Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History.
Identifieur interne : 000E20 ( PubMed/Corpus ); précédent : 000E19; suivant : 000E21Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History.
Auteurs : Ying Tao ; Mang Shi ; Christina Chommanard ; Krista Queen ; Jing Zhang ; Wanda Markotter ; Ivan V. Kuzmin ; Edward C. Holmes ; Suxiang TongSource :
- Journal of virology [ 1098-5514 ] ; 2017.
English descriptors
- KwdEn :
- Amino Acid Sequence, Animals, Chiroptera (virology), Conserved Sequence, Coronavirus Infections (epidemiology), Coronavirus Infections (veterinary), Coronavirus NL63, Human, Epidemiological Monitoring, Evolution, Molecular, Genetic Variation, Genome, Viral, Kenya (epidemiology), Phylogeny, Phylogeography, Prevalence, Recombination, Genetic, Respiratory Tract Infections (epidemiology), Respiratory Tract Infections (veterinary), Sequence Analysis, DNA, Viral Proteins (chemistry), Viral Proteins (genetics).
- MESH :
- chemical , chemistry : Viral Proteins.
- epidemiology : Coronavirus Infections, Kenya, Respiratory Tract Infections.
- chemical , genetics : Viral Proteins.
- veterinary : Coronavirus Infections, Respiratory Tract Infections.
- virology : Chiroptera.
- Amino Acid Sequence, Animals, Conserved Sequence, Coronavirus NL63, Human, Epidemiological Monitoring, Evolution, Molecular, Genetic Variation, Genome, Viral, Phylogeny, Phylogeography, Prevalence, Recombination, Genetic, Sequence Analysis, DNA.
Abstract
Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in Triaenops bats and 229E-like viruses circulating in Hipposideros bats, with the breakpoint located near 5' and 3' ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination "hot spot" in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances.IMPORTANCE Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with Triaenops afer and Hipposideros sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.
DOI: 10.1128/JVI.01953-16
PubMed: 28077633
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History.</title><author><name sortKey="Tao, Ying" sort="Tao, Ying" uniqKey="Tao Y" first="Ying" last="Tao">Ying Tao</name><affiliation><nlm:affiliation>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Shi, Mang" sort="Shi, Mang" uniqKey="Shi M" first="Mang" last="Shi">Mang Shi</name><affiliation><nlm:affiliation>Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Chommanard, Christina" sort="Chommanard, Christina" uniqKey="Chommanard C" first="Christina" last="Chommanard">Christina Chommanard</name><affiliation><nlm:affiliation>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Queen, Krista" sort="Queen, Krista" uniqKey="Queen K" first="Krista" last="Queen">Krista Queen</name><affiliation><nlm:affiliation>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Jing" sort="Zhang, Jing" uniqKey="Zhang J" first="Jing" last="Zhang">Jing Zhang</name><affiliation><nlm:affiliation>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Markotter, Wanda" sort="Markotter, Wanda" uniqKey="Markotter W" first="Wanda" last="Markotter">Wanda Markotter</name><affiliation><nlm:affiliation>Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.</nlm:affiliation></affiliation></author><author><name sortKey="Kuzmin, Ivan V" sort="Kuzmin, Ivan V" uniqKey="Kuzmin I" first="Ivan V" last="Kuzmin">Ivan V. Kuzmin</name><affiliation><nlm:affiliation>Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Holmes, Edward C" sort="Holmes, Edward C" uniqKey="Holmes E" first="Edward C" last="Holmes">Edward C. 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Kuzmin</name><affiliation><nlm:affiliation>Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Holmes, Edward C" sort="Holmes, Edward C" uniqKey="Holmes E" first="Edward C" last="Holmes">Edward C. Holmes</name><affiliation><nlm:affiliation>Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Tong, Suxiang" sort="Tong, Suxiang" uniqKey="Tong S" first="Suxiang" last="Tong">Suxiang Tong</name><affiliation><nlm:affiliation>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA sot1@cdc.gov.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Journal of virology</title><idno type="eISSN">1098-5514</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Chiroptera (virology)</term><term>Conserved Sequence</term><term>Coronavirus Infections (epidemiology)</term><term>Coronavirus Infections (veterinary)</term><term>Coronavirus NL63, Human</term><term>Epidemiological Monitoring</term><term>Evolution, Molecular</term><term>Genetic Variation</term><term>Genome, Viral</term><term>Kenya (epidemiology)</term><term>Phylogeny</term><term>Phylogeography</term><term>Prevalence</term><term>Recombination, Genetic</term><term>Respiratory Tract Infections (epidemiology)</term><term>Respiratory Tract Infections (veterinary)</term><term>Sequence Analysis, DNA</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Coronavirus Infections</term><term>Kenya</term><term>Respiratory Tract Infections</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Coronavirus Infections</term><term>Respiratory Tract Infections</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chiroptera</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Conserved Sequence</term><term>Coronavirus NL63, Human</term><term>Epidemiological Monitoring</term><term>Evolution, Molecular</term><term>Genetic Variation</term><term>Genome, Viral</term><term>Phylogeny</term><term>Phylogeography</term><term>Prevalence</term><term>Recombination, Genetic</term><term>Sequence Analysis, DNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in <i>Triaenops</i> bats and 229E-like viruses circulating in <i>Hipposideros</i> bats, with the breakpoint located near 5' and 3' ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination "hot spot" in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances.<b>IMPORTANCE</b> Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with <i>Triaenops afer</i> and <i>Hipposideros</i> sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28077633</PMID><DateCompleted><Year>2017</Year><Month>05</Month><Day>29</Day></DateCompleted><DateRevised><Year>2019</Year><Month>03</Month><Day>29</Day></DateRevised><Article PubModel="Electronic-Print"><Journal><ISSN IssnType="Electronic">1098-5514</ISSN><JournalIssue CitedMedium="Internet"><Volume>91</Volume><Issue>5</Issue><PubDate><Year>2017</Year><Month>03</Month><Day>01</Day></PubDate></JournalIssue><Title>Journal of virology</Title><ISOAbbreviation>J. Virol.</ISOAbbreviation></Journal><ArticleTitle>Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">e01953-16</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1128/JVI.01953-16</ELocationID><Abstract><AbstractText>Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in <i>Triaenops</i> bats and 229E-like viruses circulating in <i>Hipposideros</i> bats, with the breakpoint located near 5' and 3' ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination "hot spot" in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances.<b>IMPORTANCE</b> Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with <i>Triaenops afer</i> and <i>Hipposideros</i> sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.</AbstractText><CopyrightInformation>Copyright © 2017 American Society for Microbiology.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tao</LastName><ForeName>Ying</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Mang</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chommanard</LastName><ForeName>Christina</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Queen</LastName><ForeName>Krista</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Jing</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Markotter</LastName><ForeName>Wanda</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kuzmin</LastName><ForeName>Ivan V</ForeName><Initials>IV</Initials><AffiliationInfo><Affiliation>Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Holmes</LastName><ForeName>Edward C</ForeName><Initials>EC</Initials><AffiliationInfo><Affiliation>Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tong</LastName><ForeName>Suxiang</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA sot1@cdc.gov.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>02</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Virol</MedlineTA><NlmUniqueID>0113724</NlmUniqueID><ISSNLinking>0022-538X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014764">Viral Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><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="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000662" MajorTopicYN="Y">veterinary</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058957" MajorTopicYN="N">Coronavirus NL63, Human</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D062665" MajorTopicYN="N">Epidemiological Monitoring</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007630" MajorTopicYN="N">Kenya</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058974" MajorTopicYN="N">Phylogeography</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015995" MajorTopicYN="N">Prevalence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="N">Recombination, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012141" MajorTopicYN="N">Respiratory Tract Infections</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000662" MajorTopicYN="Y">veterinary</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014764" MajorTopicYN="N">Viral 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