Complete genome analysis of a SARS-like bat coronavirus identified in the Republic of Korea.
Identifieur interne : 000918 ( PubMed/Checkpoint ); précédent : 000917; suivant : 000919Complete genome analysis of a SARS-like bat coronavirus identified in the Republic of Korea.
Auteurs : Yongkwan Kim [Corée du Sud] ; Kidong Son [Corée du Sud] ; Young-Sik Kim [Corée du Sud] ; Sook-Young Lee [Corée du Sud] ; Weonhwa Jheong [Corée du Sud] ; Jae-Ku Oem [Corée du Sud]Source :
- Virus genes [ 1572-994X ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Virus du SRAS.
- virologie : Chiroptera.
- Analyse de séquence de protéine, Animaux, Génome viral, Humains, Phylogénie, République de Corée, Spécificité d'espèce, Typage moléculaire.
English descriptors
- KwdEn :
- Animals, Betacoronavirus (classification), Betacoronavirus (genetics), Betacoronavirus (isolation & purification), Chiroptera (virology), Genome, Viral, Humans, Molecular Typing, Phylogeny, Republic of Korea, SARS Virus (genetics), Sequence Analysis, Protein, Species Specificity, Whole Genome Sequencing.
- MESH :
- geographic : Republic of Korea.
- classification : Betacoronavirus.
- genetics : Betacoronavirus, SARS Virus.
- isolation & purification : Betacoronavirus.
- virology : Chiroptera.
- Animals, Genome, Viral, Humans, Molecular Typing, Phylogeny, Sequence Analysis, Protein, Species Specificity, Whole Genome Sequencing.
Abstract
Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.
DOI: 10.1007/s11262-019-01668-w
PubMed: 31076983
Affiliations:
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Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon</wicri:regionArea><wicri:noRegion>Incheon</wicri:noRegion></affiliation></author><author><name sortKey="Son, Kidong" sort="Son, Kidong" uniqKey="Son K" first="Kidong" last="Son">Kidong Son</name><affiliation wicri:level="1"><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon</wicri:regionArea><wicri:noRegion>Incheon</wicri:noRegion></affiliation></author><author><name sortKey="Kim, Young Sik" sort="Kim, Young Sik" uniqKey="Kim Y" first="Young-Sik" last="Kim">Young-Sik Kim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju</wicri:regionArea><wicri:noRegion>Jeonju</wicri:noRegion></affiliation></author><author><name sortKey="Lee, Sook Young" sort="Lee, Sook Young" uniqKey="Lee S" first="Sook-Young" last="Lee">Sook-Young Lee</name><affiliation wicri:level="1"><nlm:affiliation>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju</wicri:regionArea><wicri:noRegion>Jeonju</wicri:noRegion></affiliation></author><author><name sortKey="Jheong, Weonhwa" sort="Jheong, Weonhwa" uniqKey="Jheong W" first="Weonhwa" last="Jheong">Weonhwa Jheong</name><affiliation wicri:level="1"><nlm:affiliation>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon</wicri:regionArea><wicri:noRegion>Incheon</wicri:noRegion></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 wicri:level="1"><nlm:affiliation>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea. jku0623@jbnu.ac.kr.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju</wicri:regionArea><wicri:noRegion>Jeonju</wicri:noRegion></affiliation></author></analytic><series><title level="j">Virus genes</title><idno type="eISSN">1572-994X</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Betacoronavirus (classification)</term><term>Betacoronavirus (genetics)</term><term>Betacoronavirus (isolation & purification)</term><term>Chiroptera (virology)</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Typing</term><term>Phylogeny</term><term>Republic of Korea</term><term>SARS Virus (genetics)</term><term>Sequence Analysis, Protein</term><term>Species Specificity</term><term>Whole Genome Sequencing</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence de protéine</term><term>Animaux</term><term>Chiroptera (virologie)</term><term>Génome viral</term><term>Humains</term><term>Phylogénie</term><term>République de Corée</term><term>Spécificité d'espèce</term><term>Typage moléculaire</term><term>Virus du SRAS (génétique)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Republic of Korea</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Chiroptera</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chiroptera</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Typing</term><term>Phylogeny</term><term>Sequence Analysis, Protein</term><term>Species Specificity</term><term>Whole Genome Sequencing</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence de protéine</term><term>Animaux</term><term>Génome viral</term><term>Humains</term><term>Phylogénie</term><term>République de Corée</term><term>Spécificité d'espèce</term><term>Typage moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31076983</PMID><DateCompleted><Year>2019</Year><Month>11</Month><Day>19</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>24</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1572-994X</ISSN><JournalIssue CitedMedium="Internet"><Volume>55</Volume><Issue>4</Issue><PubDate><Year>2019</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Virus genes</Title><ISOAbbreviation>Virus Genes</ISOAbbreviation></Journal><ArticleTitle>Complete genome analysis of a SARS-like bat coronavirus identified in the Republic of Korea.</ArticleTitle><Pagination><MedlinePgn>545-549</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s11262-019-01668-w</ELocationID><Abstract><AbstractText>Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.</AbstractText></Abstract><AuthorList CompleteYN="Y"><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, Republic of Korea.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, 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, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Young-Sik</ForeName><Initials>YS</Initials><AffiliationInfo><Affiliation>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Sook-Young</ForeName><Initials>SY</Initials><AffiliationInfo><Affiliation>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, 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, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Oem</LastName><ForeName>Jae-Ku</ForeName><Initials>JK</Initials><AffiliationInfo><Affiliation>Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea. jku0623@jbnu.ac.kr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>NRF-2018R1D1A1B07041764</GrantID><Agency>National Research Foundation of Korea</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>05</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Virus Genes</MedlineTA><NlmUniqueID>8803967</NlmUniqueID><ISSNLinking>0920-8569</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000073640" MajorTopicYN="N">Betacoronavirus</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="D002685" MajorTopicYN="N">Chiroptera</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="Y">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058889" MajorTopicYN="N">Molecular Typing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056910" MajorTopicYN="N" Type="Geographic">Republic of Korea</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020539" MajorTopicYN="N">Sequence Analysis, Protein</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000073336" MajorTopicYN="N">Whole Genome Sequencing</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Bat</Keyword><Keyword MajorTopicYN="N">Frame shift</Keyword><Keyword MajorTopicYN="N">SARS-like coronavirus</Keyword><Keyword MajorTopicYN="N">Whole genome</Keyword><Keyword MajorTopicYN="N">Zoonotic disease</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate 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sort="Son, Kidong" uniqKey="Son K" first="Kidong" last="Son">Kidong Son</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Complete genome analysis of a SARS-like bat coronavirus identified in the Republic of Korea.
}}
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HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:31076983" \
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