Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing
Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing
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DOI：
10.1128/msphere.00807-19
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发表时间：
2020-01-01
期刊：
影响因子：
4.8
通讯作者：
Zhou, Peng
中科院分区：
文献类型：
--
作者：
Li, Bei;Si, Hao-Rui;Zhou, Peng
来自蝙蝠的冠状病毒（cov）在本世纪引发了两次大流行。严重急性呼吸综合征(SARS)-冠状病毒和中东呼吸综合征(MERS)-冠状病毒均起源于蝙蝠，蝙蝠冠状病毒极有可能在未来引发疫情。积极监测对于预测和减轻这些病毒在人类中的出现既紧迫又至关重要。考虑到蝙蝠冠状病毒的高遗传多样性，下一代测序（NGS）是目前用于病毒发现的首选方法，以确保对其进行公正的测序。然而，无偏NGS是一种昂贵的方法，并且由于监测现场样本中存在高背景水平的非病毒序列，容易丢失低丰度的冠状病毒序列。在这里，我们采用了一种基于捕获的NGS方法，使用针对大多数冠状病毒物种的诱饵。利用该技术，我们通过提高检测灵敏度，有效地降低了测序成本。在本研究中，我们发现了9个蝙蝠冠状病毒的全基因组，并揭示了其中8个冠状病毒的遗传多样性。积极监测对于预测和减轻人类和牲畜中蝙蝠源性冠状病毒的出现既紧迫又至关重要。然而，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是许多监测研究的常见做法，不能反映这种多样性。另一方面，NGS是一种昂贵的方法，容易丢失低丰度的冠状病毒序列。在这里，我们采用基于捕获的NGS方法，使用针对所有cov的诱饵。我们的工作表明，对蝙蝠冠状病毒进行有针对性的、具有成本效益的大规模基因组水平监测现在是高度可行的。
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.