Use of microarrays to assess viral diversity: from genotype to phenotype.
The diversity among the coccolithovirus strains held in the Plymouth Virus Collection (PVC) was assessed using three complementary techniques: phylogeny based on DNA polymerase and major capsid protein gene sequence; host range; and a new, microarray-based genome-wide approach. The PVC is composed of three groups of strains that are geographically and temporally distinct. Virus strains clustered according to these groups in all three diversity assessments. Furthermore, the microarray approach based on genomic content showed that two strains, previously considered as identical to others in the PVC, are actually distinct. These results show the importance of genome-wide surveys for assessing strain diversity. Not only has the microarray provided an alternative to the phylogeny-derived pattern for virus evolution, it has also begun to provide some clues to the genes that may be responsible for the different phenotypes displayed by these viruses.
Allen
Michael J
MJ
Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.
Martinez-Martinez
Joaquin
J
Schroeder
Declan C
DC
Somerfield
Paul J
PJ
Wilson
William H
WH
D036022:Capsid Proteins / Q000235:genetics; D004279:DNA, Viral / Q000032:analysis; D004259:DNA-Directed DNA Polymerase; D056890:Eukaryota / Q000821:virology; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D017862:Phycodnaviridae / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny
D036022:Capsid Proteins; D004279:DNA, Viral; D004259:DNA-Directed DNA Polymerase