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DC Field | Value | Language |
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dc.contributor.author | Yinfeng Zhang | en_US |
dc.contributor.author | Chris Wymant | en_US |
dc.contributor.author | Oliver Laeyendecker | en_US |
dc.contributor.author | M. Kathryn Grabowski | en_US |
dc.contributor.author | Matthew Hall | en_US |
dc.contributor.author | Sarah Hudelson | en_US |
dc.contributor.author | Estelle Piwowar-Manning | en_US |
dc.contributor.author | Marybeth McCauley | en_US |
dc.contributor.author | Theresa Gamble | en_US |
dc.contributor.author | Mina C. Hosseinipour | en_US |
dc.contributor.author | Nagalingeswaran Kumarasamy | en_US |
dc.contributor.author | James G. Hakim | en_US |
dc.contributor.author | Johnstone Kumwenda | en_US |
dc.contributor.author | Lisa A. Mills | en_US |
dc.contributor.author | Breno R. Santos | en_US |
dc.contributor.author | Beatriz Grinsztejn | en_US |
dc.contributor.author | Jose H. Pilotto | en_US |
dc.contributor.author | Suwat Chariyalertsak | en_US |
dc.contributor.author | Joseph Makhema | en_US |
dc.contributor.author | Ying Q. Chen | en_US |
dc.contributor.author | Myron S. Cohen | en_US |
dc.contributor.author | Christophe Fraser | en_US |
dc.contributor.author | Susan H. Eshleman | en_US |
dc.date.accessioned | 2022-10-16T07:25:07Z | - |
dc.date.available | 2022-10-16T07:25:07Z | - |
dc.date.issued | 2021-01-01 | en_US |
dc.identifier.issn | 15376591 | en_US |
dc.identifier.issn | 10584838 | en_US |
dc.identifier.other | 2-s2.0-85100359827 | en_US |
dc.identifier.other | 10.1093/cid/ciz1247 | en_US |
dc.identifier.uri | https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85100359827&origin=inward | en_US |
dc.identifier.uri | http://cmuir.cmu.ac.th/jspui/handle/6653943832/77244 | - |
dc.description.abstract | Background: 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.subject | Medicine | en_US |
dc.title | Evaluation of phylogenetic methods for inferring the direction of human immunodeficiency virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052 | en_US |
dc.type | Journal | en_US |
article.title.sourcetitle | Clinical Infectious Diseases | en_US |
article.volume | 72 | en_US |
article.stream.affiliations | FHI 360 | en_US |
article.stream.affiliations | Botswana Harvard AIDS Institute Partnership | en_US |
article.stream.affiliations | The Voluntary Health Services, Chennai | en_US |
article.stream.affiliations | UNC Project-Malawi | en_US |
article.stream.affiliations | University of Malawi College of Medicine | en_US |
article.stream.affiliations | Hospital Nossa Senhora da Conceicao | en_US |
article.stream.affiliations | Godfrey Huggins School of Medicine | en_US |
article.stream.affiliations | Fundacao Oswaldo Cruz | en_US |
article.stream.affiliations | The University of North Carolina at Chapel Hill | en_US |
article.stream.affiliations | Instituto Nacional de Infectologia Evandro Chagas (INI) | en_US |
article.stream.affiliations | Centers for Disease Control and Prevention | en_US |
article.stream.affiliations | Nuffield Department of Medicine | en_US |
article.stream.affiliations | Fred Hutchinson Cancer Research Center | en_US |
article.stream.affiliations | Johns Hopkins School of Medicine | en_US |
article.stream.affiliations | Chiang Mai University | en_US |
Appears in Collections: | CMUL: Journal Articles |
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