Viral discovery and sequence recovery using DNA microarrays

David Wang, Anatoly Urisman, Yu Tsueng Liu, Michael Springer, Thomas Ksiazek, Dean D. Erdman, Elaine R. Mardis, Matthew Hickenbotham, Vincent Magrini, James Eldred, J. Phillipe Latreille, Richard K. Wilson, Don Ganem, Joseph L. DeRisi

Research output: Contribution to journalArticle

307 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
JournalPLoS Biology
Volume1
Issue number2
DOIs
StatePublished - 2003
Externally publishedYes

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Microarrays
Oligonucleotide Array Sequence Analysis
Viruses
Recovery
viruses
DNA
Emerging Communicable Diseases
Severe Acute Respiratory Syndrome
Coronavirus
Coronavirinae
emerging diseases
hybridization
Genes
genome
conserved sequences
Conserved Sequence
Viral Genome
Nucleic Acid Databases
Pathogens
Disease Outbreaks

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Wang, D., Urisman, A., Liu, Y. T., Springer, M., Ksiazek, T., Erdman, D. D., ... DeRisi, J. L. (2003). Viral discovery and sequence recovery using DNA microarrays. PLoS Biology, 1(2). https://doi.org/10.1371/journal.pbio.0000002

Viral discovery and sequence recovery using DNA microarrays. / Wang, David; Urisman, Anatoly; Liu, Yu Tsueng; Springer, Michael; Ksiazek, Thomas; Erdman, Dean D.; Mardis, Elaine R.; Hickenbotham, Matthew; Magrini, Vincent; Eldred, James; Latreille, J. Phillipe; Wilson, Richard K.; Ganem, Don; DeRisi, Joseph L.

In: PLoS Biology, Vol. 1, No. 2, 2003.

Research output: Contribution to journalArticle

Wang, D, Urisman, A, Liu, YT, Springer, M, Ksiazek, T, Erdman, DD, Mardis, ER, Hickenbotham, M, Magrini, V, Eldred, J, Latreille, JP, Wilson, RK, Ganem, D & DeRisi, JL 2003, 'Viral discovery and sequence recovery using DNA microarrays', PLoS Biology, vol. 1, no. 2. https://doi.org/10.1371/journal.pbio.0000002
Wang, David ; Urisman, Anatoly ; Liu, Yu Tsueng ; Springer, Michael ; Ksiazek, Thomas ; Erdman, Dean D. ; Mardis, Elaine R. ; Hickenbotham, Matthew ; Magrini, Vincent ; Eldred, James ; Latreille, J. Phillipe ; Wilson, Richard K. ; Ganem, Don ; DeRisi, Joseph L. / Viral discovery and sequence recovery using DNA microarrays. In: PLoS Biology. 2003 ; Vol. 1, No. 2.
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