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Genetic and evolutionary analysis of emerging H3N2 canine influenza virus.

Identifieur interne : 000110 ( Main/Exploration ); précédent : 000109; suivant : 000111

Genetic and evolutionary analysis of emerging H3N2 canine influenza virus.

Auteurs : Gairu Li [République populaire de Chine] ; Ruyi Wang [République populaire de Chine] ; Cheng Zhang [République populaire de Chine] ; Shilei Wang [République populaire de Chine] ; Wanting He [République populaire de Chine] ; Junyan Zhang [République populaire de Chine] ; Jie Liu [République populaire de Chine] ; Yuchen Cai [République populaire de Chine] ; Jiyong Zhou [République populaire de Chine] ; Shuo Su [République populaire de Chine]

Source :

RBID : pubmed:29691381

Descripteurs français

English descriptors

Abstract

The H3N2 canine influenza virus (CIV) originated from an avian species. Since its emergence, it has circulated in multiple states and has caused pandemics among dog populations; however, no comprehensive studies have explored the causes driving these ongoing cases. The study of the codon usage patterns of viruses can reveal the genetic changes required for the viruses to adapt to new hosts and the external environment. Here we performed a thorough genetic, evolutionary, and codon usage analysis. We identified three evolutionary H3N2 CIV clades from a timescaled phylogenetic tree, namely, Origin, China, and Korea/USA, by principal component analysis (PCA). Additionally, we found a low codon usage bias and that mutation pressure, natural selection, and dinucleotide abundance shape the codon usage bias of H3N2 CIVs, with natural selection being more crucial than the others. Moreover, the human codon adaptation index was similar to that of dogs (the natural host) and cats. In addition, the H3N2 CIV similarity index values were higher than those of the avian influenza virus (AIV), suggesting viral adaptation to the host. Therefore, H3N2 CIVs may pose a potential risk to public health in the future, and further epidemiologic, evolutionary, and pathogenetic studies are required.

DOI: 10.1038/s41426-018-0079-0
PubMed: 29691381
PubMed Central: PMC5915587


Affiliations:


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Le document en format XML

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<term>Adaptation, Biological (genetics)</term>
<term>Animals (MeSH)</term>
<term>China (epidemiology)</term>
<term>Codon (MeSH)</term>
<term>Communicable Diseases, Emerging (epidemiology)</term>
<term>Communicable Diseases, Emerging (transmission)</term>
<term>Communicable Diseases, Emerging (virology)</term>
<term>Dog Diseases (epidemiology)</term>
<term>Dog Diseases (virology)</term>
<term>Dogs (virology)</term>
<term>Evolution, Molecular (MeSH)</term>
<term>Host-Pathogen Interactions (MeSH)</term>
<term>Humans (MeSH)</term>
<term>Influenza A Virus, H3N2 Subtype (genetics)</term>
<term>Influenza A Virus, H3N2 Subtype (isolation & purification)</term>
<term>Influenza A Virus, H3N2 Subtype (pathogenicity)</term>
<term>Influenza, Human (virology)</term>
<term>Mutation (MeSH)</term>
<term>Orthomyxoviridae Infections (epidemiology)</term>
<term>Orthomyxoviridae Infections (veterinary)</term>
<term>Orthomyxoviridae Infections (virology)</term>
<term>Phylogeny (MeSH)</term>
<term>Selection, Genetic (MeSH)</term>
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<keywords scheme="KwdFr" xml:lang="fr">
<term>Adaptation biologique (génétique)</term>
<term>Animaux (MeSH)</term>
<term>Chiens (virologie)</term>
<term>Chine (épidémiologie)</term>
<term>Codon (MeSH)</term>
<term>Grippe humaine (virologie)</term>
<term>Humains (MeSH)</term>
<term>Infections à Orthomyxoviridae (médecine vétérinaire)</term>
<term>Infections à Orthomyxoviridae (virologie)</term>
<term>Infections à Orthomyxoviridae (épidémiologie)</term>
<term>Interactions hôte-pathogène (MeSH)</term>
<term>Maladies des chiens (virologie)</term>
<term>Maladies des chiens (épidémiologie)</term>
<term>Maladies transmissibles émergentes (transmission)</term>
<term>Maladies transmissibles émergentes (virologie)</term>
<term>Maladies transmissibles émergentes (épidémiologie)</term>
<term>Mutation (MeSH)</term>
<term>Phylogenèse (MeSH)</term>
<term>Sous-type H3N2 du virus de la grippe A (génétique)</term>
<term>Sous-type H3N2 du virus de la grippe A (isolement et purification)</term>
<term>Sous-type H3N2 du virus de la grippe A (pathogénicité)</term>
<term>Sélection génétique (MeSH)</term>
<term>Évolution moléculaire (MeSH)</term>
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<keywords scheme="MESH" type="chemical" xml:lang="en">
<term>Codon</term>
</keywords>
<keywords scheme="MESH" qualifier="epidemiology" xml:lang="en">
<term>China</term>
<term>Communicable Diseases, Emerging</term>
<term>Dog Diseases</term>
<term>Orthomyxoviridae Infections</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Adaptation, Biological</term>
<term>Influenza A Virus, H3N2 Subtype</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Adaptation biologique</term>
<term>Sous-type H3N2 du virus de la grippe A</term>
</keywords>
<keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en">
<term>Influenza A Virus, H3N2 Subtype</term>
</keywords>
<keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr">
<term>Sous-type H3N2 du virus de la grippe A</term>
</keywords>
<keywords scheme="MESH" qualifier="médecine vétérinaire" xml:lang="fr">
<term>Infections à Orthomyxoviridae</term>
</keywords>
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<term>Influenza A Virus, H3N2 Subtype</term>
</keywords>
<keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr">
<term>Sous-type H3N2 du virus de la grippe A</term>
</keywords>
<keywords scheme="MESH" qualifier="transmission" xml:lang="en">
<term>Communicable Diseases, Emerging</term>
</keywords>
<keywords scheme="MESH" qualifier="veterinary" xml:lang="en">
<term>Orthomyxoviridae Infections</term>
</keywords>
<keywords scheme="MESH" qualifier="virologie" xml:lang="fr">
<term>Chiens</term>
<term>Grippe humaine</term>
<term>Infections à Orthomyxoviridae</term>
<term>Maladies des chiens</term>
<term>Maladies transmissibles émergentes</term>
</keywords>
<keywords scheme="MESH" qualifier="virology" xml:lang="en">
<term>Communicable Diseases, Emerging</term>
<term>Dog Diseases</term>
<term>Dogs</term>
<term>Influenza, Human</term>
<term>Orthomyxoviridae Infections</term>
</keywords>
<keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr">
<term>Chine</term>
<term>Infections à Orthomyxoviridae</term>
<term>Maladies des chiens</term>
<term>Maladies transmissibles émergentes</term>
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<term>Animals</term>
<term>Evolution, Molecular</term>
<term>Host-Pathogen Interactions</term>
<term>Humans</term>
<term>Mutation</term>
<term>Phylogeny</term>
<term>Selection, Genetic</term>
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<term>Animaux</term>
<term>Codon</term>
<term>Humains</term>
<term>Interactions hôte-pathogène</term>
<term>Mutation</term>
<term>Phylogenèse</term>
<term>Sélection génétique</term>
<term>Évolution moléculaire</term>
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<front>
<div type="abstract" xml:lang="en">The H3N2 canine influenza virus (CIV) originated from an avian species. Since its emergence, it has circulated in multiple states and has caused pandemics among dog populations; however, no comprehensive studies have explored the causes driving these ongoing cases. The study of the codon usage patterns of viruses can reveal the genetic changes required for the viruses to adapt to new hosts and the external environment. Here we performed a thorough genetic, evolutionary, and codon usage analysis. We identified three evolutionary H3N2 CIV clades from a timescaled phylogenetic tree, namely, Origin, China, and Korea/USA, by principal component analysis (PCA). Additionally, we found a low codon usage bias and that mutation pressure, natural selection, and dinucleotide abundance shape the codon usage bias of H3N2 CIVs, with natural selection being more crucial than the others. Moreover, the human codon adaptation index was similar to that of dogs (the natural host) and cats. In addition, the H3N2 CIV similarity index values were higher than those of the avian influenza virus (AIV), suggesting viral adaptation to the host. Therefore, H3N2 CIVs may pose a potential risk to public health in the future, and further epidemiologic, evolutionary, and pathogenetic studies are required.</div>
</front>
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<Article PubModel="Electronic">
<Journal>
<ISSN IssnType="Electronic">2222-1751</ISSN>
<JournalIssue CitedMedium="Internet">
<Volume>7</Volume>
<Issue>1</Issue>
<PubDate>
<Year>2018</Year>
<Month>Apr</Month>
<Day>25</Day>
</PubDate>
</JournalIssue>
<Title>Emerging microbes & infections</Title>
<ISOAbbreviation>Emerg Microbes Infect</ISOAbbreviation>
</Journal>
<ArticleTitle>Genetic and evolutionary analysis of emerging H3N2 canine influenza virus.</ArticleTitle>
<Pagination>
<MedlinePgn>73</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1038/s41426-018-0079-0</ELocationID>
<Abstract>
<AbstractText>The H3N2 canine influenza virus (CIV) originated from an avian species. Since its emergence, it has circulated in multiple states and has caused pandemics among dog populations; however, no comprehensive studies have explored the causes driving these ongoing cases. The study of the codon usage patterns of viruses can reveal the genetic changes required for the viruses to adapt to new hosts and the external environment. Here we performed a thorough genetic, evolutionary, and codon usage analysis. We identified three evolutionary H3N2 CIV clades from a timescaled phylogenetic tree, namely, Origin, China, and Korea/USA, by principal component analysis (PCA). Additionally, we found a low codon usage bias and that mutation pressure, natural selection, and dinucleotide abundance shape the codon usage bias of H3N2 CIVs, with natural selection being more crucial than the others. Moreover, the human codon adaptation index was similar to that of dogs (the natural host) and cats. In addition, the H3N2 CIV similarity index values were higher than those of the avian influenza virus (AIV), suggesting viral adaptation to the host. Therefore, H3N2 CIVs may pose a potential risk to public health in the future, and further epidemiologic, evolutionary, and pathogenetic studies are required.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Li</LastName>
<ForeName>Gairu</ForeName>
<Initials>G</Initials>
<AffiliationInfo>
<Affiliation>MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Wang</LastName>
<ForeName>Ruyi</ForeName>
<Initials>R</Initials>
<AffiliationInfo>
<Affiliation>MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhang</LastName>
<ForeName>Cheng</ForeName>
<Initials>C</Initials>
<AffiliationInfo>
<Affiliation>MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Wang</LastName>
<ForeName>Shilei</ForeName>
<Initials>S</Initials>
<AffiliationInfo>
<Affiliation>MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>He</LastName>
<ForeName>Wanting</ForeName>
<Initials>W</Initials>
<AffiliationInfo>
<Affiliation>MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhang</LastName>
<ForeName>Junyan</ForeName>
<Initials>J</Initials>
<AffiliationInfo>
<Affiliation>MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Liu</LastName>
<ForeName>Jie</ForeName>
<Initials>J</Initials>
<AffiliationInfo>
<Affiliation>MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Cai</LastName>
<ForeName>Yuchen</ForeName>
<Initials>Y</Initials>
<AffiliationInfo>
<Affiliation>MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhou</LastName>
<ForeName>Jiyong</ForeName>
<Initials>J</Initials>
<AffiliationInfo>
<Affiliation>MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Su</LastName>
<ForeName>Shuo</ForeName>
<Initials>S</Initials>
<AffiliationInfo>
<Affiliation>MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China. shuosu@njau.edu.cn.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic">
<Year>2018</Year>
<Month>04</Month>
<Day>25</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>United States</Country>
<MedlineTA>Emerg Microbes Infect</MedlineTA>
<NlmUniqueID>101594885</NlmUniqueID>
<ISSNLinking>2222-1751</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D003062">Codon</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D000220" MajorTopicYN="N">Adaptation, Biological</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D002681" MajorTopicYN="N">China</DescriptorName>
<QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D003062" MajorTopicYN="N">Codon</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D021821" MajorTopicYN="N">Communicable Diseases, Emerging</DescriptorName>
<QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName>
<QualifierName UI="Q000635" MajorTopicYN="N">transmission</QualifierName>
<QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D004283" MajorTopicYN="N">Dog Diseases</DescriptorName>
<QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName>
<QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D004285" MajorTopicYN="N">Dogs</DescriptorName>
<QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D054884" MajorTopicYN="N">Host-Pathogen Interactions</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D053122" MajorTopicYN="N">Influenza A Virus, H3N2 Subtype</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName>
<QualifierName UI="Q000472" MajorTopicYN="N">pathogenicity</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D007251" MajorTopicYN="N">Influenza, Human</DescriptorName>
<QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D009154" MajorTopicYN="N">Mutation</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D009976" MajorTopicYN="N">Orthomyxoviridae Infections</DescriptorName>
<QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName>
<QualifierName UI="Q000662" MajorTopicYN="Y">veterinary</QualifierName>
<QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D012641" MajorTopicYN="N">Selection, Genetic</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
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<History>
<PubMedPubDate PubStatus="received">
<Year>2017</Year>
<Month>12</Month>
<Day>20</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted">
<Year>2018</Year>
<Month>03</Month>
<Day>20</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised">
<Year>2018</Year>
<Month>03</Month>
<Day>19</Day>
</PubMedPubDate>
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<Year>2018</Year>
<Month>4</Month>
<Day>26</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<Year>2018</Year>
<Month>4</Month>
<Day>25</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<Year>2018</Year>
<Month>11</Month>
<Day>16</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<name sortKey="Li, Gairu" sort="Li, Gairu" uniqKey="Li G" first="Gairu" last="Li">Gairu Li</name>
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<name sortKey="Cai, Yuchen" sort="Cai, Yuchen" uniqKey="Cai Y" first="Yuchen" last="Cai">Yuchen Cai</name>
<name sortKey="He, Wanting" sort="He, Wanting" uniqKey="He W" first="Wanting" last="He">Wanting He</name>
<name sortKey="Liu, Jie" sort="Liu, Jie" uniqKey="Liu J" first="Jie" last="Liu">Jie Liu</name>
<name sortKey="Su, Shuo" sort="Su, Shuo" uniqKey="Su S" first="Shuo" last="Su">Shuo Su</name>
<name sortKey="Wang, Ruyi" sort="Wang, Ruyi" uniqKey="Wang R" first="Ruyi" last="Wang">Ruyi Wang</name>
<name sortKey="Wang, Shilei" sort="Wang, Shilei" uniqKey="Wang S" first="Shilei" last="Wang">Shilei Wang</name>
<name sortKey="Zhang, Cheng" sort="Zhang, Cheng" uniqKey="Zhang C" first="Cheng" last="Zhang">Cheng Zhang</name>
<name sortKey="Zhang, Junyan" sort="Zhang, Junyan" uniqKey="Zhang J" first="Junyan" last="Zhang">Junyan Zhang</name>
<name sortKey="Zhou, Jiyong" sort="Zhou, Jiyong" uniqKey="Zhou J" first="Jiyong" last="Zhou">Jiyong Zhou</name>
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