Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host-shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from 42 locations in the contact region between clades for TULV infection by RT-PCR. Sequencing yielded 23 TULV Central North and 21 TULV Central South genomes which differed by 14.9-18.5% at the nucleotide and 2.2-3.7% at the amino acid level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis and genomic SNPs showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating of the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.

中文翻译：

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对单一啮齿动物宿主谱系内的早期图拉汉坦病毒物种的全基因组支持

病毒的进化分化最常见的驱动因素是与其宿主的共同分化或宿主转移后的传播隔离。然而，目前仍不清楚的是，指定病毒物种内不同的系统发育分支是否代表高进化率或早期病毒物种的功能等效副产品。在这里，我们使用来自图拉正汉坦病毒（TULV）中两个广泛的系统发育分支的基因组数据来测试这些替代方案，该分支位于其天然啮齿动物宿主普通田鼠田鼠的单一进化谱系中。我们通过 RT-PCR 检查了进化枝之间接触区域 42 个位置的田鼠的 TULV 感染情况。测序产生了 23 个 TULV Central North 和 21 个 TULV Central South 基因组，其核苷酸水平差异为 14.9-18.5%，氨基酸水平差异为 2.2-3.7%，没有证据表明进化枝之间存在重组或重配。地理斜线分析表明，在连续景观中，近亲 TULV 分支之间存在突然的（<1 公里宽）过渡。这一转变位于 M. arvalis 的中央线粒体谱系内，基因组 SNP 显示宿主群体逐渐混合。TULV中部从北向南过渡期间宿主的基因组分化比宿主两个进化谱系之间附近的杂交区的基因组分化要弱得多。我们认为，这些近亲 TULV 分支代表了功能独特的早期物种，它们可能受到宿主遗传多态性的不同影响。这凸显了自然病毒接触区作为研究导致或限制 RNA 病毒传播的遗传和进化因素的系统的潜力。