Geospatial and phylogenetic clustering of acute and recent HIV infections in Lilongwe, Malawi
Year: 2025
Type: article
Study design: Observational Study
Abstract: HIV transmission during early HIV infection impedes efforts to end HIV as a public health threat, as diagnosis typically occurs after this period of elevated transmission risk. To guide diagnosis and prevention strategies, we evaluated the geospatial and phylogenetic clustering of acute and recent HIV infection in Lilongwe, Malawi. We identified people with acute (pre-seroconversion) HIV infection (AHI) and a random sample of people with post-acute HIV infection who presented to a sexually transmitted infections (STI) clinic in Lilongwe, Malawi between 2015 and 2019. We evaluated infection recency in people with post-acute HIV using a LAg-Avidity assay. We mapped the household locations of people with AHI and identified geospatial clusters using a flexible scan statistic. We constructed consensus sequences from deep sequencing reads to identify phylogenetic clusters through genetic distance thresholds and maximum likelihood trees. We identified 141 people with AHI, 30 people with recent HIV, and 652 people with chronic (non-recent) HIV. We identified four geospatial clusters that contained the residences of 30% of clinic attendees with AHI, despite comprising just 0.8% of the populated land area and 3.5% of the population. We also identified fourteen distinct two-person phylogenetic clusters. Ten of the fourteen were male-female pairs, nine of which were clinic referral pairs. The remaining four were same-sex pairs who had not referred each other to the clinic and may have been missing network intermediaries. Three of the fourteen phylogenetic pairs consisted of only acute/recent members, and zero phylogenetic linkages were located within geospatial clusters. AHI detection programs anchored in STI clinic populations and their neighborhoods could facilitate identification of early HIV infection, enabling treatment initiation and transmission prevention efforts during this most infectious period. Future studies of intervention packages and deployment approaches can help inform the optimal design and implementation of AHI-focused strategies for reducing HIV incidence.
Source: PLOS Global Public Health
Authors: Griffin J. Bell, Kimberly A. Powers, Oliver Ratmann, Ann M. Dennis, Pearson Mmodzi, Mitch Matoga, Edward Jere, Jane S. Chen, Courtney N. Maierhofer, Sarah E. Rutstein, Kathryn E. Lancaster, Maganizo B. Chagomerana, Naomi Bonongwe, Esther Mathiya, Beatrice Ndalama, David Bonsall, Sharon S. Weir, Mina C. Hosseinipour, Michael Emch, Myron S. Cohen, Irving F. Hoffman, William C. Miller
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $2,496
Funders: Alfasigma USA, Bill and Melinda Gates Foundation, Brain and Behavior Research Foundation, Kavli Foundation, Amgen, Pfizer, World Health Organization, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, City University of Hong Kong, Biocon, University of Bern, Wellcome Trust, UK Research and Innovation, Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía, Fresenius Kabi, Ho Chi Minh City University of Technology and Education, Fondation Pour l'Audition, Saskatchewan Health Research Foundation, National Institute for Health and Care Research, British Academy, European Commission, Commonwealth Scientific and Industrial Research Organisation, National Research Foundation, Indian Council of Medical Research, European Foundation for the Study of Diabetes, Deutsche Forschungsgemeinschaft, Ministry of Education, Culture, Sports, Science and Technology, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, National Natural Science Foundation of China, ZonMw, Chinese Academy of Sciences, Fundación Científica Asociación Española Contra el Cáncer, Universidad Nacional de Colombia, Generalitat de Catalunya, Nederlandse Organisatie voor Wetenschappelijk Onderzoek, National Research Foundation of Korea, Okinawa Institute of Science and Technology Graduate University, Princess Nourah Bint Abdulrahman University, Studienstiftung des Deutschen Volkes, Vetenskapsrådet, Ministerio de Ciencia e Innovación, Norges Forskningsråd, Waddenfonds, Kao Corporation, Global Affairs Canada, Fidia Farmaceutici, Zorginstituut Nederland, Canada First Research Excellence Fund, Versus Arthritis, Stan Perron Charitable Foundation, National Institutes of Health, Agency for Healthcare Research and Quality, National Oceanic and Atmospheric Administration, Mathison Centre for Mental Health Research and Education, School of Nursing and Health Sciences, University of Dundee, Cumming School of Medicine, University of Calgary, Center for Research Computing, University of Pittsburgh, Canadian Institutes of Health Research, Engineering and Physical Sciences Research Council, National Medical Research Council, Health Research Council of New Zealand, Japan Society for the Promotion of Science, Instituto de Salud Carlos III, Agencia Estatal de Investigación, National Key Research and Development Program of China, Spanish National Plan for Scientific and Technical Research and Innovation, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, National Heart, Lung, and Blood Institute, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases, National Center for Advancing Translational Sciences, Institute of Infection and Immunity, H2020 European Research Council, Samsung Bioepis, Shark Conservation Fund, Health Data Research UK, Unitaid, National Yang Ming Chiao Tung University
OpenAlex ID: W4415934985