The advent of the DNA-microarray based methods has led to discovery and …

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Biology Articles » Molecular Biology » Viral Discovery and Sequence Recovery Using DNA Microarrays

Abstract

- Viral Discovery and Sequence Recovery Using DNA Microarrays

Viral Discovery and Sequence Recovery Using DNA Microarrays

David Wang¹, Anatoly Urisman¹, Yu-Tsueng Liu², Michael Springer¹, Thomas G. Ksiazek³, Dean D. Erdman³, Elaine R. Mardis⁴, Matthew Hickenbotham⁴, Vincent Magrini⁴, James Eldred⁴, J. Phillipe Latreille⁴, Richard K. Wilson⁴, Don Ganem², Joseph L. DeRisi^1*

1 Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America, , 2 Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America, , 3 National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America, , 4 Department of Genetics, Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, United States of America

Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery. We describe herein a DNA microarray-based platform for novel virus identification and characterization. Central to this approach was a DNA microarray designed to detect a wide range of known viruses as well as novel members of existing viral families; this microarray contained the most highly conserved 70mer sequences from every fully sequenced reference viral genome in GenBank. During an outbreak of severe acute respiratory syndrome (SARS) in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient. To further characterize this new virus, approximately 1 kb of the unknown virus genome was cloned by physically recovering viral sequences hybridized to individual array elements. Sequencing of these fragments confirmed that the virus was indeed a new member of the coronavirus family. This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease.

Source: PLoS Biol. 2003 Nov;1(2):E2. Epub 2003 Nov 17.

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