Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats.
Identifieur interne : 000909 ( PubMed/Corpus ); précédent : 000908; suivant : 000910Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats.
Auteurs : Ning Wang ; Chuming Luo ; Haizhou Liu ; Xinglou Yang ; Ben Hu ; Wei Zhang ; Bei Li ; Yan Zhu ; Guangjian Zhu ; Xurui Shen ; Cheng Peng ; Zhengli ShiSource :
- Viruses [ 1999-4915 ] ; 2019.
English descriptors
- KwdEn :
- Alphacoronavirus (classification), Alphacoronavirus (isolation & purification), Animals, China, Chiroptera (virology), Coronavirus Infections (veterinary), Coronavirus Infections (virology), Evolution, Molecular, Genetic Variation, Genome, Viral, High-Throughput Nucleotide Sequencing, Open Reading Frames (genetics), Phylogeny, Sequence Analysis, DNA, Viral Proteins (genetics).
- MESH :
- chemical , genetics : Viral Proteins.
- geographic : China.
- classification : Alphacoronavirus.
- genetics : Open Reading Frames.
- isolation & purification : Alphacoronavirus.
- veterinary : Coronavirus Infections.
- virology : Chiroptera, Coronavirus Infections.
- Animals, Evolution, Molecular, Genetic Variation, Genome, Viral, High-Throughput Nucleotide Sequencing, Phylogeny, Sequence Analysis, DNA.
Abstract
Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes, ORF4a and ORF4b were found between the spike gene and the envelope gene, while ORF8 gene was found downstream of the nucleocapsid gene. All the putative genes were further confirmed by reverse-transcription analyses. One unique gene at the 3' end of the BtCoV/Rh/YN2012 genome, ORF9, exhibits ~30% amino acid identity to ORF7a of the SARS-related coronavirus. Functional analysis showed ORF4a protein can activate IFN-β production, whereas ORF3a can regulate NF-κB production. We also screened the spike-mediated virus entry using the spike-pseudotyped retroviruses system, although failed to find any fully permissive cells. Our results expand the knowledge on the genetic diversity of bat coronaviruses. Continuous screening of bat viruses will help us further understand the important role played by bats in coronavirus evolution and transmission.
DOI: 10.3390/v11040379
PubMed: 31022925
Links to Exploration step
pubmed:31022925Le document en format XML
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last="Zhu">Guangjian Zhu</name><affiliation><nlm:affiliation>EcoHealth Alliance, New York, NY 10001, USA. zhugj609@126.com.</nlm:affiliation></affiliation></author><author><name sortKey="Shen, Xurui" sort="Shen, Xurui" uniqKey="Shen X" first="Xurui" last="Shen">Xurui Shen</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. pukulovesu@163.com.</nlm:affiliation></affiliation></author><author><name sortKey="Peng, Cheng" sort="Peng, Cheng" uniqKey="Peng C" first="Cheng" last="Peng">Cheng Peng</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. pengcheng@wh.iov.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Shi, Zhengli" sort="Shi, Zhengli" uniqKey="Shi Z" first="Zhengli" last="Shi">Zhengli Shi</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. zlshi@wh.iov.cn.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:31022925</idno><idno type="pmid">31022925</idno><idno type="doi">10.3390/v11040379</idno><idno type="wicri:Area/PubMed/Corpus">000909</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000909</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats.</title><author><name sortKey="Wang, Ning" sort="Wang, Ning" uniqKey="Wang N" first="Ning" last="Wang">Ning Wang</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. wuzhongxiaoliu@163.com.</nlm:affiliation></affiliation></author><author><name sortKey="Luo, Chuming" sort="Luo, Chuming" uniqKey="Luo C" first="Chuming" last="Luo">Chuming Luo</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. chine.lcm@163.com.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Haizhou" sort="Liu, Haizhou" uniqKey="Liu H" first="Haizhou" last="Liu">Haizhou Liu</name><affiliation><nlm:affiliation>Center for Emerging Infectious Disease, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. liuhz@wh.iov.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Yang, Xinglou" sort="Yang, Xinglou" uniqKey="Yang X" first="Xinglou" last="Yang">Xinglou Yang</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. yangxl@wh.iov.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Hu, Ben" sort="Hu, Ben" uniqKey="Hu B" first="Ben" last="Hu">Ben Hu</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. ouihaagendazs@hotmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Wei" sort="Zhang, Wei" uniqKey="Zhang W" first="Wei" last="Zhang">Wei Zhang</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. happyzhang_2007@163.com.</nlm:affiliation></affiliation></author><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 and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. shenqi0622@126.com.</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 and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. zhuyan@wh.iov.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Zhu, Guangjian" sort="Zhu, Guangjian" uniqKey="Zhu G" first="Guangjian" last="Zhu">Guangjian Zhu</name><affiliation><nlm:affiliation>EcoHealth Alliance, New York, NY 10001, USA. zhugj609@126.com.</nlm:affiliation></affiliation></author><author><name sortKey="Shen, Xurui" sort="Shen, Xurui" uniqKey="Shen X" first="Xurui" last="Shen">Xurui Shen</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. pukulovesu@163.com.</nlm:affiliation></affiliation></author><author><name sortKey="Peng, Cheng" sort="Peng, Cheng" uniqKey="Peng C" first="Cheng" last="Peng">Cheng Peng</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. pengcheng@wh.iov.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Shi, Zhengli" sort="Shi, Zhengli" uniqKey="Shi Z" first="Zhengli" last="Shi">Zhengli Shi</name><affiliation><nlm:affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. zlshi@wh.iov.cn.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Viruses</title><idno type="eISSN">1999-4915</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alphacoronavirus (classification)</term><term>Alphacoronavirus (isolation & purification)</term><term>Animals</term><term>China</term><term>Chiroptera (virology)</term><term>Coronavirus Infections (veterinary)</term><term>Coronavirus Infections (virology)</term><term>Evolution, Molecular</term><term>Genetic Variation</term><term>Genome, Viral</term><term>High-Throughput Nucleotide Sequencing</term><term>Open Reading Frames (genetics)</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Viral Proteins (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Alphacoronavirus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Open Reading Frames</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Alphacoronavirus</term></keywords><keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chiroptera</term><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Evolution, Molecular</term><term>Genetic Variation</term><term>Genome, Viral</term><term>High-Throughput Nucleotide Sequencing</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes, <i>ORF4a</i> and <i>ORF4b</i> were found between the spike gene and the envelope gene, while <i>ORF8</i> gene was found downstream of the nucleocapsid gene. All the putative genes were further confirmed by reverse-transcription analyses. One unique gene at the 3' end of the BtCoV/Rh/YN2012 genome, <i>ORF9</i>, exhibits ~30% amino acid identity to <i>ORF7a</i> of the SARS-related coronavirus. Functional analysis showed ORF4a protein can activate IFN-β production, whereas ORF3a can regulate NF-κB production. We also screened the spike-mediated virus entry using the spike-pseudotyped retroviruses system, although failed to find any fully permissive cells. Our results expand the knowledge on the genetic diversity of bat coronaviruses. Continuous screening of bat viruses will help us further understand the important role played by bats in coronavirus evolution and transmission.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31022925</PMID><DateCompleted><Year>2020</Year><Month>02</Month><Day>19</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>09</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1999-4915</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><Issue>4</Issue><PubDate><Year>2019</Year><Month>04</Month><Day>24</Day></PubDate></JournalIssue><Title>Viruses</Title><ISOAbbreviation>Viruses</ISOAbbreviation></Journal><ArticleTitle>Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E379</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/v11040379</ELocationID><Abstract><AbstractText>Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes, <i>ORF4a</i> and <i>ORF4b</i> were found between the spike gene and the envelope gene, while <i>ORF8</i> gene was found downstream of the nucleocapsid gene. All the putative genes were further confirmed by reverse-transcription analyses. One unique gene at the 3' end of the BtCoV/Rh/YN2012 genome, <i>ORF9</i>, exhibits ~30% amino acid identity to <i>ORF7a</i> of the SARS-related coronavirus. Functional analysis showed ORF4a protein can activate IFN-β production, whereas ORF3a can regulate NF-κB production. We also screened the spike-mediated virus entry using the spike-pseudotyped retroviruses system, although failed to find any fully permissive cells. Our results expand the knowledge on the genetic diversity of bat coronaviruses. Continuous screening of bat viruses will help us further understand the important role played by bats in coronavirus evolution and transmission.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Ning</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. wuzhongxiaoliu@163.com.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>College of Life Science, University of Chinese Academy of Sciences, Beijing 100864, China. wuzhongxiaoliu@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Chuming</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. chine.lcm@163.com.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>College of Life Science, University of Chinese Academy of Sciences, Beijing 100864, China. chine.lcm@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Haizhou</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Center for Emerging Infectious Disease, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. liuhz@wh.iov.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xinglou</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. yangxl@wh.iov.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Ben</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. ouihaagendazs@hotmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Wei</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. happyzhang_2007@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Bei</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. shenqi0622@126.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Yan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. zhuyan@wh.iov.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Guangjian</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>EcoHealth Alliance, New York, NY 10001, USA. zhugj609@126.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shen</LastName><ForeName>Xurui</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. pukulovesu@163.com.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>College of Life Science, University of Chinese Academy of Sciences, Beijing 100864, China. pukulovesu@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peng</LastName><ForeName>Cheng</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. pengcheng@wh.iov.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Zhengli</ForeName><Initials>Z</Initials><Identifier Source="ORCID">0000-0001-8089-163X</Identifier><AffiliationInfo><Affiliation>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. zlshi@wh.iov.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>04</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Viruses</MedlineTA><NlmUniqueID>101509722</NlmUniqueID><ISSNLinking>1999-4915</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014764">Viral Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000073638" MajorTopicYN="N">Alphacoronavirus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002681" MajorTopicYN="N" Type="Geographic">China</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002685" MajorTopicYN="N">Chiroptera</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName><QualifierName UI="Q000662" MajorTopicYN="Y">veterinary</QualifierName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="Y">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016366" MajorTopicYN="N">Open Reading Frames</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014764" MajorTopicYN="N">Viral Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Rhinolophus bat</Keyword><Keyword MajorTopicYN="Y">alphacoronavirus</Keyword><Keyword MajorTopicYN="Y">coronavirus</Keyword><Keyword MajorTopicYN="Y">unique genes</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>03</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>04</Month><Day>14</Day></PubMedPubDate><PubMedPubDate 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