Characterizing 56 complete SARS-CoV S-gene sequences from Hong Kong
Received 11 May 2006; received in revised form 18 September 2006; accepted 6 October 2006. published online 18 November 2006.
Abstract
Background
The spike glycoprotein (S) gene of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) has been useful in analyzing the molecular epidemiology of the 2003 SARS outbreaks.
Objectives
To characterize complete SARS-CoV S-gene sequences from Hong Kong.
Study design
Fifty-six SARS-CoV S-gene sequences, obtained from patients who presented with SARS to the Prince of Wales Hospital during March–May 2003, were analysed using a maximum likelihood (ML) approach, together with 138 other (both human and animal) S-gene sequences downloaded from GenBank.
Results
The maximum-likelihood (ML) trees showed little evolution occurring within these 56 sequences. Analysis with the other sequences, showed three distinct SARS clusters, closely correlated to previously defined early, middle and late phases of the 2003 international SARS outbreaks. In addition, two new single nucleotide variations (SNVs), T21615A and T21901A, were discovered, not previously reported elsewhere.
Conclusions
The ML approach to the reconstruction of tree phylogenies is known to be superior to the more popular, less computationally and time-demanding neighbour-joining (NJ) approach. The ML analysis in this study confirms the previously reported SARS epidemiology analysed mostly using the NJ approach. The two new SNVs reported here are most likely due to the tissue-culture passaging of the clinical samples.
aDepartment of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
bDepartment of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China.
cCentre for Emerging Infectious Diseases, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
Corresponding author at: Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China. Tel.: +852 2632 3333; fax: +852 2647 3227.
ABSTRACT