Alizon M, et al. Genetic variability of the AIDS virus: nucleotide sequence analysis of two isolates from African patients. Cell. 1986;46(1):63–74. https://doi.org/10.1016/0092-8674(86)90860-3.
Amornkul PN, et al. Disease progression by infecting HIV-1 subtype in a seroconverter cohort in sub-Saharan Africa. AIDS. 2013;27(17):2775–86. https://doi.org/10.1097/QAD.0000000000000012.
Andrews S. FastQC: A quality control tool for high throughput sequence data. [Online] 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Baeten JM, et al. HIV-1 subtype D infection is associated with faster disease progression than subtype A in spite of similar plasma HIV-1 loads. J Infect Dis. 2007;195(8):1177–80. https://doi.org/10.1086/512682.
Bankevich A, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–77. https://doi.org/10.1089/cmb.2012.0021.
Bbosa N, et al. Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations. Sci Rep. 2019. https://doi.org/10.1038/s41598-018-37458-x.
Bbosa N, et al. 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(3):1–21. https://doi.org/10.3390/v12030331.
Bbosa N, Kaleebu P, Ssemwanga D. HIV subtype diversity worldwide. Curr Opin HIV AIDS. 2019;14(3):153–60. https://doi.org/10.1097/COH.0000000000000534.
Blanquart F, et al. A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda. eLife. 2016;5:1–32. https://doi.org/10.7554/elife.20492.
Bousheri S, et al. Infection with different HIV subtypes is associated with CD4 activation-associated dysfunction and apoptosis. J Acquir Immune Defic Syndr. 2009;52(5):548–52. https://doi.org/10.1097/QAI.0b013e3181c1d456.
Cane P. HIV drug resistance testing. Methods Mol Biol. 2011;665:123–32. https://doi.org/10.1007/978-1-60761-817-1_8.
Capoferri AA, et al. Recombination analysis of near full-length HIV-1 sequences and the identification of a potential new circulating recombinant form from Rakai, Uganda. AIDS Res Hum Retroviruses. 2020. https://doi.org/10.1089/aid.2019.0150.
Carswell JW. HIV infection in healthy persons in Uganda. AIDS. 1987;1(4):223–7.
Chalmet K, et al. Epidemiological study of phylogenetic transmission clusters in a local HIV-1 epidemic reveals distinct differences between subtype B and non-B infections. BMC Infect Dis. 2010. https://doi.org/10.1186/1471-2334-10-262.
Coetzer M, et al. Extreme genetic divergence is required for coreceptor switching in HIV-1 subtype C. J Acquir Immune Defic Syndr. 2011;56(1):9–15. https://doi.org/10.1097/QAI.0b013e3181f63906.
Connor RI, et al. Change in coreceptor use correlates with disease progression in HIV-1 infected individuals. J Exp Med. 1997;185(2):621–8. https://doi.org/10.3141/1543-18.
Conroy SA, et al. Changes in the distribution of HIV type 1 subtypes D and A in Rakai District, Uganda Between 1994 and 2002. AIDS Res Hum Retroviruses. 2010;26(10):1087–91. https://doi.org/10.1089/aid.2010.0054.
Daar ES, et al. Baseline HIV type 1 coreceptor tropism predicts disease progression. Clin Infect Dis. 2007;45(5):643–9. https://doi.org/10.1086/520650.
Danecek P, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):1–4. https://doi.org/10.1093/gigascience/giab008.
Depledge DP, et al. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS ONE. 2011;6(11). https://doi.org/10.1371/journal.pone.0027805.
Easterbrook PJ, et al. Impact of HIV-1 viral subtype on disease progression and response to antiretroviral therapy. J Int AIDS Soc. 2010;13(1):1–9.
Eller MA, et al. HIV type 1 disease progression to AIDS and death in a rural Ugandan cohort is primarily dependent on viral load despite variable subtype and T-cell immune activation levels. J Infect Dis. 2015;211(10):1574–84. https://doi.org/10.1093/infdis/jiu646.
Essex M. Human immunodeficiency viruses in the developing world. Adv Virus Res. 1999;53(C):71–88. https://doi.org/10.1016/S0065-3527(08)60343-7.
Faria NR, et al. The early spread and epidemic ignition of HIV-1 in human populations. Science. 2014;346(6205):56–61. https://doi.org/10.1126/science.1256739.The.
Faria NR, et al. Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. PLoS Pathog. 2019;15(12):1–23. https://doi.org/10.1371/journal.ppat.1007976.
Fraser C, et al. Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis. Proc Natl Acad Sci USA. 2007;104(44):17441–6. https://doi.org/10.1073/pnas.0708559104.
Gall A, et al. Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes. J Clin Microbiol. 2012;50(12):3838–44. https://doi.org/10.1128/JCM.01516-12.
Geretti AM. HIV-1 subtypes: epidemiology and significance for HIV management. Curr Opin Infect Dis. 2006;19:1–7. https://doi.org/10.1097/01.qco.0000200293.45532.68.
Gibson KM, et al. Validation of variant assembly using haphpipe with next-generation sequence data from viruses. Viruses. 2020. https://doi.org/10.3390/v12070758.
Grant HE, et al. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evolution. 2020;6(1):1–12. https://doi.org/10.1093/ve/veaa004.
Grant HE. Characterisation of the Ugandan HIV epidemic with full-length genome sequence data from 1986 to 2016. Edinburgh: University of Edinburgh; 2022.
Green EC, et al. Uganda’s HIV prevention success: the role of sexual behavior change and the national response. AIDS Behav. 2006;10(4):335–46. https://doi.org/10.1007/s10461-006-9073-y.
Gryseels S, et al. A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue. Proc Natl Acad Sci USA. 2020. https://doi.org/10.1073/pnas.1913682117.
Harris M, et al. Among 46 near full length HIV type 1 genome sequences from Rakai District, Uganda, subtype D and AD recombinants predominate. AIDS Res Hum Retroviruses. 2002;18(17):1281–90. https://doi.org/10.1089/088922202320886325.
Hodcroft E, et al. The contribution of viral genotype to plasma viral set-point in HIV infection. PLoS Pathog. 2014. https://doi.org/10.1371/journal.ppat.1004112.
Huang W, et al. Coreceptor tropism in human immunodeficiency virus type 1 subtype D: High prevalence of CXCR4 tropism and heterogeneous composition of viral populations. J Virol. 2007;81(15):7885–93. https://doi.org/10.1128/jvi.00218-07.
Kaleebu P, et al. Relationship between HIV-1 Env subtypes A and D and disease progression in a rural Ugandan cohort. AIDS. 2001;15(3):293–9. https://doi.org/10.1097/00002030-200102160-00001.
Kaleebu P, et al. Effect of human immunodeficiency virus (HIV) type 1 envelope subtypes A and D on disease progression in a large cohort of HIV-1-positive persons in Uganda. J Infect Dis. 2002;185(9):1244–50. https://doi.org/10.1086/340130.
Kaleebu P, et al. Relation between chemokine receptor use, disease stage, and HIV-1 subtypes A and D: results from a rural Ugandan cohort. J Acquir Immune Defic Syndr. 2007;45(1):28–33. https://doi.org/10.1097/QAI.0b013e3180385aa0.
Kalish ML, et al. Recombinant viruses and early global HIV-1 epidemic. Emerg Infect Dis. 2004;10(7):1227–34. https://doi.org/10.3201/eid1007.030904.
Kaslow R, et al. Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat Med. 1996;2(4):405–11.
Kiwanuka N, et al. Effect of human immunodeficiency virus type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection. J Infect Dis. 2008;197(5):707–13. https://doi.org/10.1086/527416.
Kiwanuka N, et al. HIV-1 viral subtype differences in the rate of CD4+ T-Cell decline. J Acquir Immune Defic Syndr. 2010;54(2):180–4. https://doi.org/10.1097/QAI.0b013e3181c98fc0.HIV-1.
Kiwuwa-Muyingo S, et al. HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: a phylogenetic and epidemiological approach. PLoS ONE. 2017;12(10):1–23. https://doi.org/10.1371/journal.pone.0185818.
Koot M, et al. Prognostic value of HIV-1 syncytium-inducing phenotype for rate of CD4+ cell depletion and progression to AIDS. Ann Intern Med. 1993;118(9):681–8. https://doi.org/10.7326/0003-4819-118-9-199305010-00004.
Kosakovsky Pond SL, et al. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol. 2009;5(11):1–21. https://doi.org/10.1371/journal.pcbi.1000581.
Krueger F. TrimGalore. [Online] 2020. https://github.com/FelixKrueger/TrimGalore.
Kuritzkes DR. HIV-1 subtype as a determinant of disease progression. J Infect Dis. 2008;197(5):638–9. https://doi.org/10.1086/527417.
Lamers SL, et al. HIV-1 subtype distribution and diversity over 18 years in Rakai, Uganda. AIDS Res Hum Retroviruses. 2020;36(6):522–6. https://doi.org/10.1089/aid.2020.0062.
Lee GQ, et al. Prevalence and clinical impacts of HIV-1 intersubtype recombinants in Uganda revealed by near-full-genome population and deep sequencing approaches. AIDS. 2017;31(17):2345–54. https://doi.org/10.1097/QAD.0000000000001619.
Lengauer T, et al. Bioinformatics prediction of HIV coreceptor usage. Nat Biotechnol. 2007;25(12):1407–10. https://doi.org/10.1038/nbt1371.
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013. https://arXiv.org/abs/1303.3997v2 [q-bio.GN].
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. 2011;17(1):10–2.
McKenna A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303. https://doi.org/10.1101/gr.107524.110.20.
McPhee E, et al. Short communication: the interaction of HIV set point viral load and subtype on disease progression. AIDS Res Hum Retroviruses. 2019;35(1):49–51. https://doi.org/10.1089/aid.2018.0165.
Mellors JW, et al. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science. 1996;272(5265):1167–70. https://doi.org/10.1126/science.272.5265.1167.
Meyerhans A, et al. Temporal fluctuations in HIV quasispecies in vivo are not reflected by sequential HIV isolations. Cell. 1989;58(5):901–10. https://doi.org/10.1016/0092-8674(89)90942-2.
Peden K, Emerman M, Montagnier L. Changes in growth properties on passage in tissue culture of viruses derived from infectious molecular clones of HIV-1LAI, HIV-1MAL, and HIV-1ELI. Virology. 1991;185(2):661–72. https://doi.org/10.1016/0042-6822(91)90537-L.
Pillay D, et al. PANGEA-HIV: Phylogenetics for generalised epidemics in Africa. Lancet Infect Dis. 2015;15(3):259–61. https://doi.org/10.1016/S1473-3099(15)70036-8.
Pollakis G, et al. Phenotypic and genotypic comparisons of CCR5- and CXCR4-tropic human immunodeficiency virus type 1 biological clones isolated from subtype C-infected individuals. J Virol. 2004;78(6):2841–52. https://doi.org/10.1128/jvi.78.6.2841-2852.2004.
Poon AFY, et al. Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data. PLoS Comput Biol. 2012. https://doi.org/10.1371/journal.pcbi.1002753.
Rambaut A, et al. The causes and consequences of HIV evolution. Nat Rev Genet. 2004;5(1):52–61. https://doi.org/10.1038/nrg1246.
Ratmann O, et al. Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda. Lancet HIV. 2020;7(3):e173–83. https://doi.org/10.1016/S2352-3018(19)30378-9.
Robertson DL, et al. HIV-1 nomenclature proposal. Science. 2000;288(5463):55. https://doi.org/10.1126/science.288.5463.55d.
Schuitemaker H, Van’Wout AB, Lusso P. Clinical significance of HIV-1 coreceptor usage. J Transl Med. 2010;9(1):1–17. https://doi.org/10.1186/1479-5876-9-S1-S5.
Sharp PM, Hahn BH. Origins of HIV and the AIDS pandemic. Cold Spring Harb Perspect Med. 2011. https://doi.org/10.1101/cshperspect.a006841.
Sing T, et al. Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther. 2007;12(7):1097–106. https://doi.org/10.1177/135965350701200709.
Ssemwanga D, et al. ‘HIV type 1 subtype distribution, multiple infections, sexual networks, and partnership histories in female sex workers in Kampala, Uganda. AIDS Res Hum Retroviruses. 2012. https://doi.org/10.1089/aid.2011.0024.
Ssemwanga D, et al. Effect of HIV-1 subtypes on disease progression in rural Uganda: a prospective clinical cohort study. PLoS ONE. 2013. https://doi.org/10.1371/journal.pone.0071768.
Ssemwanga D, et al. The molecular epidemiology and transmission dynamics of HIV type 1 in a general population cohort in Uganda. Viruses. 2020;12(11):1–17. https://doi.org/10.3390/v12111283.
Stilianos L, Doebeli M. Efficient comparative phylogenetics on large trees. Bioinformatics. 2017. https://doi.org/10.1093/bioinformatics/btx701.
Suchard MA, et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution. 2018;4(1):1–5. https://doi.org/10.1093/ve/vey016.
Thielen A, et al. Improved prediction of HIV-1 coreceptor usage with sequence information from the second hypervariable loop of gp120. J Infect Dis. 2010;202(9):1435–43. https://doi.org/10.1086/656600.
Tscherning C, et al. Differences in chemokine coreceptor usage between genetic subtypes of HIV-1. Virology. 1998;241(2):181–8. https://doi.org/10.1006/viro.1997.8980.
Vartanian JP, et al. Selection, recombination, and G to A hypermutation of human immunodeficiency virus type 1 genomes. J Virol. 1991;65(4):1779–88. https://doi.org/10.1128/jvi.65.4.1779-1788.1991.
Vasan A, et al. Different rates of disease progression of HIV type 1 infection in Tanzania based on infecting subtype. Clin Infect Dis. 2006;42(6):843–52. https://doi.org/10.1086/499952.
Wambui V, et al. Predicted HIV-1 coreceptor usage among Kenya patients shows a high tendency for subtype D to be CXCR4 tropic. AIDS Res Ther. 2012;9:1–7. https://doi.org/10.1186/1742-6405-9-22.
Ward MJ, et al. Estimating the rate of intersubtype recombination in early HIV-1 group M strains. J Virol. 2013;87(4):1967–73. https://doi.org/10.1128/JVI.02478-12.
de Wolf F, et al. Syncytium-inducing and non-syncytium-inducing capacity of human immunodeficiency virus type 1 subtypes other than B: phenotypic and genotypic characteristics. AIDS Res Hum Retroviruses. 1994;10(11):1387–400. https://doi.org/10.1089/aid.1994.10.1387.
Worobey M, et al. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature. 2008;455(7213):661–4. https://doi.org/10.1038/nature07390.
Yamaguchi J, et al. Universal target capture of HIV sequences from NGS libraries. Front Microbiol. 2018; pp. 1–13. https://doi.org/10.3389/fmicb.2018.02150.
Yebra G, et al. Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic. In: Scientific Reports. Nature Publishing Group; 2016, pp. 1–6. https://doi.org/10.1038/srep39489.
Yu G, et al. Ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8(1):28–36. https://doi.org/10.1111/2041-210X.12628.
Zhu T, et al. An African HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature. 1998;391:594–7.