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most_recent_publications.xml
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<?xml version="1.0" ?>
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<Year>2016</Year>
<Month>10</Month>
<Day>07</Day>
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<DateRevised>
<Year>2017</Year>
<Month>02</Month>
<Day>24</Day>
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<Volume>12</Volume>
<Issue>10</Issue>
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<Year>2016</Year>
<Month>Oct</Month>
</PubDate>
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<Title>PLoS computational biology</Title>
<ISOAbbreviation>PLoS Comput. Biol.</ISOAbbreviation>
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<ArticleTitle>Retrospective Parameter Estimation and Forecast of Respiratory Syncytial Virus in the United States.</ArticleTitle>
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<ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pcbi.1005133</ELocationID>
<Abstract>
<AbstractText>Recent studies have shown that systems combining mathematical modeling and Bayesian inference methods can be used to generate real-time forecasts of future infectious disease incidence. Here we develop such a system to study and forecast respiratory syncytial virus (RSV). RSV is the most common cause of acute lower respiratory infection and bronchiolitis. Advanced warning of the epidemic timing and volume of RSV patient surges has the potential to reduce well-documented delays of treatment in emergency departments. We use a susceptible-infectious-recovered (SIR) model in conjunction with an ensemble adjustment Kalman filter (EAKF) and ten years of regional U.S. specimen data provided by the Centers for Disease Control and Prevention. The data and EAKF are used to optimize the SIR model and i) estimate critical epidemiological parameters over the course of each outbreak and ii) generate retrospective forecasts. The basic reproductive number, R0, is estimated at 3.0 (standard deviation 0.6) across all seasons and locations. The peak magnitude of RSV outbreaks is forecast with nearly 70% accuracy (i.e. nearly 70% of forecasts within 25% of the actual peak), four weeks before the predicted peak. This work represents a first step in the development of a real-time RSV prediction system.</AbstractText>
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<LastName>Reis</LastName>
<ForeName>Julia</ForeName>
<Initials>J</Initials>
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<Affiliation>Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America.</Affiliation>
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<LastName>Shaman</LastName>
<ForeName>Jeffrey</ForeName>
<Initials>J</Initials>
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<Affiliation>Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America.</Affiliation>
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<CommentsCorrectionsList>
<CommentsCorrections RefType="Cites">
<RefSource>Pediatr Crit Care Med. 2007 Jul;8(4):317-23</RefSource>
<PMID Version="1">17545931</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Am J Respir Cell Mol Biol. 2010 Jun;42(6):697-705</RefSource>
<PMID Version="1">19635930</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Pediatrics. 2014 Nov;134(5):e1474-502</RefSource>
<PMID Version="1">25349312</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20425-30</RefSource>
<PMID Version="1">23184969</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>PLoS One. 2015 Mar 24;10(3):e0115674</RefSource>
<PMID Version="1">25803450</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Pediatrics. 2007 Mar;119(3):611</RefSource>
<PMID Version="1">17332214</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>PLoS Comput Biol. 2015 Jul 30;11(7):e1004383</RefSource>
<PMID Version="1">26226185</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Ann Emerg Med. 2011 Mar;57(3):191-200.e1-7</RefSource>
<PMID Version="1">21035903</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Sci Transl Med. 2015 Nov 4;7(312):312fs44</RefSource>
<PMID Version="1">26537253</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Influenza Other Respir Viruses. 2015 Sep;9(5):225-33</RefSource>
<PMID Version="1">25980600</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Am J Dis Child. 1986 Jun;140(6):543-6</RefSource>
<PMID Version="1">3706232</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Pediatr. 1976 Jul;89(1):11-5</RefSource>
<PMID Version="1">180274</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Epidemiol Infect. 2015 Mar;143(4):804-12</RefSource>
<PMID Version="1">24901443</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Antiviral Res. 2004 Sep;63(3):191-6</RefSource>
<PMID Version="1">15451187</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Ann Emerg Med. 2010 Sep;56(3):261-9</RefSource>
<PMID Version="1">20619500</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Am J Respir Crit Care Med. 2004 Apr 1;169(7):801-5</RefSource>
<PMID Version="1">14742302</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Pediatrics. 2010 Jul;126(1):e116-23</RefSource>
<PMID Version="1">20547651</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>West J Emerg Med. 2015 Jan;16(1):85-8</RefSource>
<PMID Version="1">25671015</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Pediatr Infect Dis J. 2012 Jan;31(1):5-9</RefSource>
<PMID Version="1">21817948</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Pediatrics. 2004 Sep;114(3):805-16</RefSource>
<PMID Version="1">15342857</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>PLoS Comput Biol. 2015 Aug 28;11(8):e1004382</RefSource>
<PMID Version="1">26317693</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Epidemiol Infect. 2016 Jun;144(8):1622-33</RefSource>
<PMID Version="1">26732801</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Math Biosci. 2007 Sep;209(1):222-39</RefSource>
<PMID Version="1">17335858</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Healthc Manag. 2012 May-Jun;57(3):167-80; discussion 180-1</RefSource>
<PMID Version="1">22724375</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Nat Commun. 2013;4:2837</RefSource>
<PMID Version="1">24302074</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Pediatr Pulmonol. 1998 Dec;26(6):424-8</RefSource>
<PMID Version="1">9888217</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Aging health. 2009 Dec 1;5(6):775</RefSource>
<PMID Version="1">20174457</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>PLoS One. 2010 Apr 14;5(4):e10036</RefSource>
<PMID Version="1">20418945</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Math Biosci. 2001 Aug;172(2):95-113</RefSource>
<PMID Version="1">11520501</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Ann Emerg Med. 2004 Dec;44(6):586-8</RefSource>
<PMID Version="1">15573033</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Emerg Med. 2006 Apr;30(3):269-76</RefSource>
<PMID Version="1">16677976</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>N Engl J Med. 2009 Feb 5;360(6):588-98</RefSource>
<PMID Version="1">19196675</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>PLoS Curr. 2014 Oct 31;6:null</RefSource>
<PMID Version="1">25642378</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Am J Epidemiol. 1983 Apr;117(4):467-74</RefSource>
<PMID Version="1">6404161</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Sci Transl Med. 2013 May 15;5(185):185ps8</RefSource>
<PMID Version="1">23677590</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>PLoS Pathog. 2015 Jan 08;11(1):e1004591</RefSource>
<PMID Version="1">25569275</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>PLoS Comput Biol. 2014 Apr 24;10(4):e1003583</RefSource>
<PMID Version="1">24762780</PMID>
</CommentsCorrections>
</CommentsCorrectionsList>
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<ArticleId IdType="doi">10.1371/journal.pcbi.1005133</ArticleId>
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<Year>2016</Year>
<Month>12</Month>
<Day>23</Day>
</DateCreated>
<DateRevised>
<Year>2017</Year>
<Month>02</Month>
<Day>20</Day>
</DateRevised>
<Article PubModel="Electronic">
<Journal>
<ISSN IssnType="Electronic">2045-2322</ISSN>
<JournalIssue CitedMedium="Internet">
<Volume>6</Volume>
<PubDate>
<Year>2016</Year>
<Month>Dec</Month>
<Day>23</Day>
</PubDate>
</JournalIssue>
<Title>Scientific reports</Title>
<ISOAbbreviation>Sci Rep</ISOAbbreviation>
</Journal>
<ArticleTitle>Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.</ArticleTitle>
<Pagination>
<MedlinePgn>39489</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1038/srep39489</ELocationID>
<Abstract>
<AbstractText>HIV molecular epidemiology studies analyse viral pol gene sequences due to their availability, but whole genome sequencing allows to use other genes. We aimed to determine what gene(s) provide(s) the best approximation to the real phylogeny by analysing a simulated epidemic (created as part of the PANGEA_HIV project) with a known transmission tree. We sub-sampled a simulated dataset of 4662 sequences into different combinations of genes (gag-pol-env, gag-pol, gag, pol, env and partial pol) and sampling depths (100%, 60%, 20% and 5%), generating 100 replicates for each case. We built maximum-likelihood trees for each combination using RAxML (GTR + Γ), and compared their topologies to the corresponding true tree's using CompareTree. The accuracy of the trees was significantly proportional to the length of the sequences used, with the gag-pol-env datasets showing the best performance and gag and partial pol sequences showing the worst. The lowest sampling depths (20% and 5%) greatly reduced the accuracy of tree reconstruction and showed high variability among replicates, especially when using the shortest gene datasets. In conclusion, using longer sequences derived from nearly whole genomes will improve the reliability of phylogenetic reconstruction. With low sample coverage, results can be highly variable, particularly when based on short sequences.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Yebra</LastName>
<ForeName>Gonzalo</ForeName>
<Initials>G</Initials>
<AffiliationInfo>
<Affiliation>Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Hodcroft</LastName>
<ForeName>Emma B</ForeName>
<Initials>EB</Initials>
<AffiliationInfo>
<Affiliation>Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Ragonnet-Cronin</LastName>
<ForeName>Manon L</ForeName>
<Initials>ML</Initials>
<AffiliationInfo>
<Affiliation>Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Pillay</LastName>
<ForeName>Deenan</ForeName>
<Initials>D</Initials>
<AffiliationInfo>
<Affiliation>Wellcome Trust-Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Durban, South Africa.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Brown</LastName>
<ForeName>Andrew J Leigh</ForeName>
<Initials>AJ</Initials>
<AffiliationInfo>
<Affiliation>Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<CollectiveName>PANGEA_HIV Consortium</CollectiveName>
</Author>
<Author ValidYN="Y">
<CollectiveName>ICONIC Project</CollectiveName>
</Author>
</AuthorList>
<Language>eng</Language>
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<Grant>
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<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
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<Month>12</Month>
<Day>23</Day>
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</MedlineJournalInfo>
<CommentsCorrectionsList>
<CommentsCorrections RefType="Cites">
<RefSource>J Mol Evol. 2004 Nov;59(5):709-17</RefSource>
<PMID Version="1">15693627</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS. 1992 Aug;6(8):869-74</RefSource>
<PMID Version="1">1418784</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>BMC Bioinformatics. 2013 Nov 06;14:317</RefSource>
<PMID Version="1">24191891</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Lancet Infect Dis. 2015 Mar;15(3):259-61</RefSource>
<PMID Version="1">25749217</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS. 2005 Sep 23;19(14):1551-2</RefSource>
<PMID Version="1">16135914</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS Res Hum Retroviruses. 2015 May;31(5):531-42</RefSource>
<PMID Version="1">25560745</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS. 2004 Mar 26;18(5):719-28</RefSource>
<PMID Version="1">15075506</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>BMJ. 1994 Jan 15;308(6922):171-3</RefSource>
<PMID Version="1">8312767</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Nature. 1993 Feb 25;361(6414):691</RefSource>
<PMID Version="1">8441463</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS. 1992 Sep;6(9):983-9</RefSource>
<PMID Version="1">1388911</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS Res Hum Retroviruses. 2016 May;32(5):471-4</RefSource>
<PMID Version="1">26881451</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS. 2011 May 15;25(8):1035-9</RefSource>
<PMID Version="1">21505318</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>BMC Bioinformatics. 2014 May 07;15:133</RefSource>
<PMID Version="1">24885610</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Mol Biol Evol. 2012 Aug;29(8):1969-73</RefSource>
<PMID Version="1">22367748</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>BMC Infect Dis. 2014 Jul 21;14:407</RefSource>
<PMID Version="1">25047543</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Bioinformatics. 2014 May 1;30(9):1312-3</RefSource>
<PMID Version="1">24451623</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS. 2010 May 15;24(8):1203-12</RefSource>
<PMID Version="1">20395786</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Infect Dis. 2011 Nov;204(9):1463-9</RefSource>
<PMID Version="1">21921202</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>BMJ. 2012 Aug 21;345:e5253</RefSource>
<PMID Version="1">22915687</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS Res Hum Retroviruses. 2005 Jun;21(6):575-9</RefSource>
<PMID Version="1">15989463</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10864-9</RefSource>
<PMID Version="1">8855273</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Science. 2014 Oct 3;346(6205):56-61</RefSource>
<PMID Version="1">25278604</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Infect Dis. 2016 May 1;213(9):1410-8</RefSource>
<PMID Version="1">26704616</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Sci Rep. 2016 Jun 14;6:27580</RefSource>
<PMID Version="1">27297284</PMID>
</CommentsCorrections>
</CommentsCorrectionsList>
<InvestigatorList>
<Investigator ValidYN="Y">
<LastName>Fraser</LastName>
<ForeName>Christophe</ForeName>
<Initials>C</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Kellam</LastName>
<ForeName>Paul</ForeName>
<Initials>P</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>de Oliveira</LastName>
<ForeName>Tulio</ForeName>
<Initials>T</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Dennis</LastName>
<ForeName>Ann</ForeName>
<Initials>A</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Hoppe</LastName>
<ForeName>Anne</ForeName>
<Initials>A</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Kityo</LastName>
<ForeName>Cissy</ForeName>
<Initials>C</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Frampton</LastName>
<ForeName>Dan</ForeName>
<Initials>D</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Ssemwanga</LastName>
<ForeName>Deogratius</ForeName>
<Initials>D</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Tanser</LastName>
<ForeName>Frank</ForeName>
<Initials>F</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Keshani</LastName>
<ForeName>Jagoda</ForeName>
<Initials>J</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Lingappa</LastName>
<ForeName>Jairam</ForeName>
<Initials>J</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Herbeck</LastName>
<ForeName>Joshua</ForeName>
<Initials>J</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Wawer</LastName>
<ForeName>Maria</ForeName>
<Initials>M</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Essex</LastName>
<ForeName>Max</ForeName>
<Initials>M</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Cohen</LastName>
<ForeName>Myron S</ForeName>
<Initials>MS</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Paton</LastName>
<ForeName>Nicholas</ForeName>
<Initials>N</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Ratmann</LastName>
<ForeName>Oliver</ForeName>
<Initials>O</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Kaleebu</LastName>
<ForeName>Pontiano</ForeName>
<Initials>P</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Hayes</LastName>
<ForeName>Richard</ForeName>
<Initials>R</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Fidler</LastName>
<ForeName>Sarah</ForeName>
<Initials>S</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Quinn</LastName>
<ForeName>Thomas</ForeName>
<Initials>T</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Novitsky</LastName>
<ForeName>Vladimir</ForeName>
<Initials>V</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Haywards</LastName>
<ForeName>Andrew</ForeName>
<Initials>A</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Nastouli</LastName>
<ForeName>Eleni</ForeName>
<Initials>E</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Morris</LastName>
<ForeName>Steven</ForeName>
<Initials>S</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Clark</LastName>
<ForeName>Duncan</ForeName>
<Initials>D</Initials>
</Investigator>
<Investigator ValidYN="Y">
<LastName>Kozlakidis</LastName>
<ForeName>Zisis</ForeName>
<Initials>Z</Initials>
</Investigator>
</InvestigatorList>
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<History>
<PubMedPubDate PubStatus="received">
<Year>2016</Year>
<Month>06</Month>
<Day>14</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted">
<Year>2016</Year>
<Month>11</Month>
<Day>21</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>2016</Year>
<Month>12</Month>
<Day>24</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<Year>2016</Year>
<Month>12</Month>
<Day>23</Day>
<Hour>6</Hour>
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<Year>2016</Year>
<Month>12</Month>
<Day>23</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<ArticleIdList>
<ArticleId IdType="pubmed">28008945</ArticleId>
<ArticleId IdType="pii">srep39489</ArticleId>
<ArticleId IdType="doi">10.1038/srep39489</ArticleId>
<ArticleId IdType="pmc">PMC5180198</ArticleId>
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</PubmedData>
</PubmedArticle>
<PubmedArticle>
<MedlineCitation Status="In-Data-Review" Owner="NLM">
<PMID Version="1">27774305</PMID>
<DateCreated>
<Year>2016</Year>
<Month>10</Month>
<Day>24</Day>
</DateCreated>
<DateRevised>
<Year>2017</Year>
<Month>02</Month>
<Day>20</Day>
</DateRevised>
<Article PubModel="Electronic-eCollection">
<Journal>
<JournalIssue CitedMedium="Print">
<Volume>2</Volume>
<Issue>2</Issue>
<PubDate>
<Year>2016</Year>
<Month>Jul</Month>
</PubDate>
</JournalIssue>
<Title>Virus evolution</Title>
<ISOAbbreviation>Virus Evol</ISOAbbreviation>
</Journal>
<ArticleTitle>Compartmentalized HIV rebound in the central nervous system after interruption of antiretroviral therapy.</ArticleTitle>
<Pagination>
<MedlinePgn>vew020</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>To design effective eradication strategies, it may be necessary to target HIV reservoirs in anatomic compartments other than blood. This study examined HIV RNA rebound following interruption of antiretroviral therapy (ART) in blood and cerebrospinal fluid (CSF) to determine whether the central nervous system (CNS) might serve as an independent source of resurgent viral replication. Paired blood and CSF samples were collected longitudinally from 14 chronically HIV-infected individuals undergoing ART interruption. HIV env (C2-V3), gag (p24) and pol (reverse transcriptase) were sequenced from cell-free HIV RNA and cell-associated HIV DNA in blood and CSF using the Roche 454 FLX Titanium platform. Comprehensive sequence and phylogenetic analyses were performed to search for evidence of unique or differentially represented viral subpopulations emerging in CSF supernatant as compared with blood plasma. Using a conservative definition of compartmentalization based on four distinct statistical tests, nine participants presented a compartmentalized HIV RNA rebound within the CSF after interruption of ART, even when sampled within 2 weeks from viral rebound. The degree and duration of viral compartmentalization varied considerably between subjects and between time-points within a subject. In 10 cases, we identified viral populations within the CSF supernatant at the first sampled time-point after ART interruption, which were phylogenetically distinct from those present in the paired blood plasma and mostly persisted over time (when longitudinal time-points were available). Our data suggest that an independent source of HIV RNA contributes to viral rebound within the CSF after treatment interruption. The most likely source of compartmentalized HIV RNA is a CNS reservoir that would need to be targeted to achieve complete HIV eradication.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Gianella</LastName>
<ForeName>Sara</ForeName>
<Initials>S</Initials>
<AffiliationInfo>
<Affiliation>Department of Medicine, University of California, San Diego, La Jolla, CA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Kosakovsky Pond</LastName>
<ForeName>Sergei L</ForeName>
<Initials>SL</Initials>
<AffiliationInfo>
<Affiliation>Department of Biology, Temple University, Philadelphia, PA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Oliveira</LastName>
<ForeName>Michelli F</ForeName>
<Initials>MF</Initials>
<AffiliationInfo>
<Affiliation>Department of Medicine, University of California, San Diego, La Jolla, CA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Scheffler</LastName>
<ForeName>Konrad</ForeName>
<Initials>K</Initials>
<AffiliationInfo>
<Affiliation>Department of Medicine, University of California, San Diego, La Jolla, CA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Strain</LastName>
<ForeName>Matt C</ForeName>
<Initials>MC</Initials>
<AffiliationInfo>
<Affiliation>Department of Medicine, University of California, San Diego, La Jolla, CA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>De la Torre</LastName>
<ForeName>Antonio</ForeName>
<Initials>A</Initials>
<AffiliationInfo>
<Affiliation>Departments of Neurosciences and Psychiatry, University of California, San Diego, La Jolla, CA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Letendre</LastName>
<ForeName>Scott</ForeName>
<Initials>S</Initials>
<AffiliationInfo>
<Affiliation>Department of Medicine, University of California, San Diego, La Jolla, CA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Smith</LastName>
<ForeName>Davey M</ForeName>
<Initials>DM</Initials>
<AffiliationInfo>
<Affiliation>Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, San Diego, CA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Ellis</LastName>
<ForeName>Ronald J</ForeName>
<Initials>RJ</Initials>
<AffiliationInfo>
<Affiliation>Departments of Neurosciences and Psychiatry, University of California, San Diego, La Jolla, CA, USA.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y">
<Grant>
<GrantID>K24 AI100665</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>R01 MH101012</GrantID>
<Acronym>MH</Acronym>
<Agency>NIMH NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>R25 MH081482</GrantID>
<Acronym>MH</Acronym>
<Agency>NIMH NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>R01 GM093939</GrantID>
<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>U01 AI043638</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>U01 AI068636</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>T32 AI007384</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>DP1 DA034978</GrantID>
<Acronym>DA</Acronym>
<Agency>NIDA NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>P30 AI027763</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>P30 MH062512</GrantID>
<Acronym>MH</Acronym>
<Agency>NIMH NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>P30 AI036214</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>K01 AI110181</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>U01 GM110749</GrantID>
<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>R01 MH097520</GrantID>
<Acronym>MH</Acronym>
<Agency>NIMH NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>P01 AI074621</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>UM1 AI068636</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant>
<GrantID>R24 AI106039</GrantID>
<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
</Grant>
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<Year>2016</Year>
<Month>08</Month>
<Day>03</Day>
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<Country>England</Country>
<MedlineTA>Virus Evol</MedlineTA>
<NlmUniqueID>101664675</NlmUniqueID>
<ISSNLinking>2057-1577</ISSNLinking>
</MedlineJournalInfo>
<CommentsCorrectionsList>
<CommentsCorrections RefType="Cites">
<RefSource>J Virol. 2005 Feb;79(3):1772-88</RefSource>
<PMID Version="1">15650202</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Neurovirol. 2012 Apr;18(2):81-90</RefSource>
<PMID Version="1">22528397</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Nat Med. 2003 Jun;9(6):727-8</RefSource>
<PMID Version="1">12754504</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>PLoS One. 2010 Mar 10;5(3):e9490</RefSource>
<PMID Version="1">20224823</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Acquir Immune Defic Syndr. 2007 Sep 1;46(1):39-47</RefSource>
<PMID Version="1">17972364</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS. 2012 Jan 14;26(2):157-65</RefSource>
<PMID Version="1">22045341</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Nat Med. 1999 May;5(5):512-7</RefSource>
<PMID Version="1">10229227</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>BMC Bioinformatics. 2004 Aug 19;5:113</RefSource>
<PMID Version="1">15318951</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Mol Biol Evol. 1993 May;10(3):512-26</RefSource>
<PMID Version="1">8336541</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Clin Microbiol. 2000 Feb;38(2):630-4</RefSource>
<PMID Version="1">10655358</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Infect Dis. 2014 Apr 1;209(7):1032-8</RefSource>
<PMID Version="1">24273040</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Science. 2009 Mar 6;323(5919):1304-7</RefSource>
<PMID Version="1">19265012</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Neuroimmunol. 2006 Oct;179(1-2):180-5</RefSource>
<PMID Version="1">16901548</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Proc Natl Acad Sci U S A. 2008 May 27;105(21):7552-7</RefSource>
<PMID Version="1">18490657</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Acquir Immune Defic Syndr. 2006 Sep;43(1):27-34</RefSource>
<PMID Version="1">16878047</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Neurovirol. 2005 Apr;11(2):180-9</RefSource>
<PMID Version="1">16036796</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS. 2005 Jan 3;19(1):1-14</RefSource>
<PMID Version="1">15627028</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Genetics. 1992 Oct;132(2):583-9</RefSource>
<PMID Version="1">1427045</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Genetics. 1989 Nov;123(3):603-13</RefSource>
<PMID Version="1">2599370</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>AIDS Rev. 2006 Jul-Sep;8(3):125-40</RefSource>
<PMID Version="1">17078483</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Science. 1997 Nov 14;278(5341):1291-5</RefSource>
<PMID Version="1">9360926</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Virology. 2009 Mar 1;385(1):204-8</RefSource>
<PMID Version="1">19100592</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>Mol Biol Evol. 2006 Oct;23(10):1891-901</RefSource>
<PMID Version="1">16818476</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites">
<RefSource>J Virol. 2007 Jun;81(12):6643-51</RefSource>