Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing
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 surveillan...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2020-02-01
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| Series: | mSphere |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mSphere.00807-19 |
| _version_ | 1818856743609827328 |
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| author | Bei Li Hao-Rui Si Yan Zhu Xing-Lou Yang Danielle E. Anderson Zheng-Li Shi Lin-Fa Wang Peng Zhou |
| author_facet | Bei Li Hao-Rui Si Yan Zhu Xing-Lou Yang Danielle E. Anderson Zheng-Li Shi Lin-Fa Wang Peng Zhou |
| author_sort | Bei Li |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-19T08:29:21Z |
| format | Article |
| id | doaj.art-14bff36f21f44e15b7332378423353f4 |
| institution | Directory Open Access Journal |
| issn | 2379-5042 |
| language | English |
| last_indexed | 2024-12-19T08:29:21Z |
| publishDate | 2020-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSphere |
| spelling | doaj.art-14bff36f21f44e15b7332378423353f42022-12-21T20:29:13ZengAmerican Society for MicrobiologymSphere2379-50422020-02-015110.1128/mSphere.00807-19Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation SequencingBei Li0Hao-Rui Si1Yan Zhu2Xing-Lou Yang3Danielle E. Anderson4Zheng-Li Shi5Lin-Fa Wang6Peng Zhou7CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, ChinaCAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, ChinaCAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, ChinaCAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, ChinaProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, SingaporeCAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, ChinaProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, SingaporeCAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, ChinaABSTRACT 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.https://journals.asm.org/doi/10.1128/mSphere.00807-19batcoronavirusgenomeenrichmentnext-generation sequencing |
| spellingShingle | Bei Li Hao-Rui Si Yan Zhu Xing-Lou Yang Danielle E. Anderson Zheng-Li Shi Lin-Fa Wang Peng Zhou Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing mSphere bat coronavirus genome enrichment next-generation sequencing |
| title | Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing |
| title_full | Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing |
| title_fullStr | Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing |
| title_full_unstemmed | Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing |
| title_short | Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing |
| title_sort | discovery of bat coronaviruses through surveillance and probe capture based next generation sequencing |
| topic | bat coronavirus genome enrichment next-generation sequencing |
| url | https://journals.asm.org/doi/10.1128/mSphere.00807-19 |
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