Genetic Characteristics of Coronaviruses from Korean Bats in 2016.
Identifieur interne : 000A96 ( PubMed/Corpus ); précédent : 000A95; suivant : 000A97Genetic Characteristics of Coronaviruses from Korean Bats in 2016.
Auteurs : Saemi Lee ; Seong-Deok Jo ; Kidong Son ; Injung An ; Jipseol Jeong ; Seung-Jun Wang ; Yongkwan Kim ; Weonhwa Jheong ; Jae-Ku OemSource :
- Microbial ecology [ 1432-184X ] ; 2018.
English descriptors
- KwdEn :
- MESH :
- geographic : China, Hong Kong, Republic of Korea.
- classification : Coronavirus.
- genetics : Coronavirus.
- isolation & purification : Coronavirus.
- veterinary : Coronavirus Infections.
- virology : Chiroptera, Coronavirus Infections.
- Animals, Genetic Variation, Genome, Viral, Humans, Phylogeny.
Abstract
Bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (SARS), coronavirus, and other coronaviruses found in mammals. However, little research has been conducted on bat coronaviruses in South Korea. In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. RT-PCR and sequencing were performed for specific coronavirus genes to identify the bat coronaviruses in different bat samples. Coronaviruses were detected in 2.7% (18/672) of the samples: 13 oral swabs from one species of the family Rhinolophidae, and four fecal samples and one carcass (intestine) from three species of the family Vespertiliodae. To determine the genetic relationships of the 18 sequences obtained in this study and previously known coronaviruses, the nucleotide sequences of a 392-nt region of the RNA-dependent RNA polymerase (RdRp) gene were analyzed phylogenetically. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1-99.7%) with Bat-CoV-JTMC15 reported in China. The other five sequences were most similar to MERS-like betacoronaviruses. Four nucleotide sequences displayed the highest identity (94.1-95.1%) with Bat-CoV-HKU5 from Hong Kong. The one sequence from a carcass showed the highest nucleotide identity (99%) with Bat-CoV-SC2013 from China. These results suggest that careful surveillance of coronaviruses from bats should be continued, because animal and human infections may result from the genetic variants present in bat coronavirus reservoirs.
DOI: 10.1007/s00248-017-1033-8
PubMed: 28725945
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Oem</name><affiliation><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea. jku0623@korea.kr.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:28725945</idno><idno type="pmid">28725945</idno><idno type="doi">10.1007/s00248-017-1033-8</idno><idno type="wicri:Area/PubMed/Corpus">000A96</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000A96</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genetic Characteristics of Coronaviruses from Korean Bats in 2016.</title><author><name sortKey="Lee, Saemi" sort="Lee, Saemi" uniqKey="Lee S" first="Saemi" last="Lee">Saemi Lee</name><affiliation><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Jo, Seong Deok" sort="Jo, Seong Deok" uniqKey="Jo S" first="Seong-Deok" last="Jo">Seong-Deok Jo</name><affiliation><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Son, Kidong" sort="Son, Kidong" uniqKey="Son K" first="Kidong" last="Son">Kidong Son</name><affiliation><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="An, Injung" sort="An, Injung" uniqKey="An I" first="Injung" last="An">Injung An</name><affiliation><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Jeong, Jipseol" sort="Jeong, Jipseol" uniqKey="Jeong J" first="Jipseol" last="Jeong">Jipseol Jeong</name><affiliation><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Seung Jun" sort="Wang, Seung Jun" uniqKey="Wang S" first="Seung-Jun" last="Wang">Seung-Jun Wang</name><affiliation><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Yongkwan" sort="Kim, Yongkwan" uniqKey="Kim Y" first="Yongkwan" last="Kim">Yongkwan Kim</name><affiliation><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Jheong, Weonhwa" sort="Jheong, Weonhwa" uniqKey="Jheong W" first="Weonhwa" last="Jheong">Weonhwa Jheong</name><affiliation><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Oem, Jae Ku" sort="Oem, Jae Ku" uniqKey="Oem J" first="Jae-Ku" last="Oem">Jae-Ku Oem</name><affiliation><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea. jku0623@korea.kr.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Microbial ecology</title><idno type="eISSN">1432-184X</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>China</term><term>Chiroptera (virology)</term><term>Coronavirus (classification)</term><term>Coronavirus (genetics)</term><term>Coronavirus (isolation & purification)</term><term>Coronavirus Infections (veterinary)</term><term>Coronavirus Infections (virology)</term><term>Genetic Variation</term><term>Genome, Viral</term><term>Hong Kong</term><term>Humans</term><term>Phylogeny</term><term>Republic of Korea</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term><term>Hong Kong</term><term>Republic of Korea</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Coronavirus</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>Genetic Variation</term><term>Genome, Viral</term><term>Humans</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (SARS), coronavirus, and other coronaviruses found in mammals. However, little research has been conducted on bat coronaviruses in South Korea. In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. RT-PCR and sequencing were performed for specific coronavirus genes to identify the bat coronaviruses in different bat samples. Coronaviruses were detected in 2.7% (18/672) of the samples: 13 oral swabs from one species of the family Rhinolophidae, and four fecal samples and one carcass (intestine) from three species of the family Vespertiliodae. To determine the genetic relationships of the 18 sequences obtained in this study and previously known coronaviruses, the nucleotide sequences of a 392-nt region of the RNA-dependent RNA polymerase (RdRp) gene were analyzed phylogenetically. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1-99.7%) with Bat-CoV-JTMC15 reported in China. The other five sequences were most similar to MERS-like betacoronaviruses. Four nucleotide sequences displayed the highest identity (94.1-95.1%) with Bat-CoV-HKU5 from Hong Kong. The one sequence from a carcass showed the highest nucleotide identity (99%) with Bat-CoV-SC2013 from China. These results suggest that careful surveillance of coronaviruses from bats should be continued, because animal and human infections may result from the genetic variants present in bat coronavirus reservoirs.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28725945</PMID><DateCompleted><Year>2019</Year><Month>01</Month><Day>16</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>24</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-184X</ISSN><JournalIssue CitedMedium="Internet"><Volume>75</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Microbial ecology</Title><ISOAbbreviation>Microb. Ecol.</ISOAbbreviation></Journal><ArticleTitle>Genetic Characteristics of Coronaviruses from Korean Bats in 2016.</ArticleTitle><Pagination><MedlinePgn>174-182</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00248-017-1033-8</ELocationID><Abstract><AbstractText>Bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (SARS), coronavirus, and other coronaviruses found in mammals. However, little research has been conducted on bat coronaviruses in South Korea. In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. RT-PCR and sequencing were performed for specific coronavirus genes to identify the bat coronaviruses in different bat samples. Coronaviruses were detected in 2.7% (18/672) of the samples: 13 oral swabs from one species of the family Rhinolophidae, and four fecal samples and one carcass (intestine) from three species of the family Vespertiliodae. To determine the genetic relationships of the 18 sequences obtained in this study and previously known coronaviruses, the nucleotide sequences of a 392-nt region of the RNA-dependent RNA polymerase (RdRp) gene were analyzed phylogenetically. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1-99.7%) with Bat-CoV-JTMC15 reported in China. The other five sequences were most similar to MERS-like betacoronaviruses. Four nucleotide sequences displayed the highest identity (94.1-95.1%) with Bat-CoV-HKU5 from Hong Kong. The one sequence from a carcass showed the highest nucleotide identity (99%) with Bat-CoV-SC2013 from China. These results suggest that careful surveillance of coronaviruses from bats should be continued, because animal and human infections may result from the genetic variants present in bat coronavirus reservoirs.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Saemi</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jo</LastName><ForeName>Seong-Deok</ForeName><Initials>SD</Initials><AffiliationInfo><Affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Son</LastName><ForeName>Kidong</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>An</LastName><ForeName>Injung</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jeong</LastName><ForeName>Jipseol</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Seung-Jun</ForeName><Initials>SJ</Initials><AffiliationInfo><Affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Yongkwan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jheong</LastName><ForeName>Weonhwa</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Oem</LastName><ForeName>Jae-Ku</ForeName><Initials>JK</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-4298-0604</Identifier><AffiliationInfo><Affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea. jku0623@korea.kr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Iksan, Republic of Korea. jku0623@korea.kr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>07</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Microb Ecol</MedlineTA><NlmUniqueID>7500663</NlmUniqueID><ISSNLinking>0095-3628</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><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="D017934" MajorTopicYN="N">Coronavirus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</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="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006723" MajorTopicYN="N" Type="Geographic">Hong Kong</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056910" MajorTopicYN="N" Type="Geographic">Republic of Korea</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Bats</Keyword><Keyword MajorTopicYN="N">Coronavirus</Keyword><Keyword MajorTopicYN="N">Middle East respiratory syndrome</Keyword><Keyword 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