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To quickly control infectious disease outbreaks, extensive information is required to identify the source and transmission routes, and to evaluate the effect of containment policies. Traditionally, scientists have used travel- and contact-tracing methods, but the recent SARS epidemic showed that sequence-based techniques for pathogen detection (i.e. looking for "fingerprints" of genetic material from the SARS virus) can also be important tools to help understand outbreaks. As they report in the February issue of the international open-access journal PLoS Medicine, Jianjun Liu and colleagues (from the Genome Institute of Singapore) adapted a molecular biology technique called "mass spectrometry (MS)–based genotyping", already used as a high-throughput way of detecting single nucleotide polymorphisms (small variations) in human DNA, to the analysis of the SARS virus from clinical samples.
The major breakthroughs against SARS were the discovery of the SARS coronavirus (SARS-CoV) as the etiological agent and the sequencing of the SARS genome. Liu's colleagues at the Genome Institute of Singapore had previously shown that common genetic variants in the SARS-CoV genome could be used as molecular fingerprints to help trace the route of infection. However, as "sequence analysis of large numbers of clinical samples is challenging, cumbersome, and expensive," they felt that "what is needed is a rapid, sensitive, high throughput, and cost-effective screening method." Towards this goal, Liu and colleagues now demonstrate that an MS-based technique can quickly yield accurate information on clinical isolates (in this case from the 2003 SARS outbreak in Singapore).
Citation: Liu J, Lim SL, Ruan Y, Ling AE, Ng LFP, et al. (2005) SARS transmission pattern in Singapore reassessed by viral sequence variation analysis. PLoS Med 2(2): e43.
CONTACT:
JianJun Liu
Genome Institute of Signapore
Population Genetics
60 Biopolis Street
Genome #02-01
Singapore 138672
+65-64-78-80-88
liuj3@gis.a-star.edu.sg
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