Snake arenavirus genetic diversity

Arenaviruses represent the largest family of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential.

沙粒病毒（Arenaviruses）是人类出血热病毒的最大一科，已知可侵染哺乳动物与蛇类。沙粒病毒的病毒粒子中包装有大片段（L）与小片段（S）基因组节段。对于这类分节段RNA病毒，新基因型可通过突变、重组与重配产生。尽管学界认为，一次远古重组事件推动了哺乳动物沙粒病毒新谱系的出现，但目前尚无确凿证据表明自然状态下的沙粒病毒感染中存在重组或重配事件。本研究通过宏基因组测序（metagenomic sequencing）对圈养沙粒病毒感染蛇类的病毒多样性进行了调查。从48只感染蛇类中，我们获得了210个完整或近完整的基因组节段序列，这些节段可归类为23种L型与11种S型基因型。多数受试蛇类存在多重感染，单只个体可携带多达4种不同的S型节段基因型与11种不同的L型节段基因型。这种S/L型节段的失衡现象具有普遍性：所有宿主个体的L型节段基因型数量均多于S型，且某一特定S型节段基因型在单只宿主与种群水平上均占据主导地位。我们通过实时荧光定量逆转录聚合酶链反应（qRT-PCR）与病毒分离实验验证了测序结果，且分离得到的病毒毒株在培养体系中以群落形式增殖。本研究检测到大量重组与重配事件，包括结构异常的重组节段——这类节段拥有2个基因间区与冗余序列，尽管结构非典型，但仍可稳定复制与传播。总体而言，本研究揭示的宿主内病毒多样性在范围与形式上均远超此前对沙粒病毒乃至所有病毒的观测结果。这种多样性可合理归因于亚临床感染的野生捕获蛇类在圈养环境中的混养。因此，这些发现不仅为研究沙粒病毒的进化与适应提供了独特契机，还为探究人类活动对病毒生态学、多样性与致病潜力的意外影响开辟了研究路径。