Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages Across Villages in Botswana Treatment-as-Prevention Trial
Author:
Novitsky Vlad12, Zahralban-Steele Melissa2, Moyo Sikhulile12, Nkhisang Tapiwa2, Maruapula Dorcas1, McLane Mary Fran2, Leidner Jean3, Bennett Kara4, Abeler-Dörner Lucie, Bonsall David, Fraser Christophe, Golubchik Tanya, Ayles Helen, Bowden Rory, Calvez Vincent, Fidler Sarah, Grabowski Kate, Kagaayi Joseph, Hayes Richard, Seeley Janet, Herbeck Joshua, Lingappa Jairam, Kaleebu Pontiano, Ssemwanga Deogratius, Pillay Deenan, Tanser Frank, Quinn Thomas, Rambaut Andrew, Leigh-Brown Andrew, Ratmann Oliver, Wawer Maria, Cohen Myron, Dennis Ann, D’Oliveira Tulio, Frampton Dan, Hoppe Anne, Kellam Paul, Kityo Cissy, Paton Nick, Wirth Kathleen E2, Gaolathe Tendani1, Kadima Etienne1, Chakalisa Unoda1, Pretorius Holme Molly2, Lockman Shahin125, Mmalane Mompati1, Makhema Joseph12, Gaseitsiwe Simani12, DeGruttola Victor6, Essex M12,
Affiliation:
1. Botswana Harvard AIDS Institute, Gaborone, Botswana 2. Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA 3. Goodtables Data Consulting LLC, Norman, Oklahoma, USA 4. Bennett Statistical Consulting Inc, Ballston Lake, New York, USA 5. Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA 6. Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
Abstract
Abstract
Background
Phylogenetic mapping of HIV-1 lineages circulating across defined geographical locations is promising for better understanding HIV transmission networks to design optimal prevention interventions.
Methods
We obtained near full-length HIV-1 genome sequences from people living with HIV (PLWH), including participants on antiretroviral treatment in the Botswana Combination Prevention Project, conducted in 30 Botswana communities in 2013–2018. Phylogenetic relationships among viral sequences were estimated by maximum likelihood.
Results
We obtained 6078 near full-length HIV-1C genome sequences from 6075 PLWH. We identified 984 phylogenetically distinct HIV-1 lineages (molecular HIV clusters) circulating in Botswana by mid-2018, with 2–27 members per cluster. Of these, dyads accounted for 62%, approximately 32% (n = 316) were found in single communities, and 68% (n = 668) were spread across multiple communities. Men in clusters were approximately 3 years older than women (median age 42 years, vs 39 years; P < .0001). In 65% of clusters, men were older than women, while in 35% of clusters women were older than men. The majority of identified viral lineages were spread across multiple communities.
Conclusions
A large number of circulating phylogenetically distinct HIV-1C lineages (molecular HIV clusters) suggests highly diversified HIV transmission networks across Botswana communities by 2018.
Funder
U.S. President's Emergency Plan for AIDS Relief Centers for Disease Control and Prevention National Institute of Allergy and Infectious Diseases Bill and Melinda Gates Foundation Fogarty International Center National Institutes of Health
Publisher
Oxford University Press (OUP)
Subject
Infectious Diseases,Immunology and Allergy
Cited by
11 articles.
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