851
Science. 2003 May 30;300(5624):1399-404
12730501
Lancet. 2003 Apr 19;361(9366):1319-25
12711465