Identifying the genetic mechanisms facilitating host range and virulence of a viral pathogen that threatens European amphibian biodiversity

由于传染病的出现，两栖动物正在经历灾难性的减少。在欧洲，病原体主要是病毒（拉纳病毒），我们的工作表明，在两栖动物群落中出现的拉纳病毒可能导致至少三种不同的模式：死亡率和种群下降可能是宿主特异性的，它可能影响整个宿主群落，或者感染可能是无症状的，在致命感染常见的地区共同发生。通过对病毒分离株的分析，我们已经确定这种变异与病毒系统发育有关：在西班牙，导致两栖动物群落死亡和衰退的遗传谱系与遗传上独特的无症状谱系共同循环；在英国，第三种谱系与单一宿主物种的死亡和衰退有关（常见的青蛙-感染其他宿主物种是罕见的，不会导致显著的死亡率或溢出宿主的减少）。在这里，我们建议利用这个新系统来确定哪些遗传因素导致了宿主范围和毒力的这些差异。我们的方法是三管齐下：首先，我们将对130个ranavirus基因组进行测序，以编目欧洲谱系中的遗传变异并确定候选位点。我们还将采取一种更自下而上的系统发育方法，在全球ranavirus基因组面板中识别与宿主物种差异相关的任何遗传变异。其次，我们进行了控制感染实验，以验证三种动物模型中不同的宿主范围和不同病毒分离株的毒力（选择两种无尾动物和一种尾尾动物，以涵盖我们在西班牙观察到的宿主范围）。第三，我们将产生病毒敲除，针对我们在前两个目标中确定的候选区域，并在我们的动物模型中使用重组体和野生型病毒测试有关基因功能的假设。我们的研究结果将对我们理解为什么在某些情况下病毒是如此致命的病原体做出重要贡献。在整个欧洲，拉纳病毒的出现正在增加，并正在成为拉丁美洲和马达加斯加这两个两栖动物和爬行动物生物多样性热点地区两栖动物和爬行动物生物多样性的新威胁。我们的研究将更广泛地告知流行病学界，哪些遗传因素可能对病毒利用新宿主很重要。鉴于大多数新发感染是病毒性的，并且是通过宿主跳跃出现的，我们希望我们的发现能引起这个社区的广泛兴趣。

Amphibians are experiencing catastrophic declines, caused by the emergence of infectious diseases. In Europe, the causative agent is predominantly viral (ranavirus), and our work has shown that emergence of ranavirus in amphibian communities can result in at least three different patterns: the mortality and population decline can be host-specific, it can affect the whole host community or infections can be asymptomatic, co-occurring in areas where lethal infections are common. From analysis of viral isolates we have determined that this variation correlates with viral phylogeney: in Spain, a genetic lineage responsible for amphibian community mortality and decline co-circulates with a genetically distinct asymptomatic lineage; in the UK, a third lineage is associated with death and decline of a single host species (common frogs - infection of other host species is rare and does not lead to significant mortality or decline in spill-over hosts).Here we propose to take advantage of this novel system to ascertain what genetic factors are responsible for these differences in host range and virulence. Our approach is three-pronged: first, we will sequence 130 ranavirus genomes to catalogue genetic variation amongst the European lineages and identify candidate loci. We will also take a more bottom-up phylogenetic approach, identifying any genetic variants that map with differences in host species in a global panel of ranavirus genomes. Second, we carry out controlled infection experiments to verify the different host range and virulence of different viral isolates in three animal models (two anurans and one caudate chosen to encompass the host range we have observed in Spain). Third, we will generate viral knockouts, targeting candidate regions we have identified in the first two objectives, and test hypotheses regarding gene function using recombinants and wild type virus in our animal models.Our results will be a crucial contribution to our understanding of why ranaviruses are such lethal pathogens in some circumstances. Ranavirus emergence is on the increase across Europe, and is emerging as a novel threat to amphibian and reptile biodiversity in Latin America and Madagascar, two amphibian and reptile biodiversity hotspots. Our research will more widely inform the epidemiological community as to what genetic factors may be important for viruses to exploit novel hosts. Given that most emerging infections are viral and emergence arises through host jumps, we expect our findings to be of broad interest to this community.