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Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays.
Genome Res. 2004 Mar; 14(3):398-405.GR

Abstract

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.

Authors+Show Affiliations

Genome Institute of Singapore, Singapore 138672, Republic of Singapore. wongc@gis.a-star.edu.sgNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Validation Study

Language

eng

PubMed ID

14993206

Citation

Wong, Christopher W., et al. "Tracking the Evolution of the SARS Coronavirus Using High-throughput, High-density Resequencing Arrays." Genome Research, vol. 14, no. 3, 2004, pp. 398-405.
Wong CW, Albert TJ, Vega VB, et al. Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Res. 2004;14(3):398-405.
Wong, C. W., Albert, T. J., Vega, V. B., Norton, J. E., Cutler, D. J., Richmond, T. A., Stanton, L. W., Liu, E. T., & Miller, L. D. (2004). Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Research, 14(3), 398-405.
Wong CW, et al. Tracking the Evolution of the SARS Coronavirus Using High-throughput, High-density Resequencing Arrays. Genome Res. 2004;14(3):398-405. PubMed PMID: 14993206.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. AU - Wong,Christopher W, AU - Albert,Thomas J, AU - Vega,Vinsensius B, AU - Norton,Jason E, AU - Cutler,David J, AU - Richmond,Todd A, AU - Stanton,Lawrence W, AU - Liu,Edison T, AU - Miller,Lance D, PY - 2004/3/3/pubmed PY - 2004/3/18/medline PY - 2004/3/3/entrez SP - 398 EP - 405 JF - Genome research JO - Genome Res VL - 14 IS - 3 N2 - 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. SN - 1088-9051 UR - https://www.unboundmedicine.com/medline/citation/14993206/Tracking_the_evolution_of_the_SARS_coronavirus_using_high_throughput_high_density_resequencing_arrays_ L2 - http://genome.cshlp.org/cgi/pmidlookup?view=long&pmid=14993206 DB - PRIME DP - Unbound Medicine ER -