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Evolution of a new genotype of West Nile virus in North America

A. R. McMullen, F. J. May, L. Li, H. Guzman, R. Bueno, Jr, J. A. Dennett, R. B. Tesh, A. D. T. Barrett

PREVIOUS studies of North American isolates of West Nile virus (WNV), a mosquito-borne flavivirus, suggested that the virus had reached genetic homeostasis. This study examined genetic variation in WNV strains from the Upper Texas Gulf Coast region since 2005.

WNV isolates were studied from mosquito pools or the brains of naturally infected birds collected between 2005 and 2009 in Harris County in the Upper Texas Gulf Coast region. Viral RNA was amplified by RT-PCR and the products were separated by electrophoresis. Purified PCR products were sequenced, edited and assembled, and full-length coding sequences were aligned with all published North American WNV isolates in GenBank (as of November 2010), and a single isolate using MUSCLE. Phylogenetic trees were constructed. The first 9999 nucleotides of the WNV open-reading frame were screened for recombination, and the genome was analysed for sites of positive selection.

A total of 111 isolates were included in the study, and the genomic sequences of 17 geotemporally representative isolates were determined …

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