Please use this identifier to cite or link to this item: https://www.arca.fiocruz.br/handle/icict/31429
Title: Phylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort
Authors: Rose, Rebecca
Hall, Matthew
Redd, Andrew D.
Lamers, Susanna
Barbier, Andrew E.
Porcella, Stephen F.
Hudelson, Sarah E.
Piwowar-Manning, Estelle
McCauley, Marybeth
Gamble, Theresa
Wilson, Ethan A.
Kumwenda, Johnstone
Hosseinipour, Mina C.
Hakim, James G.
Kumarasamy, Nagalingeswaran
Chariyalertsak, Suwat
Pilotto, Jose H.
Grinsztejn, Beatriz
Mills, Lisa A.
Makhema, Joseph
Santos, Breno R.
Chen, Ying Q.
Quinn, Thomas C.
Fraser, Christophe
Cohen, Myron S.
Eshleman, Susan H.
Laeyendecker, Oliver
Affilliation: BioInfoExperts. Thibodaux, LA, USA.
Oxford University. Big Data Institute. Oxford, UK.
National Institutes of Health. National Institute of Allergy and Infectious Diseases. Division of Intramural Research. Laboratory of Immunoregulation./ Johns Hopkins University. School of Medicine. Department of Medicine. Baltimore, MD, USA.
BioInfoExperts. Thibodaux, LA, USA.
BioInfoExperts. Thibodaux, LA, USA.
National Institutes of Health. National Institute of Allergy and Infectious Diseases. Division of Intramural Research. Rocky Mountain Laboratories. Research Technologies Section. Genomics Unit. Hamilton, MT, USA.
Johns Hopkins Univ. School of Medicine. Dept. of Pathology. Baltimore, MD, USA.
Johns Hopkins Univ. School of Medicine. Dept. of Pathology. Baltimore, MD, USA.
FHI360. Science Facilitation Department. Durham, NC, USA.
FHI360. Science Facilitation Department. Durham, NC, USA.
Fred Hutchinson Cancer Research Institute. Vaccine and Infectious Disease Science Division. Seattle, WA, USA.
Johns Hopkins Project. College of Medicine. Blantyre, Malawi.
Univ. of North Carolina at Chapel Hill. Dept of Medicine. Chapel Hill, NC, USA.
University of Zimbabwe. Harare, Zimbabwe.
YRGCARE Medical Centre. Chennai, India.
Chiang Mai University. Research Institute for Health Sciences. Chiang Mai, Thailand.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular./ Hospital Geral de Nova Iguaçu. Rio de Janeiro, RJ, Brasil.
Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST/AIDS. Rio de Janeiro, RJ, Brasil.
Division of HIV/AIDS Prevention. Centers for Disease Control and Prevention (CDC). / HIV Research Branch. KEMRI–CDC Research and Public Health Collaboration. Kisumu, Kenya.
Botswana Harvard AIDS Institute. Gabarone, Botswana.
Hospital Nossa Senhora da Conceição. Serviço de Infectologia. Porto Alegre, RS, Brasil.
Fred Hutchinson Cancer Research Institute. Vaccine and Infectious Disease Science Division. Seattle, WA, USA.
National Institutes of Health. National Institute of Allergy and Infectious Diseases. Division of Intramural Research. Laboratory of Immunoregulation./ Johns Hopkins University. School of Medicine. Department of Medicine./ Johns Hopkins Bloomberg. School of Public Health. Department of Epidemiology. Baltimore, MD, USA.
Oxford University. Big Data Institute. Oxford, UK.
Univ. of North Carolina at Chapel Hill. Dept of Medicine. Chapel Hill, NC, USA.
Johns Hopkins Univ. School of Medicine. Dept. of Pathology. Baltimore, MD, USA.
National Institutes of Health. National Institute of Allergy and Infectious Diseases. Division of Intramural Research. Laboratory of Immunoregulation./ Johns Hopkins University. School of Medicine. Department of Medicine./ Johns Hopkins Bloomberg. School of Public Health. Department of Epidemiology. Baltimore, MD, USA.
Abstract: BACKGROUND: We evaluated use of phylogenetic methods to predict the direction of HIV transmission. METHODS: For 33 index-partner pairs with genetically-linked infection, samples were collected from partners and indexes close to time of partners' seroconversion (SC); 31 indexes also had an earlier sample. Phylogenies were inferred using env next-generation sequences (one tree per pair/subtype). Direction of transmission (DoT) predicted from each tree was classified as correct or incorrect based on which sequences (index or partner) were closest to the root. DoT was also assessed using maximum-parsimony to infer ancestral node states for 100 bootstrap trees. RESULTS: DoT was predicted correctly for both single pair and subtype-specific trees in 22 pairs (67%) using SC samples and 23 pairs (74%) using early index samples. DoT was predicted incorrectly for four pairs (15%) using SC or early index samples. In the bootstrap analysis, DoT was predicted correctly for 18 pairs (55%) using SC samples and 24 pairs (73%) using early index samples. DoT was predicted incorrectly for seven pairs (21%) using SC samples and four pairs (13%) using early index samples. CONCLUSIONS: Phylogenetic methods based solely on tree topology of HIV env sequences, particularly without consideration of phylogenetic uncertainty, may be insufficient for determining DoT.
Keywords: Networks
Epidemiology
Viral dynamics
Issue Date: 2018
Publisher: Oxford
Citation: ROSE, R. et al. Phylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort. Journal of Infectious Diseases, p. 1-26, 2018.
DOI: 10.1093/infdis/jiy734
ISSN: 0022-1899
Copyright: restricted access
Revised document: Não
Publication status: Publicado
Appears in Collections:IOC - Preprint
INI - Preprint

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