Evolutionary Dynamics of West Nile Virus in the United States, 1999–2011: Phylogeny, Selection Pressure and Evolutionary Time-Scale Analysis

<div><p>West Nile virus (WNV), an arbovirus maintained in a bird-mosquito enzootic cycle, can infect other vertebrates including humans. WNV was first reported in the US in 1999 where, to date, three genotypes belonging to WNV lineage I have been described (NY99, WN02, SW/WN03). We report here the WNV sequences obtained from two birds, one mosquito, and 29 selected human samples acquired during the US epidemics from 2006–2011 and our examination of the evolutionary dynamics in the open-reading frame of WNV isolates reported from 1999–2011. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses and selection pressure analyses were conducted with the HyPhy package. Phylogenetic analysis identified human WNV isolates within the main WNV genotypes that have circulated in the US. Within genotype SW/WN03, we have identified a cluster with strains derived from blood donors and birds from Idaho and North Dakota collected during 2006–2007, termed here MW/WN06. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. The mean nucleotide substitution rate for WNV isolates obtained from humans was calculated to be 5.06×10⁻⁴ substitutions/site/year (s/s/y). The Bayesian skyline plot shows that after a period of high genetic variability following the introduction of WNV into the US, the WNV population appears to have reached genetic stability. The establishment of WNV in the US represents a unique opportunity to understand how an arbovirus adapts and evolves in a naïve environment. We describe a novel, well-supported cluster of WNV formed by strains collected from humans and birds from Idaho and North Dakota. Adequate genetic surveillance is essential to public health since new mutants could potentially affect viral pathogenesis, decrease performance of diagnostic assays, and negatively impact the efficacy of vaccines and the development of specific therapies.</p></div

Genetic Variability of West Nile Virus in U.S. Blood Donors from the 2012 Epidemic Season

<div><p>West Nile virus (WNV) is an arbovirus maintained in nature in a bird-mosquito enzootic cycle which can also infect other vertebrates including humans. WNV is now endemic in the United States (U.S.), causing yearly outbreaks that have resulted in an estimated total of 4–5 million human infections. Over 41,700 cases of West Nile disease, including 18,810 neuroinvasive cases and 1,765 deaths, were reported to the CDC between 1999 and 2014. In 2012, the second largest West Nile outbreak in the U.S. was reported, which caused 5,674 cases and 286 deaths. WNV continues to evolve, and three major WNV lineage I genotypes (NY99, WN02, and SW/WN03) have been described in the U.S. since introduction of the virus in 1999. We report here the WNV sequences obtained from 19 human samples acquired during the 2012 U.S. outbreak and our examination of the evolutionary dynamics in WNV isolates sequenced from 1999–2012. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses. Selection pressure analyses were performed with the HyPhy package using the Datamonkey web-server. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. Thirteen of the 19 completely sequenced isolates from 10 U.S. states were genetically similar, sharing up to 55 nucleotide mutations and 4 amino acid substitutions when compared with the prototype isolate WN-NY99. Overall, these analyses showed that following a brief contraction in 2008–2009, WNV genetic divergence in the U.S. continued to increase in 2012, and that closely related variants were found across a broad geographic range of the U.S., coincident with the second-largest WNV outbreak in U.S. history.</p></div

Evolutionary fingerprint based on 1000 distribution samples (Datamonkey server www.datamonkey.org).

<p>The plot depicts the estimate of the distribution of synonymous and non-synonymous rates inferred from alignment of WNV sequences (n = 77) from strains collected in the US in 2012. The ellipses reflect a Gaussian-approximated variance in each individual rate estimate, and colored pixels show the density of the posterior sample of the distribution for a given rate. The diagonal line represents the idealized neutral evolution scenario (ω = 1), points above the line correspond to positive selection (ω>1), and points below the line to negative selection (ω<1).</p

Selection pressure analysis of WNV strains collected in the U.S. in 2012.

<p>Selection pressure analysis of WNV strains collected in the U.S. in 2012.</p

Amino acid substitutions present in more than one of the 2012 human WNV isolates compared to the WN-NY99 (AF196835).

<p>Amino acid substitutions present in more than one of the 2012 human WNV isolates compared to the WN-NY99 (AF196835).</p

Increasing evolutionary divergence of North American WNV strains over the time of collection.

<p>Y-axis: Substitutions per site. X-axis: Years. Blue line: average divergence over sequence pairs within years; the numbers of base substitutions per site from averaging over all sequence pairs within each year are shown. Red line: divergence over sequence pairs between 1999 and other years; the numbers of base substitutions per site from averaging over all sequence pairs between 1999 and other years are shown. Green line: estimates of net evolutionary divergence between groups of sequences, 1999–2012: the numbers of base substitutions per site from estimation of net average between groups of sequences corresponding to each year are shown. Analyses were conducted in MEGA6 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004717#pntd.0004717.ref024" target="_blank">24</a>] using the Maximum Composite Likelihood model [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004717#pntd.0004717.ref046" target="_blank">46</a>].</p

Maximum clade credibility tree from Bayesian analysis of WNV strains from North America, 1999–2012 (n = 870).

<p>A) WNV genotypes are color-coded in the branches of the tree as NY99 (black), WN02 (blue), SW/WN03 (purple) and cluster MW/WN06 (red). Nodes 1 to 6 containing WNV isolates from this study are highlighted in green and shown in detail. The mean time to the most recent common ancestor (tMRCA) is shown in each principal node. The 95% highest probability densities (95% HPD) for each node age are shown as blue bars. B) Bayesian coalescent inference of genetic diversity and population dynamics using the Bayesian Skyline plot. The X axis represents years of study and the Y axis, the relative genetic diversity product of the effective population size.</p

Consensus maximum-likelihood tree of North American WNV ORFs, 1999–2012 (n = 870).

<p>WNV genotypes are color-coded as NY99 (black), INTermediate (orange), WN02 (blue), SW/WN03 (purple) and cluster MW/WN06 (red). All WNV sequences derived from this study are labeled by black diamonds, and Nodes 1 to 6 containing these sequences are highlighted in green and shown in detail. Taxon names correspond to GenBank accession numbers and years of collection. Node-specific amino acid substitutions are shown for each node (see also <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004717#pntd.0004717.s004" target="_blank">S4 Table</a>). For each node, states shown in red in the adjacent U.S. map are those from which strains have been isolated.</p

List of 2012 WNV isolates completely sequenced in this study.

<p>List of 2012 WNV isolates completely sequenced in this study.</p

Common nucleotide mutations present in the 2012 human WNV isolates, compared to the prototype strain WN-NY99 (AF196835).

<p>Common nucleotide mutations present in the 2012 human WNV isolates, compared to the prototype strain WN-NY99 (AF196835).</p