Molecular epidemiology of severe acute respiratory syndrome-associated coronavirus infections in Taiwan.
BACKGROUND
In 2003, Taiwan experienced a series of outbreaks of severe acute respiratory syndrome (SARS) and 1 laboratory-contamination accident. Here we describe a new phylogenetic analytical method to study the sources and dissemination paths of SARS-associated coronavirus (SARS-CoV) infections in Taiwan.


METHODS
A phylogenetic analytical tool for combining nucleotide sequences from 6 variable regions of a SARS-CoV genome was developed by use of 20 published SARS-CoV sequences; and this method was validated by use of 80 published SARS-CoV sequences. Subsequently, this new tool was applied to provide a better understanding of the entire complement of Taiwanese SARS-CoV isolates, including 20 previously published and 19 identified in this study. The epidemiological data were integrated with the results from the phylogenetic tree and from the nucleotide-signature pattern.


RESULTS
The topologies of phylogenetic trees generated by the new and the conventional strategies were similar, with the former having better robustness than the latter, especially in comparison with the maximum-likelihood trees: the new strategy revealed that during 2003 there were 5 waves of epidemic SARS-CoV infection, which belonged to 3 phylogenetic clusters in Taiwan.


CONCLUSIONS
The new strategy is more efficient than its conventional counterparts. The outbreaks of SARS in Taiwan originated from multiple sources.
Lan
Yu-Ching
YC
AIDS Prevention and Research Centre, National Yang-Ming University, Taiwan, Republic of China.
Liu
Tze-Tze
TT
Yang
Jyh-Yuan
JY
Lee
Cheng-Ming
CM
Chen
Yen-Ju
YJ
Chan
Yu-Jiun
YJ
Lu
Jang-Jih
JJ
Liu
Hsin-Fu
HF
Hsiung
Chao A
CA
Ho
Mei-Shang
MS
Hsiao
Kwang-Jen
KJ
Chen
Hour-Young
HY
Chen
Yi-Ming Arthur
YM
D003428:Cross Infection / Q000235:genetics / Q000635:transmission / Q000821:virology; D016679:Genome, Viral; D006801:Humans; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011336:Probability; D045473:Severe acute respiratory syndrome-related coronavirus / Q000145:classification / Q000235:genetics*; D012621:Seasons; D045169:Severe Acute Respiratory Syndrome / Q000453:epidemiology* / Q000235:genetics / Q000635:transmission; D013624:Taiwan / Q000453:epidemiology; D014195:Travel