Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing
Identifieur interne : 002500 ( Ncbi/Merge ); précédent : 002499; suivant : 002501Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing
Auteurs : Bei Li [République populaire de Chine] ; Hao-Rui Si [République populaire de Chine] ; Yan Zhu [République populaire de Chine] ; Xing-Lou Yang [République populaire de Chine] ; Danielle E. Anderson [Singapour] ; Zheng-Li Shi [République populaire de Chine] ; Lin-Fa Wang [Singapour] ; Peng Zhou [République populaire de Chine]Source :
- mSphere [ 2379-5042 ] ; 2020.
Descripteurs français
- KwdFr :
- MESH :
- isolement et purification : Coronavirus.
- virologie : Chiroptera.
- Animaux, Coronavirus, Génome viral, Séquençage nucléotidique à haut débit, Variation génétique.
English descriptors
- KwdEn :
- MESH :
- classification : Coronavirus.
- isolation & purification : Coronavirus.
- methods : High-Throughput Nucleotide Sequencing.
- virology : Chiroptera.
- Animals, Genetic Variation, Genome, Viral.
Abstract
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.
Url:
DOI: 10.1128/mSphere.00807-19
PubMed: 31996413
PubMed Central: 6992374
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PMC:6992374Le document en format XML
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<front><div type="abstract" xml:lang="en"><p>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.</p>
</div>
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</listBibl>
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</nlm:aff>
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</placeName>
</affiliation>
</author>
<author><name sortKey="Si, Hao Rui" sort="Si, Hao Rui" uniqKey="Si H" first="Hao-Rui" last="Si">Hao-Rui Si</name>
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</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
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<placeName><settlement type="city">Wuhan</settlement>
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</placeName>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>University of Chinese Academy of Sciences, Beijing, China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>University of Chinese Academy of Sciences, Beijing</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name>
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</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
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<placeName><settlement type="city">Wuhan</settlement>
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</placeName>
</affiliation>
</author>
<author><name sortKey="Yang, Xing Lou" sort="Yang, Xing Lou" uniqKey="Yang X" first="Xing-Lou" last="Yang">Xing-Lou Yang</name>
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</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Anderson, Danielle E" sort="Anderson, Danielle E" uniqKey="Anderson D" first="Danielle E." last="Anderson">Danielle E. Anderson</name>
<affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore</addr-line>
</nlm:aff>
<country xml:lang="fr">Singapour</country>
<wicri:regionArea>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore</wicri:regionArea>
<wicri:noRegion>Singapore</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Shi, Zheng Li" sort="Shi, Zheng Li" uniqKey="Shi Z" first="Zheng-Li" last="Shi">Zheng-Li Shi</name>
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</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
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<placeName><settlement type="city">Wuhan</settlement>
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</placeName>
</affiliation>
</author>
<author><name sortKey="Wang, Lin Fa" sort="Wang, Lin Fa" uniqKey="Wang L" first="Lin-Fa" last="Wang">Lin-Fa Wang</name>
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</nlm:aff>
<country xml:lang="fr">Singapour</country>
<wicri:regionArea>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore</wicri:regionArea>
<wicri:noRegion>Singapore</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Zhou, Peng" sort="Zhou, Peng" uniqKey="Zhou P" first="Peng" last="Zhou">Peng Zhou</name>
<affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing</title>
<author><name sortKey="Li, Bei" sort="Li, Bei" uniqKey="Li B" first="Bei" last="Li">Bei Li</name>
<affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Si, Hao Rui" sort="Si, Hao Rui" uniqKey="Si H" first="Hao-Rui" last="Si">Hao-Rui Si</name>
<affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>University of Chinese Academy of Sciences, Beijing, China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>University of Chinese Academy of Sciences, Beijing</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name>
<affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Yang, Xing Lou" sort="Yang, Xing Lou" uniqKey="Yang X" first="Xing-Lou" last="Yang">Xing-Lou Yang</name>
<affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Anderson, Danielle E" sort="Anderson, Danielle E" uniqKey="Anderson D" first="Danielle E." last="Anderson">Danielle E. Anderson</name>
<affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore</addr-line>
</nlm:aff>
<country xml:lang="fr">Singapour</country>
<wicri:regionArea>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore</wicri:regionArea>
<wicri:noRegion>Singapore</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Shi, Zheng Li" sort="Shi, Zheng Li" uniqKey="Shi Z" first="Zheng-Li" last="Shi">Zheng-Li Shi</name>
<affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wang, Lin Fa" sort="Wang, Lin Fa" uniqKey="Wang L" first="Lin-Fa" last="Wang">Lin-Fa Wang</name>
<affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore</addr-line>
</nlm:aff>
<country xml:lang="fr">Singapour</country>
<wicri:regionArea>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore</wicri:regionArea>
<wicri:noRegion>Singapore</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Zhou, Peng" sort="Zhou, Peng" uniqKey="Zhou P" first="Peng" last="Zhou">Peng Zhou</name>
<affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">mSphere</title>
<idno type="eISSN">2379-5042</idno>
<imprint><date when="2020">2020</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>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.</p>
</div>
</front>
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<pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing.</title>
<author><name sortKey="Li, Bei" sort="Li, Bei" uniqKey="Li B" first="Bei" last="Li">Bei Li</name>
<affiliation wicri:level="3"><nlm:affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
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<region type="région">Hubei</region>
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<author><name sortKey="Si, Hao Rui" sort="Si, Hao Rui" uniqKey="Si H" first="Hao-Rui" last="Si">Hao-Rui Si</name>
<affiliation wicri:level="3"><nlm:affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
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<author><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name>
<affiliation wicri:level="3"><nlm:affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
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<region type="région">Hubei</region>
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<author><name sortKey="Yang, Xing Lou" sort="Yang, Xing Lou" uniqKey="Yang X" first="Xing-Lou" last="Yang">Xing-Lou Yang</name>
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<author><name sortKey="Zhou, Peng" sort="Zhou, Peng" uniqKey="Zhou P" first="Peng" last="Zhou">Peng Zhou</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing.</title>
<author><name sortKey="Li, Bei" sort="Li, Bei" uniqKey="Li B" first="Bei" last="Li">Bei Li</name>
<affiliation wicri:level="3"><nlm:affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
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</placeName>
</affiliation>
</author>
<author><name sortKey="Si, Hao Rui" sort="Si, Hao Rui" uniqKey="Si H" first="Hao-Rui" last="Si">Hao-Rui Si</name>
<affiliation wicri:level="3"><nlm:affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
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</placeName>
</affiliation>
</author>
<author><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name>
<affiliation wicri:level="3"><nlm:affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
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</placeName>
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</author>
<author><name sortKey="Yang, Xing Lou" sort="Yang, Xing Lou" uniqKey="Yang X" first="Xing-Lou" last="Yang">Xing-Lou Yang</name>
<affiliation wicri:level="3"><nlm:affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan</wicri:regionArea>
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</placeName>
</affiliation>
</author>
<author><name sortKey="Anderson, Danielle E" sort="Anderson, Danielle E" uniqKey="Anderson D" first="Danielle E" last="Anderson">Danielle E. Anderson</name>
<affiliation wicri:level="1"><nlm:affiliation>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.</nlm:affiliation>
<country xml:lang="fr">Singapour</country>
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</affiliation>
</author>
<author><name sortKey="Shi, Zheng Li" sort="Shi, Zheng Li" uniqKey="Shi Z" first="Zheng-Li" last="Shi">Zheng-Li Shi</name>
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<author><name sortKey="Wang, Lin Fa" sort="Wang, Lin Fa" uniqKey="Wang L" first="Lin-Fa" last="Wang">Lin-Fa Wang</name>
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<author><name sortKey="Zhou, Peng" sort="Zhou, Peng" uniqKey="Zhou P" first="Peng" last="Zhou">Peng Zhou</name>
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<idno type="eISSN">2379-5042</idno>
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<term>Chiroptera (virology)</term>
<term>Coronavirus (classification)</term>
<term>Coronavirus (isolation & purification)</term>
<term>Genetic Variation</term>
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<term>Variation génétique</term>
</keywords>
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</keywords>
<keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Coronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term>
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</keywords>
<keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chiroptera</term>
</keywords>
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<term>Genetic Variation</term>
<term>Genome, Viral</term>
</keywords>
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<term>Coronavirus</term>
<term>Génome viral</term>
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<front><div type="abstract" xml:lang="en">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.<b>IMPORTANCE</b>
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.</div>
</front>
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