{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T15:30:38Z","timestamp":1770996638067,"version":"3.50.1"},"reference-count":76,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2020,11,10]],"date-time":"2020-11-10T00:00:00Z","timestamp":1604966400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC\/DFID Concordat agreement and is also part of the EDCTP2 programme supported by the European Union","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The General Population Cohort (GPC) in south-western Uganda has a low HIV-1 incidence rate (&lt;1%). However, new infections continue to emerge. In this research, 3796 HIV-1 pol sequences (GPC: n = 1418, non-GPC sites: n = 1223, Central Uganda: n = 1010 and Eastern Uganda: n = 145) generated between 2003\u20132015 were analysed using phylogenetic methods with demographic data to understand HIV-1 transmission in this cohort and inform the epidemic response. HIV-1 subtype A1 was the most prevalent strain in the GPC area (GPC and non-GPC sites) (39.8%), central (45.9%) and eastern (52.4%) Uganda. However, in the GPC alone, subtype D was the predominant subtype (39.1%). Of the 524 transmission clusters identified by Cluster Picker, all large clusters (\u22655 individuals, n = 8) involved individuals from the GPC. In a multivariate analysis, clustering was strongly associated with being female (adjusted Odds Ratio, aOR = 1.28; 95% CI, 1.06\u20131.54), being &gt;25 years (aOR = 1.52; 95% CI, 1.16\u20132.0) and being a resident in the GPC (aOR = 6.90; 95% CI, 5.22\u20139.21). Phylogeographic analysis showed significant viral dissemination (Bayes Factor test, BF &gt; 3) from the GPC without significant viral introductions (BF &lt; 3) into the GPC. The findings suggest localized HIV-1 transmission in the GPC. Intensifying geographically focused combination interventions in the GPC would contribute towards controlling HIV-1 infections.<\/jats:p>","DOI":"10.3390\/v12111283","type":"journal-article","created":{"date-parts":[[2020,11,10]],"date-time":"2020-11-10T10:47:28Z","timestamp":1605005248000},"page":"1283","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9675-4234","authenticated-orcid":false,"given":"Deogratius","family":"Ssemwanga","sequence":"first","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda"},{"name":"Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1280-675X","authenticated-orcid":false,"given":"Nicholas","family":"Bbosa","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8527-6222","authenticated-orcid":false,"given":"Rebecca N.","family":"Nsubuga","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6549-3550","authenticated-orcid":false,"given":"Alfred","family":"Ssekagiri","sequence":"additional","affiliation":[{"name":"Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Kapaata","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Nannyonjo","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Faridah","family":"Nassolo","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Karabarinde","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0199-1518","authenticated-orcid":false,"given":"Joseph","family":"Mugisha","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0583-5272","authenticated-orcid":false,"given":"Janet","family":"Seeley","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda"},{"name":"Department of Global Health and Development, London School of Hygiene and Tropical Medicine, 15-17 Tavistock Place, London WC1H 9SH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3472-3667","authenticated-orcid":false,"given":"Gonzalo","family":"Yebra","sequence":"additional","affiliation":[{"name":"The Roslin Institute, Royal (Dick) School of Veterinary Medicine, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5700-3128","authenticated-orcid":false,"given":"Andrew","family":"Leigh Brown","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pontiano","family":"Kaleebu","sequence":"additional","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda"},{"name":"Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,11,10]]},"reference":[{"key":"ref_1","unstructured":"(2020, March 20). UNAIDS DATA. Available online: https:\/\/www.unaids.org\/sites\/default\/files\/media_asset\/2019-UNAIDS-data_en.pdf."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/S0140-6736(02)09331-5","article-title":"Declining HIV-1 incidence and associated prevalence over 10 years in a rural population in south-west Uganda: A cohort study","volume":"360","author":"Mbulaiteye","year":"2002","journal-title":"Lancet"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1007\/s10461-006-9073-y","article-title":"Uganda\u2019s HIV Prevention Success: The Role of Sexual Behavior Change and the National Response","volume":"10","author":"Green","year":"2006","journal-title":"AIDS Behav."},{"key":"ref_4","unstructured":"Uganda Ministry of Health and ICF International (2012). 2011 Uganda AIDS Indicator Survey: Key Findings, MOH and ICF International."},{"key":"ref_5","unstructured":"Ministry of Health Uganda (2017). Population-Based HIV Impact Assessement (UPHIA) 2016\u20132017. Summary Sheet: Preliminary Findings, Ministry of Health Uganda."},{"key":"ref_6","unstructured":"Ministry of Health and Uganda AIDS Commission (2014). Multi-Sectoral HIV Programming for MARPS in Uganda: Review of Profiles, Sizes and Programme Coverage, Ministry of Health and Uganda AIDS Commission. Review Report."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1136\/sextrans-2015-052179","article-title":"Heterogeneity of HIV incidence: A comparative analysis between fishing communities and in a neighbouring rural general population, Uganda, and implications for HIV control","volume":"92","author":"Kamali","year":"2016","journal-title":"Sex. Transm. Infect."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1136\/sti.2010.046805","article-title":"HIV and syphilis prevalence and associated risk factors among fishing communities of Lake Victoria, Uganda","volume":"87","author":"Asiki","year":"2011","journal-title":"Sex. Transm. Infect."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Kiwanuka, N., Ssetaala, A., Ssekandi, I., Nalutaaya, A., Kitandwe, P.K., Ssempiira, J., Bagaya, B.S., Balyegisawa, A., Kaleebu, P., and Hahn, J. (2017). Population attributable fraction of incident HIV infections associated with alcohol consumption in fishing communities around Lake Victoria, Uganda. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0171200"},{"key":"ref_10","unstructured":"Mazzeo, J. (2004). Dynamics of HIV\/AIDS in the Fishing Communities of Benin and Uganda. Food Agric. Organ. HIV\/AIDS Program, Unpublished Work."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Tumwesigye, N.M., Atuyambe, L., Wanyenze, R.K., Kibira, S.P., Li, Q., Wabwire-Mangen, F., and Wagner, G. (2012). Alcohol consumption and risky sexual behaviour in the fishing communities: Evidence from two fish landing sites on Lake Victoria in Uganda. BMC Public Health, 12.","DOI":"10.1186\/1471-2458-12-1069"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1097\/QAI.0b013e3182777167","article-title":"Alcohol use, mycoplasma genitalium, and other STIs associated With HIV incidence among women at high risk in Kampala, Uganda","volume":"62","author":"Vandepitte","year":"2013","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Kasamba, I., Nash, S., Seeley, J., and Weiss, H.A. (2019). HIV incidence among women at high risk of HIV infection attending a dedicated clinic in Kampala, Uganda: 2008\u20132017. Sex. Transm. Dis.","DOI":"10.1097\/OLQ.0000000000000978"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1097\/OLQ.0b013e3182099545","article-title":"HIV and other sexually transmitted infections in a cohort of women involved in high-risk sexual behavior in Kampala, Uganda","volume":"38","author":"Vandepitte","year":"2011","journal-title":"Sex. Transm. Dis."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"E1","DOI":"10.1111\/tmi.12415","article-title":"The Medical Research Council (UK)\/Uganda Virus Research Institute Uganda Research Unit on AIDS--\u201925 years of research through partnerships\u2019","volume":"20","author":"Kaleebu","year":"2015","journal-title":"Trop. Med. Int. Health"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1093\/ije\/dys234","article-title":"The general population cohort in rural south-western Uganda: A platform for communicable and non-communicable disease studies","volume":"42","author":"Asiki","year":"2013","journal-title":"Int J. Epidemiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1097\/QAD.0b013e32830a7502","article-title":"HIV prevalence and incidence are no longer falling in southwest Uganda: Evidence from a rural population cohort 1989\u20132005","volume":"22","author":"Shafer","year":"2008","journal-title":"AIDS"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1097\/00002030-199401000-00013","article-title":"HIV-1 incidence and HIV-1-associated mortality in a rural Ugandan population cohort","volume":"8","author":"Mulder","year":"1994","journal-title":"AIDS"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/S0140-6736(97)01474-8","article-title":"HIV-1 disease progression and AIDS-defining disorders in rural Uganda","volume":"350","author":"Morgan","year":"1997","journal-title":"Lancet"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1089\/aid.2012.0170","article-title":"HIV-1 subtype distribution trends and evidence of transmission clusters among incident cases in a rural clinical cohort in southwest Uganda, 2004\u20132010","volume":"29","author":"Kapaata","year":"2013","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1093\/ije\/25.5.1077","article-title":"Incidence of HIV-1 infection in adults and socio-demographic characteristics of seroconverters in a rural population in Uganda: 1990\u20131994","volume":"25","author":"Kamali","year":"1996","journal-title":"Int. J. Epidemiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1097\/00002030-199402000-00014","article-title":"Risk factors for HIV-1 infection in adults in a rural Ugandan community: A case-control study","volume":"8","author":"Malamba","year":"1994","journal-title":"AIDS"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1038\/s41598-018-37458-x","article-title":"Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations","volume":"9","author":"Bbosa","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Bbosa, N., Ssemwanga, D., Ssekagiri, A., Xi, X., Mayanja, Y., Bahemuka, U., Seeley, J., Pillay, D., Abeler-D\u00f6rner, L., and Golubchik, T. (2020). Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts\/Groups in Uganda. Viruses, 12.","DOI":"10.3390\/v12030331"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Kaleebu, P., Kirungi, W., Watera, C., Asio, J., Lyagoba, F., Lutalo, T., Kapaata, A.A., Nanyonga, F., Parry, C.M., and Magambo, B. (2015). Virological Response and Antiretroviral Drug Resistance Emerging during Antiretroviral Therapy at Three Treatment Centers in Uganda. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0145536"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1097\/QAD.0b013e328346260f","article-title":"Transmitted antiretroviral drug resistance among newly HIV-1 diagnosed young individuals in Kampala","volume":"25","author":"Ndembi","year":"2011","journal-title":"AIDS"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1086\/648590","article-title":"Viral rebound and emergence of drug resistance in the absence of viral load testing: A randomized comparison between zidovudine-lamivudine plus Nevirapine and zidovudine-lamivudine plus Abacavir","volume":"201","author":"Ndembi","year":"2010","journal-title":"J. Infect. Dis."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1936","DOI":"10.1128\/JCM.06689-11","article-title":"Automating HIV Drug Resistance Genotyping with RECall, a Freely Accessible Sequence Analysis Tool","volume":"50","author":"Woods","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1080\/10635150802429642","article-title":"A rapid bootstrap algorithm for the RAxML Web servers","volume":"57","author":"Stamatakis","year":"2008","journal-title":"Syst. Biol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e144","DOI":"10.1093\/nar\/gku739","article-title":"COMET: Adaptive context-based modeling for ultrafast HIV-1 subtype identification","volume":"42","author":"Struck","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.meegid.2013.04.032","article-title":"Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools","volume":"19","author":"Faria","year":"2013","journal-title":"Infect. Genet. Evol."},{"key":"ref_32","unstructured":"Los Alamos National Laboratory (LANL) (2020, April 12). HIV Sequence Database Main Page, Available online: https:\/\/www.hiv.lanl.gov\/content\/sequence\/HIV\/mainpage.html."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"Larkin","year":"2007","journal-title":"Bioinformatics"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2334","DOI":"10.1093\/bioinformatics\/btm331","article-title":"ViroBLAST: A stand-alone BLAST web server for flexible queries of multiple databases and user\u2019s datasets","volume":"23","author":"Deng","year":"2007","journal-title":"Bioinformatics"},{"key":"ref_35","unstructured":"(2020, February 15). ElimDupes, Available online: https:\/\/www.hiv.lanl.gov\/content\/sequence\/ELIMDUPES\/elimdupes.html."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"783","DOI":"10.2307\/2408678","article-title":"Confidence limits on phylogenies: An approach using the bootstrap","volume":"39","author":"Felsenstein","year":"1985","journal-title":"Evolution"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Ragonnet-Cronin, M., Hodcroft, E., Hu\u00e9, S., Fearnhill, E., Delpech, V., Brown, A.J.L., and Lycett, S. (2013). UK HIV Drug Resistance Database Automated analysis of phylogenetic clusters. BMC Bioinf., 14.","DOI":"10.1186\/1471-2105-14-317"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1093\/molbev\/msy016","article-title":"HIV-TRACE (TRAnsmission Cluster Engine): A Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens","volume":"35","author":"Weaver","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Kiwuwa-Muyingo, S., Nazziwa, J., Ssemwanga, D., Ilmonen, P., Njai, H., Ndembi, N., Parry, C., Kitandwe, P.K., Gershim, A., and Mpendo, J. (2017). HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0185818"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1099\/vir.0.000107","article-title":"Analysis of the history and spread of HIV-1 in Uganda using phylodynamics","volume":"96","author":"Yebra","year":"2015","journal-title":"J. Gen. Virol."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Lemey, P., Rambaut, A., Drummond, A.J., and Suchard, M.A. (2009). Bayesian phylogeography finds its roots. PLoS Comput. Biol., 5.","DOI":"10.1371\/journal.pcbi.1000520"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/molbev\/mss243","article-title":"Accurate model selection of relaxed molecular clocks in bayesian phylogenetics","volume":"30","author":"Baele","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/molbev\/msj021","article-title":"Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences","volume":"23","author":"Shapiro","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1007\/BF02352289","article-title":"Maximum-Likelihood Models for Combined Analyses of Multiple Sequence Data","volume":"42","author":"Yang","year":"1996","journal-title":"J. Mol. Evol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/molbev\/mss265","article-title":"Improving Bayesian population dynamics inference: A coalescent-based model for multiple loci","volume":"30","author":"Gill","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"vew003","DOI":"10.1093\/ve\/vew003","article-title":"The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study","volume":"2","author":"Hall","year":"2016","journal-title":"Virus Evol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1093\/molbev\/msn090","article-title":"Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics","volume":"25","author":"Minin","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"R399","DOI":"10.1016\/j.cub.2016.03.071","article-title":"Molecular clocks","volume":"26","author":"Lee","year":"2016","journal-title":"Curr. Biol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1093\/oxfordjournals.molbev.a026389","article-title":"Estimation of primate speciation dates using local molecular clocks","volume":"17","author":"Yoder","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Drummond, A.J., Ho, S.Y.W., Phillips, M.J., and Rambaut, A. (2006). Relaxed Phylogenetics and Dating with Confidence. PLoS Biol., 4.","DOI":"10.1371\/journal.pbio.0040088"},{"key":"ref_53","unstructured":"(2020, May 30). Tracer Is a Program for Analysing the Trace Files Generated by Bayesian MCMC Runs (that Is, the Continuous Parameter Values Sampled from the Chain). Available online: http:\/\/tree.bio.ed.ac.uk\/software\/tracer\/."},{"key":"ref_54","unstructured":"(2020, May 30). Bayesian Evolutionary Analysis Sampling Trees. Available online: http:\/\/beast.bio.ed.ac.uk\/TreeAnnotator\/."},{"key":"ref_55","unstructured":"(2020, May 31). FigTree Is Designed as a Graphical Viewer of Phylogenetic Trees and as a Program for Producing Publication-Ready Figures. Available online: http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"2910","DOI":"10.1093\/bioinformatics\/btr481","article-title":"SPREAD: Spatial phylogenetic reconstruction of evolutionary dynamics","volume":"27","author":"Bielejec","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-020-59944-x","article-title":"Characterisation of HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread","volume":"10","author":"Nazziwa","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1086\/651951","article-title":"Molecular Epidemiology Reveals Long-Term Changes in HIV Type 1 Subtype B Transmission in Switzerland","volume":"201","author":"Kouyos","year":"2010","journal-title":"J. Infect. Dis."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1093\/infdis\/jir550","article-title":"UK HIV Drug Resistance Collaboration Transmission network parameters estimated from HIV sequences for a nationwide epidemic","volume":"204","author":"Lycett","year":"2011","journal-title":"J. Infect. Dis."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/j.coviro.2011.10.003","article-title":"Toward a quantitative understanding of viral phylogeography","volume":"1","author":"Faria","year":"2011","journal-title":"Curr. Opin. Virol."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Lu, L., Lycett, S.J., and Leigh Brown, A.J. (2014). Determining the phylogenetic and phylogeographic origin of highly pathogenic avian influenza (H7N3) in Mexico. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0107330"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"609","DOI":"10.3201\/eid0606.000609","article-title":"Predominance of HIV-1 subtype A and D infections in Uganda","volume":"6","author":"Hu","year":"2000","journal-title":"Emerg. Infect. Dis."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1089\/aid.2011.0024","article-title":"HIV type 1 subtype distribution, multiple infections, sexual networks, and partnership histories in female sex workers in Kampala, Uganda","volume":"28","author":"Ssemwanga","year":"2012","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1089\/088922200309052","article-title":"Molecular epidemiology of HIV type 1 in a rural community in southwest Uganda","volume":"16","author":"Kaleebu","year":"2000","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1089\/aid.2009.0127","article-title":"Geographic HIV Type 1 Subtype Distribution in Rakai District, Uganda","volume":"25","author":"Redd","year":"2009","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Bulage, L., Ssewanyana, I., Nankabirwa, V., Nsubuga, F., Kihembo, C., Pande, G., Ario, A.R., Matovu, J.K., Wanyenze, R.K., and Kiyaga, C. (2017). Factors Associated with Virological Non-suppression among HIV-Positive Patients on Antiretroviral Therapy in Uganda, August 2014\u2013July 2015. BMC Infect. Dis., 17.","DOI":"10.1186\/s12879-017-2428-3"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1080\/17441692.2015.1074715","article-title":"Mobility among youth in Rakai, Uganda: Trends, characteristics, and associations with behavioural risk factors for HIV","volume":"12","author":"Schuyler","year":"2017","journal-title":"Glob. Public Health"},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Ratmann, O., Kagaayi, J., Hall, M., Golubchick, T., Kigozi, G., Xi, X., Wymant, C., Nakigozi, G., Abeler-D\u00f6rner, L., and Bonsall, D. (2020). Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: A population-based study in Rakai, Uganda. Lancet HIV.","DOI":"10.1016\/S2352-3018(19)30378-9"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"2345","DOI":"10.1097\/QAD.0000000000001619","article-title":"Prevalence and clinical impacts of HIV-1 intersubtype recombinants in Uganda revealed by near-full-genome population and deep sequencing approaches","volume":"31","author":"Lee","year":"2017","journal-title":"AIDS"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1097\/COH.0000000000000534","article-title":"HIV subtype diversity worldwide","volume":"14","author":"Bbosa","year":"2019","journal-title":"Curr. Opin. HIV AIDS"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"e25398","DOI":"10.1002\/jia2.25398","article-title":"Who are the missing men? Characterising men who never tested for HIV from population-based surveys in six sub-Saharan African countries","volume":"22","author":"Quinn","year":"2019","journal-title":"J. Int. AIDS Soc."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1080\/09540121.2016.1164806","article-title":"Men \u201cmissing\u201d from population-based HIV testing: Insights from qualitative research","volume":"28","author":"Camlin","year":"2016","journal-title":"AIDS Care"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1007\/s00239-001-0034-9","article-title":"The effect of recombination on the accuracy of phylogeny estimation","volume":"54","author":"Posada","year":"2002","journal-title":"J. Mol. Evol."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Lu, L., Leigh Brown, A.J., and Lycett, S.J. (2017). Quantifying predictors for the spatial diffusion of avian influenza virus in China. BMC Evol. Biol., 17.","DOI":"10.1186\/s12862-016-0845-3"},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Duchatel, F., de Bronsvoort, B.M.C., and Lycett, S. (2019). Phylogeographic Analysis and Identification of Factors Impacting the Diffusion of Foot-and-Mouth Disease Virus in Africa. Front. Ecol. Evol., 7.","DOI":"10.3389\/fevo.2019.00371"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"e181","DOI":"10.1016\/S2352-3018(18)30009-2","article-title":"Migration and risk of HIV acquisition in Rakai, Uganda: A population-based cohort study","volume":"5","author":"Olawore","year":"2018","journal-title":"Lancet HIV"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/11\/1283\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:31:26Z","timestamp":1760178686000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/11\/1283"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,11,10]]},"references-count":76,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2020,11]]}},"alternative-id":["v12111283"],"URL":"https:\/\/doi.org\/10.3390\/v12111283","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,11,10]]}}}