Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing.
Identifieur interne : 000833 ( PubMed/Corpus ); précédent : 000832; suivant : 000834Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing.
Auteurs : Bei Li ; Hao-Rui Si ; Yan Zhu ; Xing-Lou Yang ; Danielle E. Anderson ; Zheng-Li Shi ; Lin-Fa Wang ; Peng ZhouSource :
- mSphere [ 2379-5042 ] ; 2020.
English descriptors
- KwdEn :
- MESH :
- classification : Coronavirus.
- isolation & purification : Coronavirus.
- methods : High-Throughput Nucleotide Sequencing.
- virology : Chiroptera.
- Animals, Genetic Variation, Genome, Viral.
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.
DOI: 10.1128/mSphere.00807-19
PubMed: 31996413
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Anderson</name><affiliation><nlm:affiliation>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.</nlm:affiliation></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><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></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><nlm:affiliation>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore linfa.wang@duke-nus.edu.sg peng.zhou@wh.iov.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Zhou, Peng" sort="Zhou, Peng" uniqKey="Zhou P" first="Peng" last="Zhou">Peng Zhou</name><affiliation><nlm:affiliation>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.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:31996413</idno><idno type="pmid">31996413</idno><idno type="doi">10.1128/mSphere.00807-19</idno><idno type="wicri:Area/PubMed/Corpus">000833</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000833</idno></publicationStmt><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><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></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><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></affiliation></author><author><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name><affiliation><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></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><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></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><nlm:affiliation>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.</nlm:affiliation></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><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></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><nlm:affiliation>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore linfa.wang@duke-nus.edu.sg peng.zhou@wh.iov.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Zhou, Peng" sort="Zhou, Peng" uniqKey="Zhou P" first="Peng" last="Zhou">Peng Zhou</name><affiliation><nlm:affiliation>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.</nlm:affiliation></affiliation></author></analytic><series><title level="j">mSphere</title><idno type="eISSN">2379-5042</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Chiroptera (virology)</term><term>Coronavirus (classification)</term><term>Coronavirus (isolation & purification)</term><term>Genetic Variation</term><term>Genome, Viral</term><term>High-Throughput Nucleotide Sequencing (methods)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chiroptera</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Genetic Variation</term><term>Genome, Viral</term></keywords></textClass></profileDesc></teiHeader><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></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31996413</PMID><DateCompleted><Year>2020</Year><Month>03</Month><Day>18</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>18</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2379-5042</ISSN><JournalIssue CitedMedium="Internet"><Volume>5</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>01</Month><Day>29</Day></PubDate></JournalIssue><Title>mSphere</Title><ISOAbbreviation>mSphere</ISOAbbreviation></Journal><ArticleTitle>Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">e00807-19</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1128/mSphere.00807-19</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>Copyright © 2020 Li et al.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y" EqualContrib="Y"><LastName>Li</LastName><ForeName>Bei</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y" EqualContrib="Y"><LastName>Si</LastName><ForeName>Hao-Rui</ForeName><Initials>HR</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>University of Chinese Academy of Sciences, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Yan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xing-Lou</ForeName><Initials>XL</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Anderson</LastName><ForeName>Danielle E</ForeName><Initials>DE</Initials><AffiliationInfo><Affiliation>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Zheng-Li</ForeName><Initials>ZL</Initials><Identifier Source="ORCID">0000-0001-8089-163X</Identifier><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Lin-Fa</ForeName><Initials>LF</Initials><Identifier Source="ORCID">0000-0003-2752-0535</Identifier><AffiliationInfo><Affiliation>Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore linfa.wang@duke-nus.edu.sg peng.zhou@wh.iov.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Peng</ForeName><Initials>P</Initials><Identifier Source="ORCID">0000-0001-9863-4201</Identifier><AffiliationInfo><Affiliation>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.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>01</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>mSphere</MedlineTA><NlmUniqueID>101674533</NlmUniqueID><ISSNLinking>2379-5042</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>mSphere. 2020 Mar 18;5(2):</RefSource><PMID Version="1">32188751</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002685" MajorTopicYN="N">Chiroptera</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017934" MajorTopicYN="N">Coronavirus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">bat</Keyword><Keyword MajorTopicYN="Y">coronavirus</Keyword><Keyword MajorTopicYN="Y">enrichment</Keyword><Keyword 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