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Title: Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort
Authors: Rebecca Rose
Matthew Hall
Andrew D. Redd
Susanna Lamers
Andrew E. Barbier
Stephen F. Porcella
Sarah E. Hudelson
Estelle Piwowar-Manning
Marybeth McCauley
Theresa Gamble
Ethan A. Wilson
Johnstone Kumwenda
Mina C. Hosseinipour
James G. Hakim
Nagalingeswaran Kumarasamy
Suwat Chariyalertsak
Jose H. Pilotto
Beatriz Grinsztejn
Lisa A. Mills
Joseph Makhema
Breno R. Santos
Ying Q. Chen
Thomas C. Quinn
Christophe Fraser
Myron S. Cohen
Susan H. Eshleman
Oliver Laeyendecker
Keywords: Medicine
Issue Date: 26-Sep-2019
Abstract: © The Author(s) 2018. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: BACKGROUND: We evaluated use of phylogenetic methods to predict the direction of human immunodeficiency virus (HIV) transmission. METHODS: For 33 pairs of HIV-infected patients (hereafter, "index patients") and their partners who acquired genetically linked HIV infection during the study, samples were collected from partners and index patients close to the time when the partner seroconverted (hereafter, "SC samples"); for 31 pairs, samples collected from the index patient at an earlier time point (hereafter, "early index samples") were also available. Phylogenies were inferred using env next-generation sequences (1 tree per pair/subtype). The direction of transmission (DoT) predicted from each tree was classified as correct or incorrect on the basis of which sequences (those from the index patient or the 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%) by using SC samples and in 23 pairs (74%) by using early index samples. DoT was predicted incorrectly for 4 pairs (15%) by using SC or early index samples. In the bootstrap analysis, DoT was predicted correctly for 18 pairs (55%) by using SC samples and for 24 pairs (73%) by using early index samples. DoT was predicted incorrectly for 7 pairs (21%) by using SC samples and for 4 pairs (13%) by using early index samples. CONCLUSIONS: Phylogenetic methods based solely on the tree topology of HIV env sequences, particularly without consideration of phylogenetic uncertainty, may be insufficient for determining DoT.
ISSN: 15376613
Appears in Collections:CMUL: Journal Articles

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