Coronaviruses (CoVs) of bat origin have caused two pandemics in this century. Severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV both originated from bats, and it is highly likely that bat coronaviruses will cause future outbreaks. Active surveillance is both urgent and essential to predict and mitigate the emergence of these viruses in humans. Next-generation sequencing (NGS) is currently the preferred methodology for virus discovery to ensure unbiased sequencing of bat CoVs, considering their high genetic diversity. However, unbiased NGS is an expensive methodology and is prone to missing low-abundance CoV sequences due to the high background level of nonviral sequences present in surveillance field samples. Here, we employ a capture-based NGS approach using baits targeting most of the CoV species. Using this technology, we effectively reduced sequencing costs by increasing the sensitivity of detection. We discovered nine full genomes of bat CoVs in this study and revealed great genetic diversity for eight of them.IMPORTANCE Active surveillance is both urgent and essential to predict and mitigate the emergence of bat-origin CoV in humans and livestock. However, great genetic diversity increases the chance of homologous recombination among CoVs. Performing targeted PCR, a common practice for many surveillance studies, would not reflect this diversity. NGS, on the other hand, is an expensive methodology and is prone to missing low-abundance CoV sequences. Here, we employ a capture-based NGS approach using baits targeting all CoVs. Our work demonstrates that targeted, cost-effective, large-scale, genome-level surveillance of bat CoVs is now highly feasible.

中文翻译：

---

通过监视和基于探针捕获的下一代测序发现蝙蝠冠状病毒。

蝙蝠起源的冠状病毒（CoV）在本世纪引起了两次大流行。严重急性呼吸综合症（SARS）-CoV和中东呼吸综合症（MERS）-CoV均起源于蝙蝠，蝙蝠冠状病毒很可能会导致未来爆发。主动监视对于预测和减轻人类中这些病毒的出现既紧急又必不可少。考虑到蝙蝠冠状病毒的高度遗传多样性，目前，下一代测序（NGS）是病毒发现的首选方法，可确保蝙蝠冠状病毒的无偏测序。但是，无偏倚的NGS是一种昂贵的方法，由于存在于监测现场样品中的非病毒序列的背景水平很高，因此容易丢失低丰度的CoV序列。在这里，我们采用基于捕获的NGS方法，使用针对大多数CoV物种的诱饵。使用这项技术，我们通过提高检测灵敏度有效地降低了测序成本。在这项研究中，我们发现了蝙蝠冠状病毒的9个完整基因组，并揭示了其中8个的巨大遗传多样性。重要信息主动监测对于预测和减轻人类和牲畜中蝙蝠起源的冠状病毒的出现既紧急又必不可少。但是，巨大的遗传多样性增加了冠状​​病毒之间同源重组的机会。进行靶向PCR，这是许多监视研究的普遍做法，不会反映出这种多样性。另一方面，NGS是一种昂贵的方法，容易丢失低丰度的CoV序列。在这里，我们采用针对所有CoV的诱饵，基于捕获的NGS方法。我们的工作表明，针对性强，具有成本效益的大规模，