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Methods

Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays

¹ Genome Institute of Singapore, Singapore 138672, Republic of Singapore ² NimbleGen Systems, Inc., Madison, Wisconsin 53711, USA ³ Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA

Mutations in the SARS-Coronavirus (SARS-CoV) can alter its clinical presentation, and the study of its mutation patterns in human populations can facilitate contact tracing. Here, we describe the development and validation of an oligonucleotide resequencing array for interrogating the entire 30-kb SARS-CoV genome in a rapid, cost-effective fashion. Using this platform, we sequenced SARS-CoV genomes from Vero cell culture isolates of 12 patients and directly from four patient tissues. The sequence obtained from the array is highly reproducible, accurate (>99.99% accuracy) and capable of identifying known and novel variants of SARS-CoV. Notably, we applied this technology to a field specimen of probable SARS and rapidly deduced its infectious source. We demonstrate that array-based resequencing-by-hybridization is a fast, reliable, and economical alternative to capillary sequencing for obtaining SARS-CoV genomic sequence on a population scale, making this an ideal platform for the global monitoring of SARS-CoV and other small-genome pathogens.

⁴ Corresponding authors.
E-MAIL wongc{at}gis.a-star.edu.sg; FAX +65-64789060. E-MAIL millerl{at}gis.a-star.edu.sg; FAX +65-64789060.

[Supplemental material is available online at www.genome.org and http://www.gis.a-star.edu.sg/homepage/toolssup.jsp.]

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