West Nile virus population genetics and evolution

Abstract

West Nile virus (WNV) (Flaviviridae: Flavivirus) is transmitted from mosquitoes to birds, but can cause fatal encephalitis in infected humans. Since its introduction into North America in New York in 1999, it has spread throughout the western hemisphere. Multiple outbreaks have also occurred in Europe over the last 20 years. This review highlights recent efforts to understand how host pressures impact viral population genetics, genotypic and phenotypic changes which have occurred in the WNV genome as it adapts to this novel environment, and molecular epidemiology of WNV worldwide. Future research directions are also discussed.

Fig. 1

Worldwide map with countries where West Nile virus has been isolated colored as follows: Lineage Ia in light blue; lineage Ib in medium blue; lineage Ic in dark blue, lineage II in red, lineage III or “Rabensburg” virus in purple, lineage IV in orange, recent Spanish lineage (Vazquez et al., 2010) in green, and Koutango virus is colored yellow. Hatched coloring indicates more than one lineage has been isolated from that country. Lineage I distribution is adapted from May et al., 2011, other lineage isolates adapted from Charrel et al., 2003; Vazquez et al., 2010. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Radial phylogram showing relationships between different lineages of WNV. Complete coding sequences were downloaded from Genbank and aligned manually in BioEdit. Strains used and accession numbers are as follows: JEV, NC_001437; NY99, lineage Ia, NC_009942; Kunjin, paKUN, lineage Ib, AY274505.1; Indi804994, Indian lineage Ic, DQ256376.1; 956, lineage II, NC_001563; Rabensburg, lineage III, AY765264.1; RussianLEIV, lineage IV, strain Krnd88-190, AY277251.1; Koutango virus, EU082200.1. Bayesian phylogeny is shown, generated with MrBayes 3.1.2 run with a general time reversible (GTR) model with gamma shaped rate variation and invariable sites (Ronquist and Huelsenbeck, 2003). Two Markov chain Monte Carlo (MCMC) tree searches of 5000,000 generations each were run in parallel with sampling one in every 1000 trees. Radial 50% majority-rule consensus tree is shown based on the last 3750 trees. Posterior probabilities are given as numbers at each node.