Stochastic lattice-based modelling of malaria dynamics.

BACKGROUND: The transmission of malaria is highly variable and depends on a range of climatic and anthropogenic factors. In addition, the dispersal of Anopheles mosquitoes is a key determinant that affects the persistence and dynamics of malaria. Simple, lumped-population models of malaria prevalence have been insufficient for predicting the complex responses of malaria to environmental changes. METHODS AND RESULTS: A stochastic lattice-based model that couples a mosquito dispersal and a susceptible-exposed-infected-recovered epidemics model was developed for predicting the dynamics of malaria in heterogeneous environments. The It[Formula: see text] approximation of stochastic integrals with respect to Brownian motion was used to derive a model of stochastic differential equations. The results show that stochastic equations that capture uncertainties in the life cycle of mosquitoes and interactions among vectors, parasites, and hosts provide a mechanism for the disruptions of malaria. Finally, model simulations for a case study in the rural area of Kilifi county, Kenya are presented. CONCLUSIONS: A stochastic lattice-based integrated malaria model has been developed. The applicability of the model for capturing the climate-driven hydrologic factors and demographic variability on malaria transmission has been demonstrated.

Hospitalizations for Substance Abuse Disorders Before and After Hurricane Katrina: Spatial Clustering and Area-Level Predictors, New Orleans, 2004 and 2008.

INTRODUCTION: Identifying at-risk groups is a challenge in post-disaster psychosocial response. Geospatial techniques can support the design and deployment of targeted and tailored interventions. This study compared spatial patterns in the distribution of hospitalizations for substance abuse disorders and associated area-level predictors before and after Hurricane Katrina in New Orleans, Louisiana. METHODS: We used hospital data from the Louisiana Department of Health and Hospitals for 2004 (pre-Katrina) and 2008 (post-Katrina). Data were assessed by using descriptive statistics, multivariable Poisson regression, and geospatial analysis. We assessed hospitalizations by US Census block group in relation to the presence of blighted properties (ie, buildings declared an imminent health threat, in danger of collapse, or a public nuisance), race of residents (white or nonwhite), presence of nondisplaced residents (measured by the number of households receiving mail in 2008), and depth of water levels. RESULTS: The hospitalization rate for substance abuse disorders was 7.13 per 1,000 population for 2004 and 9.65 per 1,000 for 2008. The concentration of hospitalizations shifted geographically from block groups exposed to floods (levee breaches) in 2004 to the center of the city in 2008. Post Katrina, predictors for hospitalizations were presence of blighted properties, nonwhite populations, and presence of nondisplaced residents. Distance from flooded areas (high water depth) and levee breaches was negatively associated with hospitalizations. Men were more likely than women to be hospitalized during both periods (78%, 2004; 63%, 2008), and the percentage of the hospitalized white population increased from 2004 (28.8%) to 2008 (44.9%). CONCLUSION: Geographic patterns of hospitalizations for substance abuse disorders shifted in post-Katrina New Orleans from flood-exposed areas to less exposed areas in the center of the city; however, poverty was a main predictor for hospitalizations during both periods. Approaches used in this study are generalizable to other disaster areas and to other psychological vulnerabilities (eg, anxiety).

Application of GIS in public health in India: A literature-based review, analysis, and recommendations.

The implementation of geospatial technologies and methods for improving health has become widespread in many nations, but India's adoption of these approaches has been fairly slow. With a large population, ongoing public health challenges, and a growing economy with an emphasis on innovative technologies, the adoption of spatial approaches to disease surveillance, spatial epidemiology, and implementation of health policies in India has great potential for both success and efficacy. Through our evaluation of scientific papers selected through a structured key phrase review of the National Center for Biotechnology Information on the database PubMed, we found that current spatial approaches to health research in India are fairly descriptive in nature, but the use of more complex models and statistics is increasing. The institutional home of the authors is skewed regionally, with Delhi and South India more likely to show evidence of use. The need for scientists engaged in spatial health analysis to first digitize basic data, such as maps of road networks, hydrological features, and land use, is a strong impediment to efficiency, and their work would certainly advance more quickly without this requirement.

Identification of Avian and Hemoparasite DNA in Blood-Engorged Abdomens of Culex pipiens (Diptera; Culicidae) from a West Nile Virus Epidemic region in Suburban Chicago, Illinois.

Multiple mosquito-borne parasites cocirculate in nature and potentially interact. To understand the community of parasites cocirculating with West Nile virus (WNV), we screened the bloodmeal content of Culex pipiens L. mosquitoes for three common types of hemoparasites. Blood-fed Cx. pipiens were collected from a WNV-epidemic area in suburban Chicago, IL, from May to September 2005 through 2010. DNA was extracted from dissected abdomens and subject to PCR and direct sequencing to identify the vertebrate host. RNA was extracted from the head or thorax and screened for WNV using quantitative reverse transcriptase PCR. Seventy-nine engorged females with avian host origin were screened using PCR and amplicon sequencing for filarioid nematodes, Haemosporida, and trypanosomatids. Filarioid nematodes were identified in 3.8% of the blooded abdomens, Plasmodium sp. in 8.9%, Haemoproteus in 31.6%, and Trypanosoma sp. in 6.3%. The sequences from these hemoparasite lineages were highly similar to sequences from birds in prior studies in suburban Chicago. Overall, 50.6% of blood-fed Culex pipiens contained hemoparasite DNA in their abdomen, presumably from current or prior bloodmeals. Additionally, we detected hemoparasite DNA in the blooded abdomen of three of 10 Cx. pipiens infected with WNV.

Host group formation decreases exposure to vector-borne disease: a field experiment in a 'hotspot' of West Nile virus transmission.

Animals can decrease their individual risk of predation by forming groups. The encounter-dilution hypothesis extends the potential benefits of gregariousness to biting insects and vector-borne disease by predicting that the per capita number of insect bites should decrease within larger host groups. Although vector-borne diseases are common and can exert strong selective pressures on hosts, there have been few tests of the encounter-dilution effect in natural systems. We conducted an experimental test of the encounter-dilution hypothesis using the American robin (Turdus migratorius), a common host species for the West Nile virus (WNV), a mosquito-borne pathogen. By using sentinel hosts (house sparrows, Passer domesticus) caged in naturally occurring communal roosts in the suburbs of Chicago, we assessed sentinel host risk of WNV exposure inside and outside of roosts. We also estimated per capita host exposure to infected vectors inside roosts and outside of roosts. Sentinel birds caged inside roosts seroconverted to WNV more slowly than those outside of roosts, suggesting that social groups decrease per capita exposure to infected mosquitoes. These results therefore support the encounter-dilution hypothesis in a vector-borne disease system. Our results suggest that disease-related selective pressures on sociality may depend on the mode of disease transmission.

Multi-Year Comparison of Community- and Species-Level West Nile Virus Antibody Prevalence in Birds from Atlanta, Georgia and Chicago, Illinois, 2005-2016.

West Nile virus (WNV) is prevalent in the United States but shows considerable variation in transmission intensity. The purpose of this study was to compare patterns of WNV seroprevalence in avian communities sampled in Atlanta, Georgia and Chicago, Illinois during a 12-year period (Atlanta 2010-2016; Chicago 2005-2012) to reveal regional patterns of zoonotic activity of WNV. WNV antibodies were measured in wild bird sera using ELISA and serum neutralization methods, and seroprevalence among species, year, and location of sampling within each city were compared using binomial-distributed generalized linear mixed-effects models. Seroprevalence was highest in year-round and summer-resident species compared with migrants regardless of region; species explained more variance in seroprevalence within each city. Northern cardinals were the species most likely to test positive for WNV in each city, whereas all other species, on average, tested positive for WNV in proportion to their sample size. Despite similar patterns of seroprevalence among species, overall seroprevalence was higher in Atlanta (13.7%) than in Chicago (5%). Location and year of sampling had minor effects, with location explaining more variation in Atlanta and year explaining more variation in Chicago. Our findings highlight the nature and magnitude of regional differences in WNV urban ecology.

Weather variability affects abundance of larval Culex (Diptera: Culicidae) in storm water catch basins in suburban Chicago.

Culex pipiens L. (Diptera: Culicidae) and Culex restuans Theobald are the primary enzootic and bridge vectors of West Nile virus in the eastern United States north of 36 degrees latitude. Recent studies of the natural history of these species have implicated catch basins and underground storm drain systems as important larval development sites in urban and suburban locales. Although the presence of larvae in these habitats is well-documented, the influence of abiotic factors on the ecology of Culex larvae developing in them remains poorly understood. Therefore, we examined the effects of multiple abiotic factors and their interactions on abundance of Culex larvae in catch basins in the Chicago, IL, metropolitan area. Low precipitation and high mean daily temperature were associated with high larval abundance, whereas there was no correlation between catch basin depth or water depth and larval abundance. Rainfall was an especially strong predictor of presence or absence of larvae in the summer of 2010, a season with an unusually high precipitation. Regression tree methods were used to build a schematic decision tree model of the interactions among these factors. This practical, visual representation of key predictors of high larval production may be used by local mosquito abatement districts to target limited resources to treat catch basins when they are particularly likely to produce West Nile virus vectors.

Effects of Scale on Modeling West Nile Virus Disease Risk.

Modeling vector-borne diseases is best conducted when heterogeneity among interacting biotic and abiotic processes is captured. However, the successful integration of these complex processes is difficult, hindered by a lack of understanding of how these relationships influence disease transmission across varying scales. West Nile virus (WNV) is the most important mosquito-borne disease in the United States. Vectored by Culex mosquitoes and maintained in the environment by avian hosts, the virus can spill over into humans and horses, sometimes causing severe neuroinvasive illness. Several modeling studies have evaluated drivers of WNV disease risk, but nearly all have done so at broad scales and have reported mixed results of the effects of common explanatory variables. As a result, fine-scale relationships with common explanatory variables, particularly climatic, socioeconomic, and human demographic, remain uncertain across varying spatial extents. Using an interdisciplinary approach and an ongoing 12-year study of the Chicago region, this study evaluated the factors explaining WNV disease risk at high spatiotemporal resolution, comparing the human WNV model and covariate performance across three increasing spatial extents: ultrafine, local, and county scales. Our results demonstrate that as spatial extent increased, model performance increased. In addition, only six of the 23 assessed covariates were included in best-fit models of at least two scales. These results suggest that the mechanisms driving WNV ecology are scale-dependent and covariate importance increases as extent decreases. These tools may be particularly helpful for public health, mosquito, and disease control personnel in predicting and preventing disease within local and fine-scale jurisdictions, before spillover occurs.

Comparing Contributions of Passive and Active Tick Collection Methods to Determine Establishment of Ticks of Public Health Concern Within Illinois.

In Illinois, between 1990 and 2017, tick-borne diseases in humans increased 10-fold, yet we have insufficient information on when and where people are exposed to vector ticks (Ixodida: Ixodidae). The aims of our research were to compare contributions of passive and active tick collection methods in determining establishment of ticks of public health concern and obtain information on tick distributions within Illinois. We used three surveillance strategies within the Illinois Tick Inventory Collaboration Network to gather information about the ticks of public health concern: 1) passive collection (voluntary submission by the public); 2) systematic collection (biweekly active surveillance); and 3) special collections (active collections in locations of special interest). Of collected adult and nymphal ticks, 436 were from passive collections, 142 from systematic collections, and 1,270 from special collections. Tick species distribution status changed in 36 counties. Our data provide noteworthy updates to distribution maps for use by public health agencies to develop prevention and control strategies. Additionally, the program built a network of collaborations and partnerships to support future tick surveillance efforts within Illinois and highlighted how the combination of the three surveillance strategies can be used to determine geographic spread of ticks, pinpoint locations in need of more surveillance, and help with long-term efforts that support phenology studies.

Examining the Relationship Between Low Birth Weight Occurrence and Passive Measures of Environmental Arsenic by Census Tract in Escambia and Santa Rosa Counties, Florida.

Arsenic is a public health concern because of its widespread distribution and high toxicity, even when doses are small. Low birth weight (LBW) occurrence, birth weights less than 2500 g, may be associated with prenatal exposure of arsenic from environmental factors and consuming contaminated drinking water and food. The objective of this study was to examine whether mothers living in areas of Escambia and Santa Rosa counties with varying levels of background arsenic in surface soil and water were associated with the occurrence of LBW. Inverse distance weight in ArcGIS was used to interpolate arsenic concentrations from environmental samples and estimate arsenic concentrations by census tracts in the two counties. After excluding multiple births and displaced geocoding addresses, birth data were obtained for the years of 2005 (n = 5845), 2010 (n = 5569), and 2015 (n = 5770) from the Bureau of Vital Statistics at the Florida Department of Health to assess temporal differences. Generalized linear models were used to analyze and compare the association between child and maternal demographic information, socioeconomic characteristics, and the environmental estimates of arsenic with LBW. No significant association was found between environmental arsenic concentration and LBW, suggesting that environmental contamination of the pregnant mother's census tract may not be a useful proxy in assessing risk for LBW.

The drivers of West Nile virus human illness in the Chicago, Illinois, USA area: Fine scale dynamic effects of weather, mosquito infection, social, and biological conditions.

West Nile virus (WNV) has consistently been reported to be associated with human cases of illness in the region near Chicago, Illinois. However, the number of reported cases of human illness varies across years, with intermittent outbreaks. Several dynamic factors, including temperature, rainfall, and infection status of vector mosquito populations, are responsible for much of these observed variations. However, local landscape structure and human demographic characteristics also play a key role. The geographic and temporal scales used to analyze such complex data affect the observed associations. Here, we used spatial and statistical modeling approaches to investigate the factors that drive the outcome of WNV human illness on fine temporal and spatial scales. Our approach included multi-level modeling of long-term weekly data from 2005 to 2016, with weekly measures of mosquito infection, human illness and weather combined with more stable landscape and demographic factors on the geographical scale of 1000m hexagons. We found that hot weather conditions, warm winters, and higher MIR in earlier weeks increased the probability of an area of having a WNV human case. Higher population and the proportion of urban light intensity in an area also increased the probability of observing a WNV human case. A higher proportion of open water sources, percentage of grass land, deciduous forests, and housing built post 1990 decreased the probability of having a WNV case. Additionally, we found that cumulative positive mosquito pools up to 31 weeks can strongly predict the total annual human WNV cases in the Chicago region. This study helped us to improve our understanding of the fine-scale drivers of spatiotemporal variability of human WNV cases.

Avian host community structure and prevalence of West Nile virus in Chicago, Illinois.

Vertebrate host diversity has been postulated to mediate prevalence of zoonotic, vector-borne diseases, such that as diversity increases, transmission dampens. This "dilution effect" is thought to be caused by distribution of infective bites to incompetent reservoir hosts. We quantified avian species richness, avian seroprevalence for antibodies to West Nile virus (WNV), and infection of WNV in Culex mosquitoes, in the Chicago metropolitan area, Illinois, USA, a region of historically high WNV activity. Results indicated high overall avian seroprevalence and variation in seroprevalence across host species; however, there was no negative correlation between avian richness and Culex infection rate or between richness and infection status in individual birds. Bird species with high seroprevalence, especially northern cardinals and mourning doves, may be important sentinels for WNV in Chicago, since they were common and widespread among all study sites. Overall, our results suggest no net effect of increasing species richness to West Nile virus transmission in Chicago. Other intrinsic and extrinsic factors, such as variation in mosquito host preference, reservoir host competence, temperature, and precipitation, may be more important than host diversity for driving interannual variation in WNV transmission. These results from a fine-scale study call into question the generality of a dilution effect for WNV at coarser spatial scales.

Molecular phylogenetic analysis of a geographically and temporally matched set of Candida albicans isolates from humans and nonmigratory wildlife in central Illinois.

This study explored whether wildlife species serve as the reservoir for human Candida albicans strains in a given geographic area. C. albicans isolates were collected from nonmigratory wildlife admitted to the University of Illinois Wildlife Medical Clinic. A geographically and temporally matched set of C. albicans oral isolates was collected from healthy human volunteers. Multilocus sequence typing was used to assign strains to genetic clades. Clade 1 isolates, particularly diploid sequence type 69 (DST 69), were most common in humans. Clade 1 strains were less frequently recovered from wildlife, while clade 8 strains, particularly DST 90, were overrepresented in the wildlife collection. All instances where a wildlife and human isolate shared the same DST occurred within clade 1. Clade distributions between human and wildlife isolates were significantly different, demonstrating population isolation between the groups. These differences may indicate limited strain transfer between groups or differential selection of C. albicans isolates in humans and wildlife. Wildlife strains had an amphotericin B MIC significantly lower than that of human isolates; strains with increased susceptibility were from several clades. C. albicans isolates were collected from domestic animals to provide comparisons with human and wildlife data sets. C. albicans isolation from canine and feline oral and anal swabs was infrequent; companion animal isolates were closely related to clade 1 human isolates. Collectively, the data suggest a greater likelihood of C. albicans transfer from humans to animals than from animals to humans. The nontransient human population may maintain the connection between geography and the C. albicans genetic groups recovered from humans.

Predicting the direct and indirect impacts of climate change on malaria in coastal Kenya.

BACKGROUND: The transmission of malaria is highly variable and depends on a range of climatic and anthropogenic factors. This study investigates the combined, i.e. direct and indirect, impacts of climate change on the dynamics of malaria through modifications in: (i) the sporogonic cycle of Plasmodium induced by air temperature increase, and (ii) the life cycle of Anopheles vector triggered by changes in natural breeding habitat arising from the altered moisture dynamics resulting from acclimation responses of vegetation under climate change. The study is performed for a rural region in Kilifi county, Kenya. METHODS AND FINDINGS: We use a stochastic lattice-based malaria (SLIM) model to make predictions of changes in Anopheles vector abundance, the life cycle of Plasmodium parasites, and thus malaria transmission under projected climate change in the study region. SLIM incorporates a nonlinear temperature-dependence of malaria parasite development to estimate the extrinsic incubation period of Plasmodium. It is also linked with a spatially distributed eco-hydrologic modeling framework to capture the impacts of climate change on soil moisture dynamics, which served as a key determinant for the formation and persistence of mosquito larval habitats on the land surface. Malaria incidence data collected from 2008 to 2013 is used for SLIM model validation. Projections of climate change and human population for the region are used to run the models for prediction scenarios. Under elevated atmospheric CO2 concentration ([CO2]) only, modeled results reveal wetter soil moisture in the root zone due to the suppression of transpiration from vegetation acclimation, which increases the abundance of Anopheles vectors and the risk of malaria. When air temperature increases are also considered along with elevated [CO2], the life cycle of Anopheles vector and the extrinsic incubation period of Plasmodium parasites are shortened nonlinearly. However, the reduction of soil moisture resulting from higher evapotranspiration due to air temperature increase also reduces the larval habitats of the vector. Our findings show the complicated role of vegetation acclimation under elevated [CO2] on malaria dynamics and indicate an indirect but ignored impact of air temperature increase on malaria transmission through reduction in larval habitats and vector density. CONCLUSIONS: Vegetation acclimation triggered by elevated [CO2] under climate change increases the risk of malaria. In addition, air temperature increase under climate change has opposing effects on mosquito larval habitats and the life cycles of both Anopheles vectors and Plasmodium parasites. The indirect impacts of temperature change on soil moisture dynamics are significant and should be weighed together with the direct effects of temperature change on the life cycles of mosquitoes and parasites for future malaria prediction and control.

Rapid amplification of West Nile virus: the role of hatch-year birds.

Epizootic transmission of West Nile virus (WNV) often intensifies rapidly leading to increasing risk of human infection, but the processes underlying amplification remain poorly understood. We quantified epizootic WNV transmission in communities of mosquitoes and birds in the Chicago, Illinois (USA) region during 2005 and 2006. Using quantitative polymerase chain reaction (PCR) methods, we detected WNV in 227 of 1195 mosquito pools (19%) in 2005 and 205 of 1685 (12%) in 2006; nearly all were Culex pipiens. In both years, mosquito infection rates increased rapidly in the second half of July to a peak of 59/1000 mosquitoes in 2005 and 33/1000 in 2006, and then declined slowly. Viral RNA was detected in 11 of 998 bird sera (1.1%) in 2005 and 3 of 1285 bird sera (<1%) in 2006; 11 of the 14 virus-positive birds were hatch-year birds. Of 540 hatch-year birds, 100 (18.5%) were seropositive in 2005, but only 2.8% (14/493) tested seropositive in 2006 for WNV antibodies using inhibition enzyme-linked immunosorbent assay (ELISA). We observed significant time series cross-correlations between mosquito infection rate and proportion of virus-positive birds, proportion of hatch-year birds captured in mist nets (significant in 2006 only), seroprevalence of hatch-year birds, and number of human cases in both seasons. These associations, coupled with the predominance of WNV infection and seropositivity in hatch-year birds, indicate a key role for hatch-year birds in the amplification of epizootic transmission of WNV, and in increasing human infection risk by facilitating local viral amplification.

Culex pipiens (Diptera: Culicidae): a bridge vector of West Nile virus to humans.

Host-feeding patterns of Culex pipiens L. collected in southwest suburban Chicago in 2005 were studied using polymerase chain reaction (PCR) and DNA sequencing techniques. Culex spp. mosquitoes, most identified to Cx. pipiens and the remainder to Cx. restuans by PCR, had fed on 18 avian species, most commonly American robin (Turdus migratorious), house sparrow (Passer domesticus), and mourning dove (Zenaida macroura). Additional blood meals were derived from four mammal species, primarily humans and raccoons (Procyon lotor). During a West Nile virus (WNV) epidemic in 2005, West Nile virus (WNV) RNA was detected in heads and thoraces of five Cx. pipiens (n = 335, 1.5%) using quantitative PCR. The hosts of these virus-infected, blood-fed mosquitoes included two American robins, one house sparrow, and one human. This is the first report of a WNV-infected Cx. pipiens mosquito collected during an epidemic of WNV that was found to have bitten a human. These results fulfill a criterion for incrimination of Cx. pipiens as a bridge vector.

The spread of mosquito-borne viruses in modern times: A spatio-temporal analysis of dengue and chikungunya.

Since the 1970s, mosquito-borne pathogens have spread to previously disease-free areas, as well as causing increased illness in endemic areas. In particular, dengue and chikungunya viruses, transmitted primarily by Aedes aegypti and secondarily by Aedes albopictus mosquitoes, represent a threat for up to a third of the world population, and are a growing public health concern. In this study, we assess the spatial and temporal factors related to the occurrences of historic dengue and chikungunya outbreaks in 76 nations focused geographically on the Indian Ocean, with outbreak data from 1959 to 2009. First, we describe the historical spatial and temporal patterns of outbreaks of dengue and chikungunya in the focal nations. Second, we use a boosted regression tree approach to assess the statistical relationships of nations' concurrent outbreak occurrences and annual occurrences with their spatial proximity to prior infections and climatic and socio-economic characteristics. We demonstrate that higher population density and shorter distances among nations with outbreaks are the dominant factors that characterize both dengue and chikungunya outbreaks. In conclusion, our analysis provides crucial insights, which can be applied to improve nations' surveillance and preparedness for future vector-borne disease epidemics.

Co-circulation of Flanders Virus and West Nile Virus in Culex Mosquitoes (Diptera: Culicidae) from Chicago, Illinois.

West Nile virus (WNV) and Flanders virus (FLAV) co-occur in regions of North America. Because both viruses are maintained in a transmission cycle involving Culex mosquitoes and birds, screening mosquitoes for FLAV has been suggested as an enhancement to WNV surveillance and epidemic prediction. Using samples collected in 2010 and 2012 in Chicago, IL, USA, we demonstrate the presence of FLAV in four out of 287 (1.4%) Culex pools. We estimated minimum infection rates for WNV and FLAV to be 5.66 and 1.22 in 2010 and 8.74 and 0.61 in 2012, respectively. FLAV occurred 1 and 3 wk prior to the peak of WNV transmission in 2010 and 2012, respectively. FLAV sequences from Chicago were genetically diverse and phylogenetically representative of lineage A viruses from across the United States.

Standardized Operational Evaluations of Catch Basin Larvicides from Seven Mosquito Control Programs in the Midwestern United States During 2017.

During June to September 2017, 7 mosquito control programs in the midwestern United States evaluated a total of 9 catch basin larvicide formulations using similar protocols. Treated basins were monitored among study sites to observe when larvicides failed to control mosquitoes in 25% or more basins within a site. Overall, when monitoring occurred within the maximum label duration of the larvicides, sites treated with a single larvicide tablet or briquet surpassed the 25% fail threshold more often than pellet and granular larvicide formulations. In 438 of the study basins, the depth from sump bottom to catch basin lid was measured. In basins that were deeper than 5 ft (1.5 m), larvicides failed to control mosquitoes significantly more often than those 5 ft or shallower.

Selective constraint and adaptive potential of West Nile virus within and among naturally infected avian hosts and mosquito vectors.

Arthropod-borne viruses are among the most genetically constrained RNA viruses, yet they have a remarkable propensity to adapt and emerge. We studied wild birds and mosquitoes naturally infected with West Nile virus (WNV) in a 'hot spot' of virus transmission in Chicago, IL, USA. We generated full coding WNV genome sequences from spatiotemporally matched bird and mosquito samples using high-throughput sequencing, allowing a molecular evolutionary assessment with deep coverage. Mean FST among samples was 0.66 (±0.02 SE) and was bimodal, with mean nucleotide diversity being higher between samples (interhost πN = 0.001; πS = 0.024) than within them (intrahost πN < 0.0001; πS < 0.001). Eight genomic sites with FST > 1.01 (in the PrM, NS2a, NS3, NS4b, and 5'-noncoding genomic regions) showed bird versus mosquito variant frequency differences of >30 per cent and/or polymorphisms fixed in ≥5 host or vector individuals, suggesting host tropism for these variants. However, phylogenetic analyses demonstrated a lack of grouping by bird or mosquito, most inter-sample differences were synonymous (mean interhost πN/πS = 0.04), and there was no significant difference between hosts and vectors in either their nucleotide diversities or levels of purifying selection (mean intrahost πN/πS = 0.28 in birds and πN/πS = 0.21 in mosquitoes). This finding contrasts with the 'trade-off' and 'selective sieve' hypotheses that have been proposed and tested in the laboratory, which predict strong host versus vector effects on WNV genetic variation, with heightened selective constraint in birds alternating with heightened viral diversity in mosquitoes. Overall, our data show WNV to be highly selectively constrained within and between both hosts and vectors but still able to vary at a limited number of sites across the genome. Such site-specific plasticity in the face of overall selective constraint may offer a mechanism whereby highly constrained viruses such as WNV and its relatives can still adapt and emerge.