| Author | Zhang, Yinfeng | |
| Author | Wymant, Chris | |
| Author | Laeyendecker, Oliver | |
| Author | Grabowski, M. Kathryn | |
| Author | Hall, Matthew | |
| Author | Hudelson, Sarah | |
| Author | Piwowar-Manning, Estelle | |
| Author | McCauley, Marybeth | |
| Author | Gamble, Theresa | |
| Author | Hosseinipour, Mina C. | |
| Author | Kumarasamy, Nagalingeswaran | |
| Author | Hakim, James G. | |
| Author | Kumwenda, Johnstone | |
| Author | Mills, Lisa A. | |
| Author | Santos, Breno R. | |
| Author | Grinsztejn, Beatriz | |
| Author | Pilotto, Jose H. | |
| Author | Chariyalertsak, Suwat | |
| Author | Makhema, Joseph | |
| Author | Chen, Ying Q. | |
| Author | Cohen, Myron S. | |
| Author | Fraser, Christophe | |
| Author | Eshleman, Susan H. | |
| Access date | 2020-01-16T15:47:54Z | |
| Available date | 2020-01-16T15:47:54Z | |
| Document date | 2020 | |
| Citation | ZHANG, Yinfeng et al.Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052. Clinical Infectious Diseases, p. 1-24, 2020. | |
| ISSN | 1058-4838 | |
| URI | https://www.arca.fiocruz.br/handle/icict/39278 | |
| Language | eng | en_US |
| Publisher | Oxford | |
| Rights | restricted access | |
| Title | Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052 | en_US |
| Type | Preprint | |
| DOI | 10.1093/cid/ciz1247 | |
| Abstract | BACKGROUND: Phylogenetic analysis can be used to assess 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 indexpartner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 trial (up to two 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 (one sample/person; group analysis) and all available samples (multi-sample 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 98/105 (93.3%) of the individual sample pairs, 99/105 (94.3%) sample pairs using group analysis, and 31 (96.9%) of the 32 couples using multi-sample 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 two individuals using whole-genome and pol NGS data. | en_US |
| Affilliation | Dept. of Pathology, Johns Hopkins Univ. School of Medicine, Baltimore, MD, USA. | |
| Affilliation | Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK | |
| Affilliation | Dept. of Medicine, Johns Hopkins Univ. School of Medicine, Baltimore, MD, USA | |
| Affilliation | Dept. of Pathology, Johns Hopkins Univ. School of Medicine, Baltimore, MD, USA | |
| Affilliation | Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK | |
| Affilliation | Dept. of Pathology, Johns Hopkins Univ. School of Medicine, Baltimore, MD, USA | |
| Affilliation | Dept. of Pathology, Johns Hopkins Univ. School of Medicine, Baltimore, MD, USA | |
| Affilliation | HPTN Leadership and Operations Center, FHI 360, Washington, DC, USA | |
| Affilliation | HPTN Leadership and Operations Center, FHI 360, Durham, NC, USA | |
| Affilliation | Division of Infectious Diseases, Univ. of North Carolina at Chapel Hill, Chapel Hill, NC, USA; UNC Project-Malawi, Institute for Global Health and Infectious Diseases, Lilongwe, Malawi | |
| Affilliation | CART CRS, Infectious Diseases Medical Centre, VHS, Chennai, India | |
| Affilliation | Dept. of Medicine, Univ. of Zimbabwe, Harare, Zimbabwe | |
| Affilliation | College of Medicine-Johns Hopkins Project, Blantyre, Malawi | |
| Affilliation | U.S. Centers for Disease Control and Prevention, HIV Research Branch, Kisumu, Kenya | |
| Affilliation | Hospital Nossa Senhora da Conceição. Departamento de Doenças Infecciosas. Porto Alegre, RS, Brasil | |
| Affilliation | Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST/AIDS. Rio de Janeiro, RJ, Brasil | |
| Affilliation | Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratorio de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, Brasil./ Hospital Geral de Nova Iguaçu. Nova Iguaçu, RJ, Brasil | |
| Affilliation | Research Institute for Health Sciences, Chiang Mai Univ., Chiang Mai, Thailand | |
| Affilliation | Botswana-Harvard AIDS Institute Partnership, Gaborone, Botswana | |
| Affilliation | Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA | |
| Affilliation | Dept. of Medicine, Univ. of North Carolina at Chapel Hill, Chapel Hill, NC, USA | |
| Affilliation | Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK | |
| Affilliation | Dept. of Pathology, Johns Hopkins Univ. School of Medicine, Baltimore, MD, USA | |
| Subject | HIV | en_US |
| Subject | HPTN 052 | en_US |
| Subject | Direction of transmission | en_US |
| Subject | Next generation sequencing | en_US |
| Subject | Phylogenetic analysis | en_US |
| Embargo date | 2030-06-01 | |
