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mSphere. 2020 Jan 29;5(1). pii: e00807-19. doi: 10.1128/mSphere.00807-19.

Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing.

Author information

1
CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
2
University of Chinese Academy of Sciences, Beijing, China.
3
Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
4
Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore linfa.wang@duke-nus.edu.sg peng.zhou@wh.iov.cn.
5
CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China linfa.wang@duke-nus.edu.sg peng.zhou@wh.iov.cn.
#
Contributed equally

Abstract

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.

KEYWORDS:

bat; coronavirus; enrichment; genome; next-generation sequencing

PMID:
31996413
PMCID:
PMC6992374
DOI:
10.1128/mSphere.00807-19
[Indexed for MEDLINE]
Free PMC Article

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