Viral discovery and sequence recovery using DNA microarrays.
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.
Wang
David
D
Department of Biochemistry and Biophysics, University of California San Francisco, USA.
Urisman
Anatoly
A
Liu
Yu-Tsueng
YT
Springer
Michael
M
Ksiazek
Thomas G
TG
Erdman
Dean D
DD
Mardis
Elaine R
ER
Hickenbotham
Matthew
M
Magrini
Vincent
V
Eldred
James
J
Latreille
J Phillipe
JP
Wilson
Richard K
RK
Ganem
Don
D
DeRisi
Joseph L
JL
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