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Int. J. Environ. Res. Public Health 2013, 10(9), 4486-4506; doi:10.3390/ijerph10094486
Article

Genetic Analysis of West Nile Virus Isolates from an Outbreak in Idaho, United States, 2006–2007

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1 Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA 2 Idaho Bureau of Laboratories, Boise, ID 83712, USA 3 Creative Testing Solutions, Tempe, AZ 85282, USA 4 American Red Cross, Gaithersburg, MD 20877, USA
* Authors to whom correspondence should be addressed.
Received: 9 July 2013 / Revised: 12 September 2013 / Accepted: 16 September 2013 / Published: 23 September 2013
(This article belongs to the Special Issue Epidemiology of West Nile Virus)
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Abstract

West Nile virus (WNV) appeared in the U.S. in 1999 and has since become endemic, with yearly summer epidemics causing tens of thousands of cases of serious disease over the past 14 years. Analysis of WNV strains isolated during the 2006–2007 epidemic seasons demonstrates that a new genetic variant had emerged coincidentally with an intense outbreak in Idaho during 2006. The isolates belonging to the new variant carry a 13 nt deletion, termed ID-Δ13, located at the variable region of the 3′UTR, and are genetically related. The analysis of deletions and insertions in the 3′UTR of two major lineages of WNV revealed the presence of conserved repeats and two indel motifs in the variable region of the 3′UTR. One human and two bird isolates from the Idaho 2006–2007 outbreaks were sequenced using Illumina technology and within-host variability was analyzed. Continued monitoring of new genetic variants is important for public health as WNV continues to evolve.
Keywords: Flavivirus; West Nile virus; genetic variation; WNV evolution; indel motifs; next generation sequencing Flavivirus; West Nile virus; genetic variation; WNV evolution; indel motifs; next generation sequencing
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Grinev, A.; Chancey, C.; Añez, G.; Ball, C.; Winkelman, V.; Williamson, P.; Foster, G.A.; Stramer, S.L.; Rios, M. Genetic Analysis of West Nile Virus Isolates from an Outbreak in Idaho, United States, 2006–2007. Int. J. Environ. Res. Public Health 2013, 10, 4486-4506.

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