Continued Evolution of West Nile Virus, Houston, Texas, USA, 2002–2012

Brian R. Mann¹, Allison R. McMullen¹, Daniele M. Swetnam, Vence Salvato, Martin Reyna, Hilda Guzman, Rudy Bueno, James A. Dennett, Robert B. Tesh, and Alan D.T. Barrett

Author affiliations: University of Texas Medical Branch, Galveston, Texas, USA (B.R. Mann, A.R. McMullen, D.M. Swetnam, H. Guzman, R.B. Tesh, A.D.T. Barrett); Harris County Public Health and Environmental Services, Houston, Texas, USA (V. Salvato, M. Reyna, R. Bueno, Jr., J.A. Dennett)

Abstract

We investigated the genetics and evolution of West Nile virus (WNV) since initial detection in the United States in 1999 on the basis of continual surveillance studies in the Houston, Texas, USA, metropolitan area (Harris County) as a surrogate model for WNV evolution on a national scale. Full-length genomic sequencing of 14 novel 2010–2012 WNV isolates collected from resident birds in Harris County demonstrates emergence of 4 independent genetic groups distinct from historical strains circulating in the greater Houston region since 2002. Phylogenetic and geospatial analyses of the 2012 WNV isolates indicate closer genetic relationship with 2003–2006 Harris County isolates than more recent 2007–2011 isolates. Inferred monophyletic relationships of these groups with several 2006–2009 northeastern US isolates supports potential introduction of a novel WNV strain in Texas since 2010. These results emphasize the need to maintain WNV surveillance activities to better understand WNV transmission dynamics in the United States.

The emergence of West Nile virus (WNV) in the Western Hemisphere in 1999 poses an ongoing public health threat in North America as the most common cause of epidemic encephalitis in the United States (1). WNV transmission is maintained in an enzootic cycle between mosquitoes and birds; equids, humans, other mammals, and some bird species act as dead-end hosts (2). Human infections are asymptomatic in 80% of cases, and West Nile fever develops in ≈20% of infected patients, which progresses to neuroinvasive disease in < 1% (3).
After introduction of WNV in the United States in 1999 (4), local transmission of the original New York genotype (NY99) in resident Culex spp. mosquito and wild bird populations fueled the geographic expansion of WNV from the northeastern region across the continental United States, north into Canada, and south into Central and South America (5–7). Subsequent introduction into Texas in 2002 resulted in 105 confirmed human infections, high mortality rates among local corvids, and a 31.2% seroconversion rate among resident birds of Harris County, Texas (Houston metropolitan area) alone (8). Uninterrupted surveillance of the related St. Louis encephalitis virus in local Culex spp. mosquito populations by the Harris County Mosquito Control Division since 1964 provided an ideal infrastructure for the expanded detection of WNV activity in the mosquito vector and the wild bird reservoir on a major bird migratory pathway. Routine collections of WNV-positive birds and mosquito pools to date have provided an outstanding opportunity to investigate WNV diversity and evolution on a fine geographic scale comparable to similar surveillance foci in the midwestern and New England regions of the United States (9–11). However, because of its geographic location, Harris County represents a different ecosystem, namely a warm year-round climate with unique resident mosquito and avian species.
Phylogenetic examination of 2002–2004 Harris County isolates confirmed rapid displacement of the NY99 genotype with the novel North American genotype (NA/WN02) in 2002 (12). Fine-scale geospatial genetic comparisons of these isolates provided further evidence of increased WNV genetic diversification in the greater Houston region relative to the homogenous distribution of the now extinct NY99 genotype (12,13). Subsequently, McMullen et al. identified the emergence of the southwestern genotype (SW/WN03) in the southwestern United States in 2003 and positive selection for the encoded NS4A-A85T and NS5-K314R amino acid substitutions in the WNV nonstructural (NS) proteins (14). To date, the NA/WN02 and SW/WN03 genotypes still appear to co-circulate.
Endemic transmission of WNV in the United States since 2006 has shown a dramatic decrease in the confirmed incidence of clinical WNV disease; < 1,100 annual human cases were reported during 2008–2011 (15). Despite identification of regional heterogeneous WNV populations, a relative stasis in WNV evolution has been observed in Harris County, consistent with the logistic molecular clock model and a decreasing viral growth rate proposed on a national scale (16–18). Notably, the current 2012 WNV transmission season demonstrates major divergence from this status quo; > 5,600 human infections have been reported nationwide (15). Incidence of clinical WNV disease in the Texas outbreak alone accounted for > 33% of the cases in the United States (1,868 cases, including 844 reports of neuroinvasive disease and 89 deaths) and > 994 confirmed cases in the greater Dallas/Fort Worth, Texas, metropolitan area and 101 cases in Harris County (15,19). These changes reflect final US and Texas and WNV cases for 2012 reported by the Centers for Disease Control and Prevention (Atlanta, GA, USA) (www.cdc.gov/media/releases/2013/a0513-west-nile.html) after submission of this report after review. Therefore, studies concerning the continued evolution of WNV in the central and southern United States remain vital for elucidating the role of dynamic genetic heterogeneity and accumulation of novel mutations in the transmission dynamics and incidence of clinical WNV disease.
We report consensus sequence analyses of 17 novel full-length 2010 (n = 1), 2011 (n = 1), and 2012 (n = 15) WNV isolates collected from WNV-positive birds and Culex spp. mosquito pools in Harris County Texas (n = 14) and the greater Dallas/Fort Worth region (n = 3). Inclusion of these new isolates with 28 additional 2002–2009 Harris County WNV isolates in phylogenetic and geospatial analyses of the greater Houston region provides an ideal model for investigating the role of ongoing WNV evolution relative to environmental and clinical incidence reported over the past decade. Furthermore, isolates from the recent WNV epidemic demonstrate closer phylogenetic relationships with original 2002–2003 Harris County isolates, inconsistent with phylogenetic trends observed until 2011 and supporting evidence for the recent introduction of a novel WNV strain(s) in Texas from another geographic region.