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...

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Autores principales:	Bei Li, Hao-Rui Si, Yan Zhu, Xing-Lou Yang, Danielle E. Anderson, Zheng-Li Shi, Lin-Fa Wang, Peng Zhou
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	bat coronavirus genome enrichment next-generation sequencing Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/14bff36f21f44e15b7332378423353f4
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spelling	oai:doaj.org-article:14bff36f21f44e15b7332378423353f42021-11-15T15:27:52ZDiscovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing10.1128/mSphere.00807-192379-5042https://doaj.org/article/14bff36f21f44e15b7332378423353f42020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00807-19https://doaj.org/toc/2379-5042ABSTRACT 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.Bei LiHao-Rui SiYan ZhuXing-Lou YangDanielle E. AndersonZheng-Li ShiLin-Fa WangPeng ZhouAmerican Society for Microbiologyarticlebatcoronavirusgenomeenrichmentnext-generation sequencingMicrobiologyQR1-502ENmSphere, Vol 5, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	bat coronavirus genome enrichment next-generation sequencing Microbiology QR1-502
spellingShingle	bat coronavirus genome enrichment next-generation sequencing Microbiology QR1-502 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
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.
format	article
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
title	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_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_sort	discovery of bat coronaviruses through surveillance and probe capture-based next-generation sequencing
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/14bff36f21f44e15b7332378423353f4
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Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing

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