节肢动物传播的病毒是遗传限制最多的RNA病毒之一,然而,他们有显著的适应和出现的倾向。我们在芝加哥病毒传播的“热点”研究了自然感染西尼罗河病毒(WNV)的野生鸟类和蚊子,IL,美国。我们使用高通量测序从时空匹配的鸟类和蚊子样本中生成了全编码WNV基因组序列,允许深度覆盖的分子进化评估。样品的平均FST为0.66(±0.02SE),为双峰,样品之间的平均核苷酸多样性(宿主间πN=0.001;πS=0.024)高于它们内部(宿主内πN<0.0001;πS<0.001)。FST>1.01的八个基因组位点(在PrM中,NS2a,NS3、NS4b、和5'-非编码基因组区域)显示鸟类与蚊子的变异频率差异>30%和/或在≥5个宿主或载体个体中固定的多态性,暗示了这些变体的宿主取向。然而,系统发育分析表明缺乏鸟类或蚊子的分组,大多数样本间差异是同义的(平均宿主间πN/πS=0.04),宿主和载体之间的核苷酸多样性或纯化选择水平均无显着差异(鸟类的平均宿主内πN/πS=0.28,蚊子的πN/πS=0.21)。这一发现与在实验室中提出和测试的“权衡”和“选择性筛选”假设形成对比,预测宿主与载体对WNV遗传变异的强烈影响,鸟类的选择性限制增强,蚊子的病毒多样性增强。总的来说,我们的数据显示WNV在宿主和载体内部和之间高度选择性地受到限制,但仍然能够在基因组中有限数量的位点发生变化.面对整体选择性约束时,这种位点特异性可塑性可能会提供一种机制,从而使诸如WNV及其亲属之类的高度受限的病毒仍然可以适应并出现。
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.