Title

Evaluation of phylogenetic inference methods to determine direction of HIV transmission

Presenter

Oliver Laeyendecker

Authors

R. Rose¹, A.D. Redd², S. Lamers¹, S.F. Porcella³, S.E. Hudelson⁴, E. Piwowar-Manning⁴, M. McCauley⁵, T. Gamble⁶, E.A. Wilson⁷, J. Kumwenda⁸, M.C. Hosseinipour⁹, J.G. Hakim¹⁰, N. Kumarasamy¹¹, S. Chariyalertsak¹², J.H. Pilotto¹³, B. Grinsztejn¹⁴, L.A. Mills¹⁵, J. Makhema¹⁶, B.R. Santos¹⁷, Y.Q. Chen⁷, T.C. Quinn², M.S. Cohen⁹, S.H. Eshleman⁴, O. Laeyendecker^2,18, HPTN 052 Study Team

Institutions

¹BioInfoExperts, Thibodaux, United States, ²NIAID, Baltimore, United States, ³Division of Intramural Research, NIAID, NIH, Hamilton, United States, ⁴Johns Hopkins Univ. School of Medicine, Pathology, Baltimore, United States, ⁵FH I360, Science Facilitation Department, Washington DC, United States, ⁶FHI 360, Science Facilitation Department, Durham, United States, ⁷Fred Hutchinson Cancer Research Institute, Vaccine and Infectious Disease Science Division, Seattle, United States, ⁸College of Medicine-Johns Hopkins Project, Blantyre, Malawi, ⁹Univ. of North Carolina at Chapel Hill, Medicine, Chapel Hill, United States, ¹⁰University of Zimbabwe, Harare, Zimbabwe, ¹¹YRGCARE Medical Centre, Chennai, India, ¹²Chiang Mai University, Research Institute for Health Sciences, Chiang Mai, Thailand, ¹³Hospital Geral de Nova Iguaçu and Laboratorio de AIDS e Imunologia Molecular (IOC/Fiocruz), Rio de Janeiro, Brazil, ¹⁴Instituto Nacional de Infectologia Evandro Chagas-INI-Fiocruz, Rio de Janeiro, Brazil, ¹⁵CDC Division of HIV/AIDS Prevention, KEMRI-CDC Research and Public Health Collaboration HIV Research Branch, Kisumu, Kenya, ¹⁶Botswana Harvard Aids Institute, Gabarone, Botswana, ¹⁷Servico de Infectologia, Hospital Nossa Senhora da Conceicao/GHC, Porto Alegro, Brazil, ¹⁸JHU, Baltimore, United States

Background: It has been postulated that the direction of HIV transmission between two individuals can be determined by phylogenetic analysis of HIV sequences. This approach may be problematic, since HIV sequences from newly-infected individuals are often more similar to index sequences from samples collected years before transmission, compared to those from samples collected at the time of transmission. We evaluated the accuracy of phylogenetic methods for determining the direction of HIV transmission by analyzing next-generation sequencing (NGS) data from index-partner pairs enrolled in the HIV Prevention Trials Network [HPTN] 052 trial. HIV-infected index and HIV-uninfected partner participants were enrolled as serodiscordant couples; samples were analyzed from couples with index-to-partner HIV transmission that was confirmed by genetic linkage studies.
Methods: NGS for HIV gp41 (HXB2 coordinates: 7691-8374) was performed using plasma samples from 39 index-partner pairs (78 samples collected within 3 months of partner seroconversion). Maximum likelihood trees were generated using the entire data set using FastTree v.2. Topological patterns of HIV from each index-partner pair were analyzed.
Results: The analysis included 9,368 consensus sequences and 521,145 total sequence reads for the 78 samples analyzed. In 10% (4/39) of couples, the phylogeny was inconsistent with the known direction of transmission. In 26% (10/39) of couples, the phylogeny results could not discern directionality. In 64% (25/39) of couples, the results correctly indicated index-to-partner transmission; in two of these 25 cases, only one index sequence was closest to the most recent common ancestor.
Conclusions: Phylogenetic analysis of NGS data obtained from samples collected within 3 months of transmission correctly determined the direction of transmission in 64% of the cases analyzed. In 36% of the cases, the phylogenetic topology did not support the known direction of infection, and in one-third of these cases the observed topology was opposite to the known direction of transmission. This demonstrates that phylogenetic topology alone may not be sufficient to accurately determine the direction of HIV transmission.