Please use this identifier to cite or link to this item: http://cmuir.cmu.ac.th/jspui/handle/6653943832/77244
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dc.contributor.authorYinfeng Zhangen_US
dc.contributor.authorChris Wymanten_US
dc.contributor.authorOliver Laeyendeckeren_US
dc.contributor.authorM. Kathryn Grabowskien_US
dc.contributor.authorMatthew Hallen_US
dc.contributor.authorSarah Hudelsonen_US
dc.contributor.authorEstelle Piwowar-Manningen_US
dc.contributor.authorMarybeth McCauleyen_US
dc.contributor.authorTheresa Gambleen_US
dc.contributor.authorMina C. Hosseinipouren_US
dc.contributor.authorNagalingeswaran Kumarasamyen_US
dc.contributor.authorJames G. Hakimen_US
dc.contributor.authorJohnstone Kumwendaen_US
dc.contributor.authorLisa A. Millsen_US
dc.contributor.authorBreno R. Santosen_US
dc.contributor.authorBeatriz Grinsztejnen_US
dc.contributor.authorJose H. Pilottoen_US
dc.contributor.authorSuwat Chariyalertsaken_US
dc.contributor.authorJoseph Makhemaen_US
dc.contributor.authorYing Q. Chenen_US
dc.contributor.authorMyron S. Cohenen_US
dc.contributor.authorChristophe Fraseren_US
dc.contributor.authorSusan H. Eshlemanen_US
dc.date.accessioned2022-10-16T07:25:07Z-
dc.date.available2022-10-16T07:25:07Z-
dc.date.issued2021-01-01en_US
dc.identifier.issn15376591en_US
dc.identifier.issn10584838en_US
dc.identifier.other2-s2.0-85100359827en_US
dc.identifier.other10.1093/cid/ciz1247en_US
dc.identifier.urihttps://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85100359827&origin=inwarden_US
dc.identifier.urihttp://cmuir.cmu.ac.th/jspui/handle/6653943832/77244-
dc.description.abstractBackground: Phylogenetic analysis can be used to assess human immunodeficiency virus (HIV) transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction. Methods: Complete next-generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 study (up to 2 samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (1 sample/person; group analysis), and all available samples (multisample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env). Results: Using whole-genome NGS data, transmission direction was inferred correctly (index to partner) for 98 of 105 (93.3%) of the individual sample pairs, 99 of 105 (94.3%) sample pairs using group analysis, and 31 of the 32 couples (96.9%) using multisample group analysis. There were no cases where the incorrect transmission direction (partner to index) was inferred. The accuracy of the method was higher with greater time between index and partner sample collection. Pol region sequences performed better than env or gag sequences for inferring transmission direction. Conclusions: We demonstrate the potential of a phylogenetic method to infer the direction of HIV transmission between 2 individuals using whole-genome and pol NGS data.en_US
dc.subjectMedicineen_US
dc.titleEvaluation of phylogenetic methods for inferring the direction of human immunodeficiency virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052en_US
dc.typeJournalen_US
article.title.sourcetitleClinical Infectious Diseasesen_US
article.volume72en_US
article.stream.affiliationsFHI 360en_US
article.stream.affiliationsBotswana Harvard AIDS Institute Partnershipen_US
article.stream.affiliationsThe Voluntary Health Services, Chennaien_US
article.stream.affiliationsUNC Project-Malawien_US
article.stream.affiliationsUniversity of Malawi College of Medicineen_US
article.stream.affiliationsHospital Nossa Senhora da Conceicaoen_US
article.stream.affiliationsGodfrey Huggins School of Medicineen_US
article.stream.affiliationsFundacao Oswaldo Cruzen_US
article.stream.affiliationsThe University of North Carolina at Chapel Hillen_US
article.stream.affiliationsInstituto Nacional de Infectologia Evandro Chagas (INI)en_US
article.stream.affiliationsCenters for Disease Control and Preventionen_US
article.stream.affiliationsNuffield Department of Medicineen_US
article.stream.affiliationsFred Hutchinson Cancer Research Centeren_US
article.stream.affiliationsJohns Hopkins School of Medicineen_US
article.stream.affiliationsChiang Mai Universityen_US
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