title: Viral discovery and sequence recovery using DNA microarrays.
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.
authors: Department of Biochemistry and Biophysics, University of California San Francisco, USA.
authors: David
authors: D
authors: Wang
authors: Anatoly
authors: A
authors: Urisman
authors: Yu-Tsueng
authors: YT
authors: Liu
authors: Michael
authors: M
authors: Springer
authors: Thomas G
authors: TG
authors: Ksiazek
authors: Dean D
authors: DD
authors: Erdman
authors: Elaine R
authors: ER
authors: Mardis
authors: Matthew
authors: M
authors: Hickenbotham
authors: Vincent
authors: V
authors: Magrini
authors: James
authors: J
authors: Eldred
authors: J Phillipe
authors: JP
authors: Latreille
authors: Richard K
authors: RK
authors: Wilson
authors: Don
authors: D
authors: Ganem
authors: Joseph L
authors: JL
authors: DeRisi
mesh_terms: D001483:Base Sequence; D021821:Communicable Diseases, Emerging / Q000175:diagnosis / Q000821:virology; D005814:Genes, Viral; D005821:Genetic Techniques; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics; D017422:Sequence Analysis, DNA; D045169:Severe Acute Respiratory Syndrome / Q000235:genetics