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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Country Level Diversity of the HIV-1 Pandemic between 1990 and 2015</title><author><name sortKey="Hemelaar, Joris" sort="Hemelaar, Joris" uniqKey="Hemelaar J" first="Joris" last="Hemelaar">Joris Hemelaar</name><affiliation><nlm:aff id="aff1"><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><addr-line>Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Loganathan, Shanghavie" sort="Loganathan, Shanghavie" uniqKey="Loganathan S" first="Shanghavie" last="Loganathan">Shanghavie Loganathan</name><affiliation><nlm:aff id="aff1"><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Elangovan, Ramyiadarsini" sort="Elangovan, Ramyiadarsini" uniqKey="Elangovan R" first="Ramyiadarsini" last="Elangovan">Ramyiadarsini Elangovan</name><affiliation><nlm:aff id="aff1"><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Yun, Jason" sort="Yun, Jason" uniqKey="Yun J" first="Jason" last="Yun">Jason Yun</name><affiliation><nlm:aff id="aff1"><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Dickson Tetteh, Leslie" sort="Dickson Tetteh, Leslie" uniqKey="Dickson Tetteh L" first="Leslie" last="Dickson-Tetteh">Leslie Dickson-Tetteh</name><affiliation><nlm:aff id="aff1"><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Kirtley, Shona" sort="Kirtley, Shona" uniqKey="Kirtley S" first="Shona" last="Kirtley">Shona Kirtley</name><affiliation><nlm:aff id="aff3"><addr-line>Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">33087461</idno><idno type="pmc">7944450</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7944450</idno><idno type="RBID">PMC:7944450</idno><idno type="doi">10.1128/JVI.01580-20</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000140</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000140</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Country Level Diversity of the HIV-1 Pandemic between 1990 and 2015</title><author><name sortKey="Hemelaar, Joris" sort="Hemelaar, Joris" uniqKey="Hemelaar J" first="Joris" last="Hemelaar">Joris Hemelaar</name><affiliation><nlm:aff id="aff1"><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><addr-line>Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Loganathan, Shanghavie" sort="Loganathan, Shanghavie" uniqKey="Loganathan S" first="Shanghavie" last="Loganathan">Shanghavie Loganathan</name><affiliation><nlm:aff id="aff1"><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Elangovan, Ramyiadarsini" sort="Elangovan, Ramyiadarsini" uniqKey="Elangovan R" first="Ramyiadarsini" last="Elangovan">Ramyiadarsini Elangovan</name><affiliation><nlm:aff id="aff1"><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Yun, Jason" sort="Yun, Jason" uniqKey="Yun J" first="Jason" last="Yun">Jason Yun</name><affiliation><nlm:aff id="aff1"><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Dickson Tetteh, Leslie" sort="Dickson Tetteh, Leslie" uniqKey="Dickson Tetteh L" first="Leslie" last="Dickson-Tetteh">Leslie Dickson-Tetteh</name><affiliation><nlm:aff id="aff1"><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Kirtley, Shona" sort="Kirtley, Shona" uniqKey="Kirtley S" first="Shona" last="Kirtley">Shona Kirtley</name><affiliation><nlm:aff id="aff3"><addr-line>Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom</addr-line></nlm:aff></affiliation></author></analytic><series><title level="j">Journal of Virology</title><idno type="ISSN">0022-538X</idno><idno type="eISSN">1098-5514</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>This is the first study to analyze global country level HIV-1 diversity from 1990 to 2015. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe and North America. The proportion of HIV-1 infections due to recombinants was highest in South-East Asia, China, and West and Central Africa. The highest proportions of URFs were found in Myanmar, Republic of the Congo, and Argentina. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to HIV vaccine development and diagnostic, drug resistance, and viral load assays.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Virol</journal-id><journal-id journal-id-type="iso-abbrev">J Virol</journal-id><journal-id journal-id-type="hwp">jvi</journal-id><journal-id journal-id-type="pmc">jvi</journal-id><journal-id journal-id-type="publisher-id">JVI</journal-id><journal-title-group><journal-title>Journal of Virology</journal-title></journal-title-group><issn pub-type="ppub">0022-538X</issn><issn pub-type="epub">1098-5514</issn><publisher><publisher-name>American Society for Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">33087461</article-id><article-id pub-id-type="pmc">7944450</article-id><article-id pub-id-type="publisher-id">01580-20</article-id><article-id pub-id-type="doi">10.1128/JVI.01580-20</article-id><article-categories><subj-group subj-group-type="heading"><subject>Genetic Diversity and Evolution</subject></subj-group></article-categories><title-group><article-title>Country Level Diversity of the HIV-1 Pandemic between 1990 and 2015</article-title><alt-title alt-title-type="running-head">Global Country Level HIV-1 Diversity</alt-title><alt-title alt-title-type="short-authors">Hemelaar et al.</alt-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid" authenticated="false">https://orcid.org/0000-0003-3523-7457</contrib-id><name><surname>Hemelaar</surname><given-names>Joris</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Loganathan</surname><given-names>Shanghavie</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Elangovan</surname><given-names>Ramyiadarsini</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yun</surname><given-names>Jason</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Dickson-Tetteh</surname><given-names>Leslie</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kirtley</surname><given-names>Shona</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><collab>WHO-UNAIDS Network for HIV Isolation and Characterization</collab></contrib><aff id="aff1"><label>a</label><addr-line>Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, John Radcliffe Hospital, Oxford, United Kingdom</addr-line></aff><aff id="aff2"><label>b</label><addr-line>Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom</addr-line></aff><aff id="aff3"><label>c</label><addr-line>Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom</addr-line></aff></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Silvestri</surname><given-names>Guido</given-names></name><role>Editor</role><aff>Emory University</aff></contrib></contrib-group><author-notes><corresp id="cor1">Address correspondence to Joris Hemelaar, <email>jorishemelaar@gmail.com</email>.</corresp><fn fn-type="other"><p><bold>Citation</bold> Hemelaar J, Loganathan S, Elangovan R, Yun J, Dickson-Tetteh L, Kirtley S, WHO-UNAIDS Network for HIV Isolation and Characterization. 2021. Country level diversity of the HIV-1 pandemic between 1990 and 2015. J Virol 95:e01580-20. <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.1128/JVI.01580-20">https://doi.org/10.1128/JVI.01580-20</ext-link>.</p></fn></author-notes><pub-date pub-type="epreprint"><day>21</day><month>10</month><year>2020</year></pub-date><pub-date pub-type="epub"><day>22</day><month>12</month><year>2020</year></pub-date><pub-date pub-type="collection"><month>1</month><year>2021</year></pub-date><volume>95</volume><issue>2</issue><elocation-id>e01580-20</elocation-id><history><date date-type="received"><day>6</day><month>8</month><year>2020</year></date><date date-type="accepted"><day>12</day><month>10</month><year>2020</year></date></history><permissions><copyright-statement>Copyright © 2020 American Society for Microbiology.</copyright-statement><copyright-year>2020</copyright-year><copyright-holder>American Society for Microbiology</copyright-holder><license license-type="asm" xlink:href="https://doi.org/10.1128/ASMCopyrightv2"><license-p><ext-link ext-link-type="uri" xlink:href="https://doi.org/10.1128/ASMCopyrightv2">All Rights Reserved</ext-link>.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="JVI.01580-20.pdf"></self-uri><abstract abstract-type="precis"><p>This is the first study to analyze global country level HIV-1 diversity from 1990 to 2015. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe and North America. The proportion of HIV-1 infections due to recombinants was highest in South-East Asia, China, and West and Central Africa. The highest proportions of URFs were found in Myanmar, Republic of the Congo, and Argentina. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to HIV vaccine development and diagnostic, drug resistance, and viral load assays.</p></abstract><abstract><title>ABSTRACT</title><p>The global diversity of HIV forms a major challenge to the development of an HIV vaccine, as well as diagnostic, drug resistance, and viral load assays, which are essential to reaching the UNAIDS 90:90:90 targets. We sought to determine country level HIV-1 diversity globally between 1990 and 2015. We assembled a global HIV-1 molecular epidemiology database through a systematic literature search and a global survey. We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published from 1 January 1990 to 31 December 2015. We collected additional unpublished data through a global survey of experts. Prevalence studies with original HIV-1 subtyping data collected between 1990 and 2015 were included. This resulted in a database with 383,519 subtyped HIV-1 samples from 116 countries over four time periods (1990 to 1999, 2000 to 2004, 2005 to 2009, and 2010 to 2015). We analyzed country-specific numbers of distinct HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in each time period. We also analyzed country-specific proportions of infections due to HIV-1 recombinants, CRFs, and URFs and calculated the Shannon diversity index for each country. Finally, we analyzed global temporal trends in each of these measures of HIV-1 diversity. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries such as Chad, Democratic Republic of the Congo, Angola, and Republic of the Congo have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe (Spain and France) and North America (United States) (up to 39 distinct HIV-1 variants in Spain). The proportion of HIV-1 infections due to recombinants was highest in Southeast Asia (>95% of infections in Viet Nam, Cambodia, and Thailand), China, and West and Central Africa, mainly due to high proportions of CRF01_AE and CRF02_AG. Other CRFs played major roles (>75% of HIV-1 infections) in Estonia (CRF06_cpx), Iran (CRF35_AD), and Algeria (CRF06_cpx). The highest proportions of URFs (>30%) were found in Myanmar, Republic of the Congo, and Argentina. Global temporal analysis showed consistent increases over time in country level numbers of distinct HIV-1 variants and proportions of CRFs and URFs, leading to increases in country level HIV-1 diversity. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to prevention and treatment efforts. HIV-1 molecular epidemiological surveillance needs to be continued and improved.</p><p><bold>IMPORTANCE</bold> This is the first study to analyze global country level HIV-1 diversity from 1990 to 2015. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe and North America. The proportion of HIV-1 infections due to recombinants was highest in South-East Asia, China, and West and Central Africa. The highest proportions of URFs were found in Myanmar, Republic of the Congo, and Argentina. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to HIV vaccine development and diagnostic, drug resistance, and viral load assays.</p></abstract><kwd-group><title>KEYWORDS</title><kwd>HIV</kwd><kwd>recombinant</kwd><kwd>circulating recombinant form</kwd><kwd>CRF</kwd><kwd>unique recombinant form</kwd><kwd>URF</kwd><kwd>molecular epidemiology</kwd><kwd>diversity</kwd></kwd-group><counts><count count="1" count-type="supplementary-material"></count><fig-count count="6"></fig-count><table-count count="1"></table-count><equation-count count="1"></equation-count><ref-count count="49"></ref-count><page-count count="15"></page-count><word-count count="9323"></word-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>January 2021</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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