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Genetic variation in West Nile virus from naturally infected mosquitoes and birds suggests quasispecies structure and strong purifying selection.

ABSTRACT: Intrahost genetic diversity was analysed in naturally infected mosquitoes and birds to determine whether West Nile virus (WNV) exists in nature as a quasispecies and to quantify selective pressures within and between hosts. WNV was sampled from ten infected birds and ten infected mosquito pools collected on Long Island, NY, USA, during the peak of the 2003 WNV transmission season. A 1938 nt fragment comprising the 3' 1159 nt of the WNV envelope (E) coding region and the 5' 779 nt of the non-structural protein 1 (NS1) coding region was amplified and cloned and 20 clones per specimen were sequenced. Results from this analysis demonstrate that WNV infections are derived from a genetically diverse population of genomes in nature. The mean nucleotide diversity was 0.016 % within individual specimens and the mean percentage of clones that differed from the consensus sequence was 19.5 %. WNV sequences in mosquitoes were significantly more genetically diverse than WNV in birds. No host-dependent bias for particular types of mutations was observed and estimates of genetic diversity did not differ significantly between E and NS1 coding sequences. Non-consensus clones obtained from two avian specimens had highly similar genetic signatures, providing preliminary evidence that WNV genetic diversity may be maintained throughout the enzootic transmission cycle, rather than arising independently during each infection. Evidence of purifying selection was obtained from both intra- and interhost WNV populations. Combined, these data support the observation that WNV populations may be structured as a quasispecies and document strong purifying natural selection in WNV populations.

SUBMITTER: Jerzak G

PROVIDER: S-EPMC2440486 | biostudies-literature | 2005 Aug

REPOSITORIES: biostudies-literature

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Genetic variation in West Nile virus from naturally infected mosquitoes and birds suggests quasispecies structure and strong purifying selection.

Jerzak Greta G Bernard Kristen A KA Kramer Laura D LD Ebel Gregory D GD

The Journal of general virology 20050801 Pt 8

Intrahost genetic diversity was analysed in naturally infected mosquitoes and birds to determine whether West Nile virus (WNV) exists in nature as a quasispecies and to quantify selective pressures within and between hosts. WNV was sampled from ten infected birds and ten infected mosquito pools collected on Long Island, NY, USA, during the peak of the 2003 WNV transmission season. A 1938 nt fragment comprising the 3' 1159 nt of the WNV envelope (E) coding region and the 5' 779 nt of the non-stru ...[more]

PMID: 16033965

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Project description:ImportanceWest Nile virus (WNV) is the leading cause of domestically acquired arboviral disease.ObjectiveTo develop real-time WNV forecasts of infected mosquitoes and human cases.Design, setting, and participantsReal-time forecasts of WNV in 4 geographically dispersed locations in the United States were generated using a WNV model-inference forecasting system previously validated with retrospective data. Analysis was performed to evaluate how observational reporting delays of mosquito WNV assay results and human medical records were associated with real-time forecast accuracy.ExposuresMosquitoes positive for WNV and human cases.Main outcomes and measuresDelays in reporting mosquito WNV assay results and human medical records and the association of these delays with real-time WNV forecast accuracy.ResultsSubstantial delays in data reporting exist for both infected mosquitoes and human WNV cases. For human cases, confirmed data (n = 37) lagged behind the onset of illness by a mean (SD) of 5.5 (2.3) weeks (range, 2-14 weeks). These human case reporting lags reduced mean forecast accuracy for the total number of human cases over the season in 110 simulated outbreaks for 2 forecasting systems by 26% and 14%, from 2 weeks before to 3 weeks after the predicted peak of infected mosquitoes. This period is the time span during which 47% of human cases are reported. Of 7064 mosquito pools, 500 (7%) tested positive; the reporting lag for these data associated with viral testing at a state laboratory was a mean (SD) of 6.6 (2.6) days (range, 4-11 days). This reporting lag was associated with decreased mean forecast accuracy for the 3 mosquito infection indicators, timing, magnitude, and season, by approximately 5% for both forecasting systems.Conclusions and relevanceDelays in reporting human WNV disease and infected mosquito information are associated with difficulties in outbreak surveillance and decreased real-time forecast accuracy. Infected mosquito lags were short enough that skillful forecasts could still be generated for mosquito infection indicators, but the human WNV case lags were too great to support accurate forecasting in real time. Forecasting WNV is potentially an important evidence-based decision support tool for public health officials and mosquito abatement districts; however, to operationalize real-time forecasting, more resources are needed to reduce human case reporting lags between illness onset and case confirmation.

Project description:BackgroundWest Nile virus (WNV), primarily vectored by mosquitoes of the genus Culex, is the most important mosquito-borne pathogen in North America, having infected thousands of humans and countless wildlife since its arrival in the USA in 1999. In locations with dedicated mosquito control programs, surveillance methods often rely on frequent testing of mosquitoes collected in a network of gravid traps (GTs) and CO2-baited light traps (LTs). Traps specifically targeting oviposition-seeking (e.g. GTs) and host-seeking (e.g. LTs) mosquitoes are vulnerable to trap bias, and captured specimens are often damaged, making morphological identification difficult.MethodsThis study leverages an alternative mosquito collection method, the human landing catch (HLC), as a means to compare sampling of potential WNV vectors to traditional trapping methods. Human collectors exposed one limb for 15 min at crepuscular periods (5:00-8:30 am and 6:00-9:30 pm daily, the time when Culex species are most actively host-seeking) at each of 55 study sites in suburban Chicago, Illinois, for two summers (2018 and 2019).ResultsA total of 223 human-seeking mosquitoes were caught by HLC, of which 46 (20.6%) were mosquitoes of genus Culex. Of these 46 collected Culex specimens, 34 (73.9%) were Cx. salinarius, a potential WNV vector species not thought to be highly abundant in upper Midwest USA. Per trapping effort, GTs and LTs collected > 7.5-fold the number of individual Culex specimens than HLC efforts.ConclusionsThe less commonly used HLC method provides important insight into the complement of human-biting mosquitoes in a region with consistent WNV epidemics. This study underscores the value of the HLC collection method as a complementary tool for surveillance to aid in WNV vector species characterization. However, given the added risk to the collector, novel mitigation methods or alternative approaches must be explored to incorporate HLC collections safely and strategically into control programs.

Project description: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 ?N?=?0.001; ?S?=?0.024) than within them (intrahost ?N?<?0.0001; ?S?<?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 ?N/?S?=?0.04), and there was no significant difference between hosts and vectors in either their nucleotide diversities or levels of purifying selection (mean intrahost ?N/?S?=?0.28 in birds and ?N/?S?=?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.

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Genetic variation in West Nile virus from naturally infected mosquitoes and birds suggests quasispecies structure and strong purifying selection.

Publications

Genetic variation in West Nile virus from naturally infected mosquitoes and birds suggests quasispecies structure and strong purifying selection.

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