Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification
Identifieur interne : 000241 ( Hal/Checkpoint ); précédent : 000240; suivant : 000242Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification
Auteurs : Nathalie Désiré [France] ; Lorenzo Cerutti ; Quentin Le Hingrat [France] ; Marine Perrier [France] ; Stefan Emler ; Vincent Calvez [France] ; Diane Descamps [France] ; Anne-Geneviève Marcelin [France] ; Stéphane Hue [Royaume-Uni] ; Benoit Visseaux [France]Source :
- Retrovirology [ 1742-4690 ] ; 2018.
Descripteurs français
- Wicri :
- topic : Nomenclature.
English descriptors
- mix :
Abstract
Background: The large and constantly evolving HIV-1 pandemic has led to an increasingly complex diversity. Because of some taxonomic difficulties among the most diverse HIV-1 subtypes, and taking advantage of the large amount of sequence data generated in the recent years, we investigated novel lineage patterns among the main HIV-1 subtypes.Results: All HIV full-length genomes available in public databases were analysed (n = 2017). Maximum likelihood phylogenies and pairwise genetic distance were obtained. Clustering patterns and mean distributions of genetic distances were compared within and across the current groups, subtypes and sub-subtypes of HIV-1 to detect and analyse any divergent lineages within previously defined HIV lineages. The level of genetic similarity observed between most HIV clades was deeply consistent with the current classification. However, both subtypes A and D showed evidence of further intra-subtype diversification not fully described by the nomenclature system at the time and could be divided into several distinct sub-subtypes.Conclusions: With this work, we propose an updated nomenclature of sub-types A and D better reflecting their current genetic diversity and evolutionary patterns. Allowing a more accurate nomenclature and classification system is a necessary step for easier subtyping of HIV strains and a better detection or follow-up of viral epidemiology shifts.
Url:
DOI: 10.1186/s12977-018-0461-y
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Hal:hal-01997960Le document en format XML
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<idno type="DOI">10.1186/s12977-018-0461-y</idno>
<series><title level="j">Retrovirology</title>
<idno type="ISSN">1742-4690</idno>
<imprint><date type="datePub">2018</date>
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<profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>Evolution</term>
<term>HIV</term>
<term>Nomenclature</term>
<term>Phylogenetic</term>
<term>Viral diversity</term>
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<front><div type="abstract" xml:lang="en"> <p>Background: The large and constantly evolving HIV-1 pandemic has led to an increasingly complex diversity. Because of some taxonomic difficulties among the most diverse HIV-1 subtypes, and taking advantage of the large amount of sequence data generated in the recent years, we investigated novel lineage patterns among the main HIV-1 subtypes.Results: All HIV full-length genomes available in public databases were analysed (n = 2017). Maximum likelihood phylogenies and pairwise genetic distance were obtained. Clustering patterns and mean distributions of genetic distances were compared within and across the current groups, subtypes and sub-subtypes of HIV-1 to detect and analyse any divergent lineages within previously defined HIV lineages. The level of genetic similarity observed between most HIV clades was deeply consistent with the current classification. However, both subtypes A and D showed evidence of further intra-subtype diversification not fully described by the nomenclature system at the time and could be divided into several distinct sub-subtypes.Conclusions: With this work, we propose an updated nomenclature of sub-types A and D better reflecting their current genetic diversity and evolutionary patterns. Allowing a more accurate nomenclature and classification system is a necessary step for easier subtyping of HIV strains and a better detection or follow-up of viral epidemiology shifts.</p>
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<hal api="V3"> <titleStmt> <title xml:lang="en">Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification</title>
<author role="aut"> <persName> <forename type="first">Nathalie</forename>
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<author role="aut"> <persName> <forename type="first">Lorenzo</forename>
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<author role="aut"> <persName> <forename type="first">Quentin</forename>
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<date type="whenModified">2020-04-09 11:56:18</date>
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<idno type="stamp" n="IPLESP" corresp="SORBONNE-UNIVERSITE">Institut Pierre Louis d'Epidémiologie et de Santé Publique</idno>
<idno type="stamp" n="SU-MEDECINE" corresp="SORBONNE-UNIVERSITE">Faculté de Médecine de Sorbonne Université</idno>
<idno type="stamp" n="IAME" corresp="UNIV-PARIS13">(Infection, Antimicrobiens, Modélisation, Evolution) - UMR 1137</idno>
<idno type="stamp" n="SORBONNE-PARIS-NORD">Université Sorbonne Paris Nord</idno>
<idno type="stamp" n="UNIV-PARIS">Université de Paris</idno>
<idno type="stamp" n="UP-SANTE">Université de Paris - Faculté de Santé</idno>
</seriesStmt>
<notesStmt> <note type="audience" n="2">International</note>
<note type="popular" n="0">No</note>
<note type="peer" n="1">Yes</note>
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<sourceDesc> <biblStruct> <analytic> <title xml:lang="en">Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification</title>
<author role="aut"> <persName> <forename type="first">Nathalie</forename>
<surname>Désiré</surname>
</persName>
<idno type="halauthorid">95255</idno>
<affiliation ref="#struct-542132"></affiliation>
<affiliation ref="#struct-413221"></affiliation>
<affiliation ref="#struct-442208"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Lorenzo</forename>
<surname>Cerutti</surname>
</persName>
<idno type="halauthorid">784845</idno>
</author>
<author role="aut"> <persName> <forename type="first">Quentin</forename>
<surname>Le Hingrat</surname>
</persName>
<idno type="halauthorid">1588688</idno>
<affiliation ref="#struct-247341"></affiliation>
<affiliation ref="#struct-459037"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Marine</forename>
<surname>Perrier</surname>
</persName>
<idno type="halauthorid">736871</idno>
<affiliation ref="#struct-247341"></affiliation>
<affiliation ref="#struct-459037"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Stefan</forename>
<surname>Emler</surname>
</persName>
<idno type="halauthorid">11388323</idno>
</author>
<author role="aut"> <persName> <forename type="first">Vincent</forename>
<surname>Calvez</surname>
</persName>
<email type="md5">6493297be5bb3423dea82e1edf02122f</email>
<email type="domain">ens-lyon.fr</email>
<idno type="idhal" notation="string">vincent-calvez</idno>
<idno type="idhal" notation="numeric">11087</idno>
<idno type="halauthorid">691354</idno>
<idno type="ORCID">https://orcid.org/0000-0002-3674-1965</idno>
<affiliation ref="#struct-542132"></affiliation>
<affiliation ref="#struct-413221"></affiliation>
<affiliation ref="#struct-442208"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Diane</forename>
<surname>Descamps</surname>
</persName>
<idno type="halauthorid">609858</idno>
<affiliation ref="#struct-247341"></affiliation>
<affiliation ref="#struct-459037"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Anne-Geneviève</forename>
<surname>Marcelin</surname>
</persName>
<idno type="halauthorid">307967</idno>
<affiliation ref="#struct-442208"></affiliation>
<affiliation ref="#struct-542132"></affiliation>
<affiliation ref="#struct-413221"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Stéphane</forename>
<surname>Hue</surname>
</persName>
<idno type="halauthorid">1366950</idno>
<affiliation ref="#struct-353798"></affiliation>
</author>
<author role="aut"> <persName> <forename type="first">Benoit</forename>
<surname>Visseaux</surname>
</persName>
<email type="md5">efb20dbb1412b64b7adf4b2c17c34841</email>
<email type="domain">aphp.fr</email>
<idno type="halauthorid">1416515</idno>
<affiliation ref="#struct-459037"></affiliation>
<affiliation ref="#struct-247341"></affiliation>
</author>
</analytic>
<monogr> <idno type="halJournalId" status="VALID">2067</idno>
<idno type="issn">1742-4690</idno>
<title level="j">Retrovirology</title>
<imprint> <publisher>BioMed Central</publisher>
<biblScope unit="volume">15</biblScope>
<biblScope unit="pp">80</biblScope>
<date type="datePub">2018</date>
<date type="dateEpub">2018-12-22</date>
</imprint>
</monogr>
<idno type="doi">10.1186/s12977-018-0461-y</idno>
</biblStruct>
</sourceDesc>
<profileDesc> <langUsage> <language ident="en">English</language>
</langUsage>
<textClass> <keywords scheme="author"> <term xml:lang="en">Phylogenetic</term>
<term xml:lang="en">Evolution</term>
<term xml:lang="en">Viral diversity</term>
<term xml:lang="en">HIV</term>
<term xml:lang="en">Nomenclature</term>
</keywords>
<classCode scheme="halDomain" n="sdv.mp.vir">Life Sciences [q-bio]/Microbiology and Parasitology/Virology</classCode>
<classCode scheme="halDomain" n="sdv.bid.spt">Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy</classCode>
<classCode scheme="halTypology" n="ART">Journal articles</classCode>
</textClass>
<abstract xml:lang="en"> <p>Background: The large and constantly evolving HIV-1 pandemic has led to an increasingly complex diversity. Because of some taxonomic difficulties among the most diverse HIV-1 subtypes, and taking advantage of the large amount of sequence data generated in the recent years, we investigated novel lineage patterns among the main HIV-1 subtypes.Results: All HIV full-length genomes available in public databases were analysed (n = 2017). Maximum likelihood phylogenies and pairwise genetic distance were obtained. Clustering patterns and mean distributions of genetic distances were compared within and across the current groups, subtypes and sub-subtypes of HIV-1 to detect and analyse any divergent lineages within previously defined HIV lineages. The level of genetic similarity observed between most HIV clades was deeply consistent with the current classification. However, both subtypes A and D showed evidence of further intra-subtype diversification not fully described by the nomenclature system at the time and could be divided into several distinct sub-subtypes.Conclusions: With this work, we propose an updated nomenclature of sub-types A and D better reflecting their current genetic diversity and evolutionary patterns. Allowing a more accurate nomenclature and classification system is a necessary step for easier subtyping of HIV strains and a better detection or follow-up of viral epidemiology shifts.</p>
</abstract>
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