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  • Open Access

Use of microarrays to assess viral diversity: from genotype to phenotype

Authors

  • Michael J. Allen,

    1. Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.
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  • Joaquin Martinez-Martinez,

    1. Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.
    2. Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK.
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    • Present address: Royal Netherlands Institute for Sea Research, NL-1790 AB Den Burg, Texel, the Netherlands. Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.

  • Declan C. Schroeder,

    1. Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK.
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  • Paul J. Somerfield,

    1. Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.
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  • William H. Wilson

    Corresponding author
    1. Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.
    2. Bigelow Laboratory for Ocean Sciences, 180 McKown Point, PO Box 475, W. Bootbay Harbor, ME 04575-0475, USA.
      *E-mail whw@pml.ac.uk; Tel. (+1) 207 633 9600; Fax (+1) 207 633 9641.
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*E-mail whw@pml.ac.uk; Tel. (+1) 207 633 9600; Fax (+1) 207 633 9641.

Summary

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.

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