The virosphere is largely unexplored and the majority of viruses are yet to be represented in public sequence databases. Bats are rich reservoirs of viruses, including several zoonoses. In this study, high throughput sequencing (HTS) of viral RNA extracted from swabs of four body sites per bat per timepoint is used to characterize the virome through a longitudinal study of a captive colony of fruit nectar bats, species Eonycteris spelaea in Singapore. Through unbiased shotgun and target enrichment sequencing, we identify both known and previously unknown viruses of zoonotic relevance and define the population persistence and temporal patterns of viruses from families that have the capacity to jump the species barrier. To our knowledge, this is the first study that combines probe-based viral enrichment with HTS to create a viral profile from multiple swab sites on individual bats and their cohort. This work demonstrates temporal patterns of the lesser dawn bat virome, including several novel viruses. Given the known risk for bat–human zoonoses, a more complete understanding of the viral dynamics in South-eastern Asian bats has significant implications for disease prevention and control. The findings of this study will be of interest to U.S. Department of Defense personnel stationed in the Asia-Pacific region and regional public health laboratories engaged in emerging infectious disease surveillance efforts.

中文翻译：

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深度测序揭示小黎明蝙蝠 (Eonycteris spelaea) 群体的颞叶 RNA 病毒组模式

病毒圈很大程度上尚未被探索，大多数病毒尚未在公共序列数据库中得到体现。蝙蝠是病毒的丰富库，其中包括几种人畜共患疾病。在这项研究中，通过对新加坡的果蜜蝙蝠（Eonycteris spelaea）的圈养群体进行纵向研究，对每个时间点从每只蝙蝠的四个身体部位的拭子中提取的病毒RNA进行高通量测序（HTS），以表征病毒组。通过无偏见的鸟枪法和目标富集测序，我们识别了已知和以前未知的人畜共患病相关病毒，并定义了具有跨越物种障碍能力的科病毒的群体持久性和时间模式。据我们所知，这是第一项将基于探针的病毒富集与 HTS 相结合的研究，从单个蝙蝠及其群体的多个拭子位点创建病毒谱。这项工作展示了小黎明蝙蝠病毒组的时间模式，包括几种新型病毒。鉴于已知的蝙蝠与人类人畜共患病的风险，更全面地了解东南亚蝙蝠的病毒动态对于疾病预防和控制具有重要意义。这项研究的结果将引起驻亚太地区的美国国防部人员和从事新发传染病监测工作的区域公共卫生实验室的兴趣。