Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, United States
Yinfeng Zhang
Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center Presbyterian Shadyside, Philadelphia, United States
Oxford Big Data Institute, Li Ka Shing Center for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, United Kingdom
Victor DeGruttola
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, United States
Eric Tchetgen Tchetgen
Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, United States
Vladimir Novitsky
Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, United States; Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
Janet Moore
Division of Global HIV/AIDS and TB, Centers for Disease Control and Prevention, Atlanta, United States
Pam Bachanas
Division of Global HIV/AIDS and TB, Centers for Disease Control and Prevention, Atlanta, United States
Tebogo Segolodi
HIV Prevention Research Unit, Centers for Disease Control and Prevention, Gaborone, Botswana
Refeletswe Lebelonyane
Ministry of Health, Republic of Botswana, Gaborone, Botswana
Molly Pretorius Holme
Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, United States
Sikhulile Moyo
Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
Joseph Makhema
Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
Shahin Lockman
Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, United States; Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Brigham and Women's Hospital, Division of Infectious Diseases, Boston, United States
Christophe Fraser
Oxford Big Data Institute, Li Ka Shing Center for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, United Kingdom
Myron Max Essex
Harvard T.H. Chan School of Public Health AIDS Initiative, Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, United States; Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, United States
On behalf of The Botswana Combination Prevention Project and PANGEA consortium
Background: Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence. Methods: To elucidate patterns of HIV spread in universal test-and-treat trials, we quantified the contribution of geographic-location, gender, age, and randomized-HIV-intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana. We sequenced HIV viral whole genomes from 5114 trial participants among the 30 trial communities. Results: Deep-sequence phylogenetic analysis revealed that most inferred HIV transmissions within the trial occurred within the same or between neighboring communities, and between similarly aged partners. Transmissions into intervention communities from control communities were more common than the reverse post-baseline (30% [12.2 – 56.7] vs. 3% [0.1 – 27.3]) than at baseline (7% [1.5 – 25.3] vs. 5% [0.9 – 22.9]) compatible with a benefit from treatment-as-prevention. Conclusions: Our findings suggest that population mobility patterns are fundamental to HIV transmission dynamics and to the impact of HIV control strategies. Funding: This study was supported by the National Institute of General Medical Sciences (U54GM088558), the Fogarty International Center (FIC) of the U.S. National Institutes of Health (D43 TW009610), and the President’s Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention (CDC) (Cooperative agreements U01 GH000447 and U2G GH001911).
