Please use this identifier to cite or link to this item: https://www.arca.fiocruz.br/handle/icict/31429
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dc.contributor.authorRose, Rebecca
dc.contributor.authorHall, Matthew
dc.contributor.authorRedd, Andrew D.
dc.contributor.authorLamers, Susanna
dc.contributor.authorBarbier, Andrew E.
dc.contributor.authorPorcella, Stephen F.
dc.contributor.authorHudelson, Sarah E.
dc.contributor.authorPiwowar-Manning, Estelle
dc.contributor.authorMcCauley, Marybeth
dc.contributor.authorGamble, Theresa
dc.contributor.authorWilson, Ethan A.
dc.contributor.authorKumwenda, Johnstone
dc.contributor.authorHosseinipour, Mina C.
dc.contributor.authorHakim, James G.
dc.contributor.authorKumarasamy, Nagalingeswaran
dc.contributor.authorChariyalertsak, Suwat
dc.contributor.authorPilotto, Jose H.
dc.contributor.authorGrinsztejn, Beatriz
dc.contributor.authorMills, Lisa A.
dc.contributor.authorMakhema, Joseph
dc.contributor.authorSantos, Breno R.
dc.contributor.authorChen, Ying Q.
dc.contributor.authorQuinn, Thomas C.
dc.contributor.authorFraser, Christophe
dc.contributor.authorCohen, Myron S.
dc.contributor.authorEshleman, Susan H.
dc.contributor.authorLaeyendecker, Oliver
dc.date.accessioned2019-02-05T15:14:44Z
dc.date.available2019-02-05T15:14:44Z
dc.date.issued2018
dc.identifier.citationROSE, 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.
dc.identifier.issn0022-1899
dc.identifier.urihttps://www.arca.fiocruz.br/handle/icict/31429
dc.language.isoeng
dc.publisherOxford
dc.rightsrestricted access
dc.titlePhylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort
dc.typeArticle
dc.identifier.doi10.1093/infdis/jiy734
dc.description.abstractenBACKGROUND: 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.
dc.creator.affilliationBioInfoExperts. Thibodaux, LA, USA.
dc.creator.affilliationOxford University. Big Data Institute. Oxford, UK.
dc.creator.affilliationNational 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.
dc.creator.affilliationBioInfoExperts. Thibodaux, LA, USA.
dc.creator.affilliationBioInfoExperts. Thibodaux, LA, USA.
dc.creator.affilliationNational 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.
dc.creator.affilliationJohns Hopkins Univ. School of Medicine. Dept. of Pathology. Baltimore, MD, USA.
dc.creator.affilliationJohns Hopkins Univ. School of Medicine. Dept. of Pathology. Baltimore, MD, USA.
dc.creator.affilliationFHI360. Science Facilitation Department. Durham, NC, USA.
dc.creator.affilliationFHI360. Science Facilitation Department. Durham, NC, USA.
dc.creator.affilliationFred Hutchinson Cancer Research Institute. Vaccine and Infectious Disease Science Division. Seattle, WA, USA.
dc.creator.affilliationJohns Hopkins Project. College of Medicine. Blantyre, Malawi.
dc.creator.affilliationUniv. of North Carolina at Chapel Hill. Dept of Medicine. Chapel Hill, NC, USA.
dc.creator.affilliationUniversity of Zimbabwe. Harare, Zimbabwe.
dc.creator.affilliationYRGCARE Medical Centre. Chennai, India.
dc.creator.affilliationChiang Mai University. Research Institute for Health Sciences. Chiang Mai, Thailand.
dc.creator.affilliationFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular./ Hospital Geral de Nova Iguaçu. Rio de Janeiro, RJ, Brasil.
dc.creator.affilliationFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST/AIDS. Rio de Janeiro, RJ, Brasil.
dc.creator.affilliationDivision of HIV/AIDS Prevention. Centers for Disease Control and Prevention (CDC). / HIV Research Branch. KEMRI–CDC Research and Public Health Collaboration. Kisumu, Kenya.
dc.creator.affilliationBotswana Harvard AIDS Institute. Gabarone, Botswana.
dc.creator.affilliationHospital Nossa Senhora da Conceição. Serviço de Infectologia. Porto Alegre, RS, Brasil.
dc.creator.affilliationFred Hutchinson Cancer Research Institute. Vaccine and Infectious Disease Science Division. Seattle, WA, USA.
dc.creator.affilliationNational 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.
dc.creator.affilliationOxford University. Big Data Institute. Oxford, UK.
dc.creator.affilliationUniv. of North Carolina at Chapel Hill. Dept of Medicine. Chapel Hill, NC, USA.
dc.creator.affilliationJohns Hopkins Univ. School of Medicine. Dept. of Pathology. Baltimore, MD, USA.
dc.creator.affilliationNational 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.
dc.subject.enNetworks
dc.subject.enEpidemiology
dc.subject.enViral dynamics
dc.peerreviewedNão
dc.publicationstatusPublicado
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INI - Preprint

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