Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: molecular epidemiology and genome evolution.
Since early March 2003, the severe acute respiratory syndrome (SARS) coronavirus (CoV) infection has claimed 346 cases and 37 deaths in Taiwan. The epidemic occurred in two stages. The first stage caused limited familial or hospital infections and lasted from early March to mid-April. All cases had clear contact histories, primarily from Guangdong or Hong Kong. The second stage resulted in a large outbreak in a municipal hospital, and quickly spread to northern and southern Taiwan from late April to mid-June. During this stage, there were some sporadic cases with untraceable contact histories. To investigate the origin and transmission route of SARS-CoV in Taiwan's epidemic, we conducted a systematic viral lineage study by sequencing the entire viral genome from ten SARS patients. SARS-CoV viruses isolated from Taiwan were found closely related to those from Guangdong and Hong Kong. In addition, all cases from the second stage belonged to the same lineage after the municipal hospital outbreak, including the patients without an apparent contact history. Analyses of these full-length sequences showed a positive selection occurring during SARS-CoV virus evolution. The mismatch distribution indicated that SARS viral genomes did not reach equilibrium and suggested a recent introduction of the viruses into human populations. The estimated genome mutation rate was approximately 0.1 per genome, demonstrating possibly one of the lowest rates among known RNA viruses.
Yeh
Shiou-Hwei
SH
Division of Molecular and Genomic Medicine, National Health Research Institutes, Taipei 115, Taiwan.
Wang
Hurng-Yi
HY
Tsai
Ching-Yi
CY
Kao
Chuan-Liang
CL
Yang
Jyh-Yuan
JY
Liu
Hwan-Wun
HW
Su
Ih-Jen
IJ
Tsai
Shih-Feng
SF
Chen
Ding-Shinn
DS
Chen
Pei-Jer
PJ
D020029:Base Pairing; D001483:Base Sequence; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012367:RNA, Viral / Q000235:genetics; D045473:Severe acute respiratory syndrome-related coronavirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D045169:Severe Acute Respiratory Syndrome / Q000453:epidemiology*; D013624:Taiwan / Q000453:epidemiology
D004279:DNA, Viral; D012367:RNA, Viral