Since its introduction to control overabundant invasive European rabbits (Oryctolagus cuniculus), the highly virulent rabbit haemorrhagic disease virus (RHDV) has caused regular annual disease outbreaks in Australian rabbit populations. Although initially reducing rabbit abundance by 60%, continent‐wide, experimental evidence has since indicated increased genetic resistance in wild rabbits that have experienced RHDV‐driven selection. To identify genetic adaptations, which explain the increased resistance to this biocontrol virus, we investigated genome‐wide SNP (single nucleotide polymorphism) allele frequency changes in a South Australian rabbit population that was sampled in 1996 (pre‐RHD genomes) and after 16 years of RHDV outbreaks. We identified several SNPs with changed allele frequencies within or close to genes potentially important for increased RHD resistance. The identified genes are known to be involved in virus infections and immune reactions or had previously been identified as being differentially expressed in healthy versus acutely RHDV‐infected rabbits. Furthermore, we show in a simulation study that the allele/genotype frequency changes cannot be explained by drift alone and that several candidate genes had also been identified as being associated with surviving RHD in a different Australian rabbit population. Our unique data set allowed us to identify candidate genes for RHDV resistance that have evolved under natural conditions, and over a time span that would not have been feasible in an experimental setting. Moreover, it provides a rare example of host genetic adaptations to virus‐driven selection in response to a suddenly emerging infectious disease.

中文翻译：

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病毒流行16年后野兔基因组的适应性变化。

自从它被引入来控制过量入侵的欧洲兔子（穴兔）），高毒力兔出血性疾病病毒（RHDV）导致澳大利亚兔子种群每年定期爆发疾病。尽管最初在整个大陆范围内将兔子的丰度降低了60％，但实验证据表明，经历过RHDV驱动选择的野兔的遗传抗性增加。为了确定遗传适应性，从而解释对这种生物防治病毒的抗性增强，我们调查了南澳大利亚兔种群的全基因组SNP（单核苷酸多态性）等位基因频率变化，该样本于1996年（RHD前基因组）和16年后抽样RHDV爆发。我们发现了几个等位基因频率内或附近的等位基因频率改变的SNP，这些基因可能对增加RHD抗性具有重要意义。已知已鉴定的基因与病毒感染和免疫反应有关，或先前已鉴定为在健康与急性RHDV感染的兔子中差异表达。此外，我们在模拟研究中显示，等位基因/基因型频率的变化不能仅通过漂移来解释，并且还已经鉴定出几个候选基因与在不同的澳大利亚兔种群中存活的RHD相关。我们独特的数据集使我们能够鉴定在自然条件下以及在实验条件下不可行的时间范围内进化出的RHDV抗性候选基因。此外，它为应对突然出现的传染病，提供了宿主基因适应病毒驱动选择的罕见例子。