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Open AccessArticle

Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda

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Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda
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Uganda Virus Research Institute, Entebbe 256, Uganda
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Department of Mathematics, Imperial College London, London SW72AZ, UK
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London School of Hygiene and Tropical Medicine (LSHTM), London WC1E 7HT, UK
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Africa Health Research Institute, Private Bag X7, Durban 4013, South Africa
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Division of Infection and Immunity, University College London, London WC1E 6BT, UK
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Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7BN, UK
*
Authors to whom correspondence should be addressed.
Viruses 2020, 12(3), 331; https://doi.org/10.3390/v12030331
Received: 14 February 2020 / Revised: 13 March 2020 / Accepted: 16 March 2020 / Published: 18 March 2020
(This article belongs to the Special Issue HIV Molecular Epidemiology for Prevention)
Across sub-Saharan Africa, key populations with elevated HIV-1 incidence and/or prevalence have been identified, but their contribution to disease spread remains unclear. We performed viral deep-sequence phylogenetic analyses to quantify transmission dynamics between the general population (GP), fisherfolk communities (FF), and women at high risk of infection and their clients (WHR) in central and southwestern Uganda. Between August 2014 and August 2017, 6185 HIV-1 positive individuals were enrolled in 3 GP and 10 FF communities, 3 WHR enrollment sites. A total of 2531 antiretroviral therapy (ART) naïve participants with plasma viral load >1000 copies/mL were deep-sequenced. One hundred and twenty-three transmission networks were reconstructed, including 105 phylogenetically highly supported source–recipient pairs. Only one pair involved a WHR and male participant, suggesting that improved population sampling is needed to assess empirically the role of WHR to the transmission dynamics. More transmissions were observed from the GP communities to FF communities than vice versa, with an estimated flow ratio of 1.56 (95% CrI 0.68–3.72), indicating that fishing communities on Lake Victoria are not a net source of transmission flow to neighboring communities further inland. Men contributed disproportionally to HIV-1 transmission flow regardless of age, suggesting that prevention efforts need to better aid men to engage with and stay in care. View Full-Text
Keywords: human immunodeficiency virus; phylogenetic analysis; deep sequences; transmission; key populations human immunodeficiency virus; phylogenetic analysis; deep sequences; transmission; key populations
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Bbosa, N.; Ssemwanga, D.; Ssekagiri, A.; Xi, X.; Mayanja, Y.; Bahemuka, U.; Seeley, J.; Pillay, D.; Abeler-Dörner, L.; Golubchik, T.; Fraser, C.; Kaleebu, P.; Ratmann, O.; on behalf of the MRC/UVRI & LSHTM Uganda Research Unit and The PANGEA Consortium. Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda. Viruses 2020, 12, 331.

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