Stenglein Mark D, Jacobson Elliott R, Chang Li-Wen, Sanders Chris, Hawkins Michelle G, Guzman David S-M, Drazenovich Tracy, Dunker Freeland, Kamaka Elizabeth K, Fisher Debbie, Reavill Drury R, Meola Linda F, Levens Gregory, DeRisi Joseph L
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America.
Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America.
PLoS Pathog. 2015 May 20;11(5):e1004900. doi: 10.1371/journal.ppat.1004900. eCollection 2015 May.
Arenaviruses are one of the largest families 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.
沙粒病毒是人类出血热病毒中最大的家族之一，已知可感染哺乳动物和蛇类。沙粒病毒在其病毒粒子中包裹着一个大（L）基因组片段和一个小（S）基因组片段。对于像这样的分段RNA病毒，新的基因型可通过突变、重组和重配产生。尽管人们认为一次古老的重组事件导致了哺乳动物沙粒病毒新谱系的出现，但在自然沙粒病毒感染中，重组和重配都尚未得到确切记录。在此，我们使用宏基因组测序来调查圈养的感染沙粒病毒的蛇体内存在的病毒多样性。从48只受感染的动物中，我们确定了210个基因组片段的完整或近乎完整序列，这些序列分为23种L基因型和11种S基因型。大多数蛇都受到多重感染，个别动物体内有多达4种不同的S片段基因型和11种不同的L片段基因型。这种S/L不平衡是典型的：在所有情况下，宿主体内的L片段基因型数量都超过S基因型，并且一种特定的S片段基因型在个体动物和群体水平上占主导地位。我们通过qRT-PCR和病毒分离证实了测序结果，并且分离株在培养物中以群体形式进行复制。检测到了许多重组和重配事件，包括具有不寻常结构的重组片段，这些片段具有2个基因间区域和多余的内容，尽管其结构不典型，但仍能够稳定复制和传播。总体而言，这代表了宿主体内病毒多样性的程度和形式远远超出了沙粒病毒或一般病毒所观察到的范围。这种多样性可能合理地归因于亚临床感染的野生捕获蛇在圈养中的混合。因此，这些发现不仅为研究沙粒病毒的进化和适应性提供了独特机会，还使得我们能够调查人为因素对病毒生态学、多样性和疾病潜力的意外影响。
