Phylogenetic studies of transmission dynamics in generalized HIV epidemics: An essential tool where the burden is greatest?
Identifieur interne : 001931 ( Pmc/Corpus ); précédent : 001930; suivant : 001932Phylogenetic studies of transmission dynamics in generalized HIV epidemics: An essential tool where the burden is greatest?
Auteurs : Ann M. Dennis ; Joshua T. Herbeck ; Andrew Leigh Brown ; Paul Kellam ; Tulio De Oliveira ; Deenan Pillay ; Christophe Fraser ; Myron S. CohenSource :
- Journal of acquired immune deficiency syndromes (1999) [ 1525-4135 ] ; 2014.
Abstract
Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population-level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics, and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics, and suggest potential solutions.
Url:
DOI: 10.1097/QAI.0000000000000271
PubMed: 24977473
PubMed Central: 4304655
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PMC:4304655Le document en format XML
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Herbeck</name><affiliation><nlm:aff id="A2">Department of Microbiology, University of Washington, Seattle, WA</nlm:aff></affiliation></author><author><name sortKey="Brown, Andrew Leigh" sort="Brown, Andrew Leigh" uniqKey="Brown A" first="Andrew Leigh" last="Brown">Andrew Leigh Brown</name><affiliation><nlm:aff id="A3">Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK</nlm:aff></affiliation></author><author><name sortKey="Kellam, Paul" sort="Kellam, Paul" uniqKey="Kellam P" first="Paul" last="Kellam">Paul Kellam</name><affiliation><nlm:aff id="A4">Wellcome Trust Sanger Institute, Cambridge, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A5">Division of Infection and Immunity, University College London, London, UK</nlm:aff></affiliation></author><author><name sortKey="De Oliveira, Tulio" sort="De Oliveira, Tulio" uniqKey="De Oliveira T" first="Tulio" last="De Oliveira">Tulio De Oliveira</name><affiliation><nlm:aff id="A6">Wellcome Trust-Africa Centre for Health and Population Studies, University of Kwazula-Natal, ZA</nlm:aff></affiliation></author><author><name sortKey="Pillay, Deenan" sort="Pillay, Deenan" uniqKey="Pillay D" first="Deenan" last="Pillay">Deenan Pillay</name><affiliation><nlm:aff id="A5">Division of Infection and Immunity, University College London, London, UK</nlm:aff></affiliation></author><author><name sortKey="Fraser, Christophe" sort="Fraser, Christophe" uniqKey="Fraser C" first="Christophe" last="Fraser">Christophe Fraser</name><affiliation><nlm:aff id="A7">Department of Infectious Disease Epidemiology, Imperial College London, London, UK</nlm:aff></affiliation></author><author><name sortKey="Cohen, Myron S" sort="Cohen, Myron S" uniqKey="Cohen M" first="Myron S." last="Cohen">Myron S. 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Dennis</name><affiliation><nlm:aff id="A1">Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC</nlm:aff></affiliation></author><author><name sortKey="Herbeck, Joshua T" sort="Herbeck, Joshua T" uniqKey="Herbeck J" first="Joshua T." last="Herbeck">Joshua T. Herbeck</name><affiliation><nlm:aff id="A2">Department of Microbiology, University of Washington, Seattle, WA</nlm:aff></affiliation></author><author><name sortKey="Brown, Andrew Leigh" sort="Brown, Andrew Leigh" uniqKey="Brown A" first="Andrew Leigh" last="Brown">Andrew Leigh Brown</name><affiliation><nlm:aff id="A3">Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK</nlm:aff></affiliation></author><author><name sortKey="Kellam, Paul" sort="Kellam, Paul" uniqKey="Kellam P" first="Paul" last="Kellam">Paul Kellam</name><affiliation><nlm:aff id="A4">Wellcome Trust Sanger Institute, Cambridge, UK</nlm:aff></affiliation><affiliation><nlm:aff id="A5">Division of Infection and Immunity, University College London, London, UK</nlm:aff></affiliation></author><author><name sortKey="De Oliveira, Tulio" sort="De Oliveira, Tulio" uniqKey="De Oliveira T" first="Tulio" last="De Oliveira">Tulio De Oliveira</name><affiliation><nlm:aff id="A6">Wellcome Trust-Africa Centre for Health and Population Studies, University of Kwazula-Natal, ZA</nlm:aff></affiliation></author><author><name sortKey="Pillay, Deenan" sort="Pillay, Deenan" uniqKey="Pillay D" first="Deenan" last="Pillay">Deenan Pillay</name><affiliation><nlm:aff id="A5">Division of Infection and Immunity, University College London, London, UK</nlm:aff></affiliation></author><author><name sortKey="Fraser, Christophe" sort="Fraser, Christophe" uniqKey="Fraser C" first="Christophe" last="Fraser">Christophe Fraser</name><affiliation><nlm:aff id="A7">Department of Infectious Disease Epidemiology, Imperial College London, London, UK</nlm:aff></affiliation></author><author><name sortKey="Cohen, Myron S" sort="Cohen, Myron S" uniqKey="Cohen M" first="Myron S." last="Cohen">Myron S. Cohen</name><affiliation><nlm:aff id="A1">Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC</nlm:aff></affiliation></author></analytic><series><title level="j">Journal of acquired immune deficiency syndromes (1999)</title><idno type="ISSN">1525-4135</idno><idno type="eISSN">1944-7884</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population-level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics, and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics, and suggest potential solutions.</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>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">100892005</journal-id><journal-id journal-id-type="pubmed-jr-id">21821</journal-id><journal-id journal-id-type="nlm-ta">J Acquir Immune Defic Syndr</journal-id><journal-id journal-id-type="iso-abbrev">J. Acquir. Immune Defic. Syndr.</journal-id><journal-title-group><journal-title>Journal of acquired immune deficiency syndromes (1999)</journal-title></journal-title-group><issn pub-type="ppub">1525-4135</issn><issn pub-type="epub">1944-7884</issn></journal-meta><article-meta><article-id pub-id-type="pmid">24977473</article-id><article-id pub-id-type="pmc">4304655</article-id><article-id pub-id-type="doi">10.1097/QAI.0000000000000271</article-id><article-id pub-id-type="manuscript">NIHMS606671</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Phylogenetic studies of transmission dynamics in generalized HIV epidemics: An essential tool where the burden is greatest?</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Dennis</surname><given-names>Ann M.</given-names></name><xref rid="FN2" ref-type="author-notes">*</xref><xref ref-type="aff" rid="A1">a</xref></contrib><contrib contrib-type="author"><name><surname>Herbeck</surname><given-names>Joshua T.</given-names></name><xref rid="FN2" ref-type="author-notes">*</xref><xref ref-type="aff" rid="A2">b</xref></contrib><contrib contrib-type="author"><name><surname>Brown</surname><given-names>Andrew Leigh</given-names></name><xref ref-type="aff" rid="A3">c</xref></contrib><contrib contrib-type="author"><name><surname>Kellam</surname><given-names>Paul</given-names></name><xref ref-type="aff" rid="A4">d</xref><xref ref-type="aff" rid="A5">e</xref></contrib><contrib contrib-type="author"><name><surname>de Oliveira</surname><given-names>Tulio</given-names></name><xref ref-type="aff" rid="A6">f</xref></contrib><contrib contrib-type="author"><name><surname>Pillay</surname><given-names>Deenan</given-names></name><xref ref-type="aff" rid="A5">e</xref></contrib><contrib contrib-type="author"><name><surname>Fraser</surname><given-names>Christophe</given-names></name><xref ref-type="aff" rid="A7">g</xref></contrib><contrib contrib-type="author"><name><surname>Cohen</surname><given-names>Myron S.</given-names></name><xref ref-type="aff" rid="A1">a</xref></contrib></contrib-group><aff id="A1"><label>a</label>Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC</aff><aff id="A2"><label>b</label>Department of Microbiology, University of Washington, Seattle, WA</aff><aff id="A3"><label>c</label>Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK</aff><aff id="A4"><label>d</label>Wellcome Trust Sanger Institute, Cambridge, UK</aff><aff id="A5"><label>e</label>Division of Infection and Immunity, University College London, London, UK</aff><aff id="A6"><label>f</label>Wellcome Trust-Africa Centre for Health and Population Studies, University of Kwazula-Natal, ZA</aff><aff id="A7"><label>g</label>Department of Infectious Disease Epidemiology, Imperial College London, London, UK</aff><author-notes><corresp id="FN1">Correspondence: Ann M. Dennis, MD, 130 Mason Farm Drive, Suite 2115, CB 7030, Chapel Hill, NC 27999-7030, <email>adennis@med.unc.edu</email>, T 919.966.2536 F 919.966.6714</corresp><fn id="FN2" fn-type="equal"><label>*</label><p>Authors contributed equally</p></fn></author-notes><pub-date pub-type="nihms-submitted"><day>1</day><month>7</month><year>2014</year></pub-date><pub-date pub-type="ppub"><day>1</day><month>10</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>01</day><month>10</month><year>2015</year></pub-date><volume>67</volume><issue>2</issue><fpage>181</fpage><lpage>195</lpage><pmc-comment>elocation-id from pubmed: 10.1097/QAI.0000000000000271</pmc-comment>
<abstract><p id="P1">Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population-level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics, and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics, and suggest potential solutions.</p></abstract><kwd-group><kwd>HIV-1</kwd><kwd>molecular epidemiology</kwd><kwd>phylogenetic</kwd><kwd>transmission networks</kwd><kwd>Sub-Saharan Africa</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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