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dc.contributor.authorMoyo, Sikhulile
dc.contributor.authorWilkinson, Eduan
dc.contributor.authorVandormael, Alain
dc.contributor.authorWang, Rui
dc.contributor.authorWeng, Jia
dc.contributor.authorKotokwe, Kenanao
dc.contributor.authorGaseitsiwe, Simani
dc.contributor.authorMusonda, Rosemary
dc.contributor.authorMakhema, Joseph
dc.contributor.authorEssex, Max
dc.contributor.authorEngelbrecht, Susan
dc.contributor.authorde Oliveira, Tulio
dc.contributor.authorNovitsky, Vladimir
dc.date.accessioned2019-10-15T18:22:16Z
dc.date.issued2017
dc.identifier.citationMoyo, Sikhulile, Eduan Wilkinson, Alain Vandormael, Rui Wang, Jia Weng, Kenanao P. Kotokwe, Simani Gaseitsiwe, et al. 2017. “Pairwise Diversity and tMRCA as Potential Markers for HIV Infection Recency.” Medicine 96 (6): e6041. https://doi.org/10.1097/md.0000000000006041.
dc.identifier.issn1549-1277
dc.identifier.issn1549-1676
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:41552034*
dc.description.abstractIntrahost human immunodeficiency virus (HIV)-1 diversity increases linearly over time. We assessed the extent to which mean pairwise distances and the time to the most recent common ancestor (tMRCA) inferred from intrahost HIV-1C env sequences were associated with the estimated time of HIV infection. Data from a primary HIV-1C infection study in Botswana were used for this analysis (N=42). A total of 2540 HIV-1C env gp120 variable loop region 1 to conserved region 5 (V1C5) of the HIV-1 envelope gp120 viral sequences were generated by single genome amplification and sequencing, with an average of 61 viral sequences per participant and 11 sequences per time point per participant. Raw pairwise distances were calculated for each time point and participant using the ape package in R software. The tMRCA was estimated using phylogenetic inference implemented in Bayesian Evolutionary Analysis by Sampling Trees v1.8.2. Pairwise distances and tMRCA were significantly associated with the estimated time since HIV infection (both P<0.001). Taking into account multiplicity of HIV infection strengthened these associations. HIV-1C env-based pairwise distances and tMRCA can be used as potential markers for HIV recency. However, the tMRCA estimates demonstrated no advantage over the pairwise distances estimates.
dc.language.isoen_US
dc.publisherPublic Library of Science
dash.licenseLAA
dc.titlePairwise diversity and tMRCA as potential markers for HIV infection recency
dc.typeJournal Article
dc.description.versionVersion of Record
dc.relation.journalPLoS Medicine
dash.depositing.authorWang, Rui::bf1a234ca95ae1f0959d1c158d4f8aa4::600
dc.date.available2019-10-15T18:22:16Z
dash.workflow.comments1Science Serial ID 80637
dc.identifier.doi10.1097/MD.0000000000006041
dash.source.volume96;6


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