1. Greene WC. A history of AIDS: Looking back to see ahead. Eur J Immunol. 2008; doi:10.1002/eji.200737441
2. Fauci AS, Marston HD. Ending AIDS--is an HIV vaccine necessary? N Engl J Med. 2014; 370:495-8. doi:10.1056/NEJMp1313771
3. UNAIDS [Internet]. Fact Sheet 2021 - Preliminary epidemiological estimates. 2021 [accessed July 2021]. Available from: https://www.unaids.org/sites/default/files/media_asset/UNAIDS_FactSheet_en.pdf.
4. UNAIDS [Internet]. Global 2019 HIV/AIDS Statistics. 2020 [accessed May 2021]. Available from: https://www.unaids.org/en/resources/documents/2020/unaids-data.
5. HSRC. The fifth South African national HIV prevalence, incidence, behaviour and communication survey, 2017: HIV impact assessment summary report. HSRC Press Cape Town; 2018.
6. Tiemessen CT, Martinson N. Elite controllers: understanding natural suppressive control of HIV-1 infection. CMEJ. 2012; 30:282-5.
7. Gulzar N, Copeland KF. CD8+ T-cells: function and response to HIV infection. Curr HIV Res. 2004; 2:23-37. doi:10.2174/1570162043485077
8. Collins DR, Gaiha GD, Walker BD. CD8+ T cells in HIV control, cure and prevention. Nature Reviews Immunology. 2020; 20:471-82. doi:10.1038/s41577-020-0274-9
9. Perdomo-Celis F, Taborda NA, Rugeles MT. CD8(+) T-Cell Response to HIV infection in the era of antiretroviral therapy. Front Immunol. 2019; 10:1896-. doi:10.3389/fimmu.2019.01896
10. McMichael AJ, Borrow P, Tomaras GD, Goonetilleke N, Haynes BF. The immune response during acute HIV-1 infection: clues for vaccine development. Nat Rev Immunol. 2010; 10:11-23. doi:10.1038/nri2674
11. Tshabalala M, Mellet J, Pepper MS. Human Leukocyte Antigen diversity: A Southern African perspective. J Immunol Res. 2015; 2015:746151. doi:10.1155/2015/746151
12. Hammond M, Anley D, editors. Tamil from Natal province South Africa. 13th International Histocompatibility Workshop; 2006; Seattle. Washington, USA: International Histocompatibility Working Group Press.
13. Allen TM, Altfeld M, Yu XG, O'Sullivan KM, Lichterfeld M, Le Gall S., et al. Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection. J Virol. 2004; 78:7069-78. doi:10.1128/jvi.78.13.7069-7078.2004
14. Draenert R, Le Gall S, Pfafferott KJ, Leslie AJ, Chetty P, Brander C., et al. Immune selection for altered antigen processing leads to cytotoxic T lymphocyte escape in chronic HIV-1 infection. J Exp Med. 2004; 199:905-15. doi:10.1084/jem.20031982
15. Kiepiela P, Ngumbela K, Thobakgale C, Ramduth D, Honeyborne I, Moodley E., et al. CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nat Med. 2007; 13:46-53. doi:10.1038/nm1520
16. Masemola A, Mashishi T, Khoury G, Mohube P, Mokgotho P, Vardas E., et al. Hierarchical targeting of subtype C human immunodeficiency virus type 1 proteins by CD8+ T cells: correlation with viral load. J Virol. 2004; 78(7):3233-43. doi:10.1128/jvi.78.7.3233-3243.2004
17. Kunwar P, Hawkins N, Dinges WL, Liu Y, Gabriel EE, Swan DA., et al. Superior control of HIV-1 replication by CD8+ T cells targeting conserved epitopes: implications for HIV vaccine design. PLoS One. 2013; 8:e64405. doi:10.1371/journal.pone.0064405
18. Borthwick N, Lin Z, Akahoshi T, Llano A, Silva-Arrieta S, Ahmed T., et al. Novel, in-natural-infection subdominant HIV-1 CD8+ T-cell epitopes revealed in human recipients of conserved-region T-cell vaccines. PloS One. 2017; 12:e0176418. doi:10.1371/journal.pone.0176418
19. Acevedo-Sáenz L, Ochoa R, Rugeles MT, Olaya-García P, Velilla-Hernández PA, Diaz FJ. Selection pressure in CD8+ T-cell epitopes in the pol gene of HIV-1 infected individuals in Colombia. A bioinformatic approach. Viruses. 2015; 7:1313-31. doi:10.3390/v7031313
20. Hsu DC, O'Connell RJ. Progress in HIV vaccine development. Hum Vaccin Immunother. 2017; 13:1018-30. doi:10.1080/21645515.2016.1276138
21. Harmon TM, Fisher KA, McGlynn MG, Stover J, Warren MJ, Teng Y., et al. Exploring the Potential Health Impact and Cost-Effectiveness of AIDS Vaccine within a Comprehensive HIV/AIDS Response in Low- and Middle-Income Countries. PLoS One. 2016; 11:e0146387. doi:10.1371/journal.pone.0146387
22. Buchbinder SP, Mehrotra DV, Duerr A, Fitzgerald DW, Mogg R, Li D., et al. Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): a double-blind, randomised, placebo-controlled, test-of-concept trial. Lancet. 2008; 372:1881-93. doi:10.1016/s0140-6736(08)61591-3
23. Gray GE, Allen M, Moodie Z, Churchyard G, Bekker LG, Nchabeleng M., et al. Safety and efficacy of the HVTN 503/Phambili study of a clade-B-based HIV-1 vaccine in South Africa: a double-blind, randomised, placebo-controlled test-of-concept phase 2b study. Lancet Infect Dis. 2011; 11:507-15. doi:10.1016/s1473-3099(11)70098-6
24. Priddy FH, Brown D, Kublin J, Monahan K, Wright DP, Lalezari J., et al. Safety and immunogenicity of a replication-incompetent adenovirus type 5 HIV-1 clade B gag/pol/nef vaccine in healthy adults. Clin Infect Dis. 2008; 46:1769-81. doi:10.1086/587993
25. Stephenson KE, Wagh K, Korber B, Barouch DH. Vaccines and broadly neutralizing antibodies for HIV-1 prevention. Annu Rev Immunol. 2020; 38:673-703. doi:10.1146/annurev-immunol-080219-023629
26. Mayaphi SH. Detection and characterisation of primary (acute and early) HIV-1 infections in an HIV hyper-endemic area [Thesis]. Pretoria: University of Pretoria; 2018.
27. LANL [Internet]. HIV molecular immunology database. Los Alamos National Laboratory (NIH); 2021. Available from: https://www.hiv.lanl.gov/content/immunology/tables/ctl_summary.html.
28. Leslie A, Matthews PC, Listgarten J, Carlson JM, Kadie C, Ndung'u T., et al. Additive contribution of HLA class I alleles in the immune control of HIV-1 infection. J Virol. 2010; 84:9879-88. doi:10.1128/JVI.00320-10
29. Carlson JM, Listgarten J, Pfeifer N, Tan V, Kadie C, Walker BD., et al. Widespread impact of HLA restriction on immune control and escape pathways of HIV-1. J Virol. 2012; 86:5230-43. doi:10.1128/JVI.06728-11
30. Loubser S, Paximadis M, Gentle NL, Puren A, Tiemessen CT. Human leukocyte antigen class I (A, B, C) and class II (DPB1, DQB1, DRB1) allele and haplotype variation in Black South African individuals. Hum Immunol. 2020; 81:6-7. doi:10.1016/j.humimm.2019.12.003
31. Paximadis M, Mathebula TY, Gentle NL, Vardas E, Colvin M, Gray CM., et al. Human Leukocyte Antigen class I (A, B, C) and II (DRB1) diversity in the black and Caucasian South African population. Hum Immunol. 2012; 73:80-92. doi:10.1016/j.humimm.2011.10.013
32. Coetzee V, Barrett L, Greeff JM, Henzi SP, Perrett DI, Wadee AA. Common HLA alleles associated with health, but not with facial attractiveness. PLoS One. 2007; 2:e640. doi:10.1371/journal.pone.0000640
33. Brumme ZL, Brumme CJ, Carlson J, Streeck H, John M, Eichbaum Q., et al. Marked epitope-and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) gag, pol, and nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. J Virol. 2008; 82:9216-27. doi:10.1128/JVI.01041-08
34. Bbosa N, Kaleebu P, Ssemwanga D. HIV subtype diversity worldwide. Curr Opin HIV AIDS. 2019; 14:153-60. doi:10.1097/coh.0000000000000534
35. Buonaguro L, Tornesello M, Buonaguro F. Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications. J Virol. 2007; 81:10209-19. doi:10.1128/JVI.00872-07
36. Jacobs GB, Wilkinson E, Isaacs S, Spies G, De Oliveira T, Seedat S., et al. HIV-1 subtypes B and C unique recombinant forms (URFs) and transmitted drug resistance identified in the Western Cape Province, South Africa. PloS One. 2014; 9:e90845. doi:10.1371/journal.pone.0090845
37. Heipertz Jr RA, Ayemoba O, Sanders-Buell E, Poltavee K, Pham P, Kijak GH., et al. Significant contribution of subtype G to HIV-1 genetic complexity in Nigeria identified by a newly developed subtyping assay specific for subtype G and CRF02_AG. Medicine. 2016; 95(32)
38. Kumar KR, Cowley MJ, Davis RL. Next-Generation Sequencing and Emerging Technologies. Semin Thromb Hemost. 2019; 45(7):661-73. doi:10.1055/s-0039-1688446
39. Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet. 2011; 52(4):413-35. doi:10.1007/s13353-011-0057-x
40. Caetano DG, Côrtes FH, Bello G, Teixeira SLM, Hoagland B, Grinsztejn B., et al. Next-generation sequencing analyses of the emergence and maintenance of mutations in CTL epitopes in HIV controllers with differential viremia control. BMC Retrovirol. 2018; 15(1):62. doi:10.1186/s12977-018-0444-z
41. Tumiotto C, Riviere L, Bellecave P, Recordon-Pinson P, Vilain-Parce A, Guidicelli GL., et al. Sanger and Next-Generation Sequencing data for characterization of CTL epitopes in archived HIV-1 proviral DNA. PLoS One. 2017; 12(9):e0185211. doi:10.1371/journal.pone.0185211
42. Kim J, De La Cruz J, Lam K, Ng H, Daar ES, Balamurugan A., et al. CD8(+) Cytotoxic T Lymphocyte Responses and Viral Epitope Escape in Acute HIV-1 Infection. Viral Immunol. 2018; 31(7):525-36. doi:10.1089/vim.2018.0040
43. Li F, Finnefrock AC, Dubey SA, Korber BT, Szinger J, Cole S., et al. Mapping HIV-1 vaccine induced T-cell responses: bias towards less-conserved regions and potential impact on vaccine efficacy in the Step study. PloS One. 2011; 6:e20479. doi:10.1371/journal.pone.0020479
44. Goonetilleke N, Liu MK, Salazar-Gonzalez JF, Ferrari G, Giorgi E, Ganusov VV., et al. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J Exp Med. 2009; 206:1253-72. doi:10.1084/jem.20090365
45. Ojwach DBA, MacMillan D, Reddy T, Novitsky V, Brumme ZL, Brockman MA., et al. Pol-Driven Replicative Capacity Impacts Disease Progression in HIV-1 Subtype C Infection. J Virol. 2018; 92(19) doi:10.1128/jvi.00811-18
46. Rhee SY, Sankaran K, Varghese V, Winters MA, Hurt CB, Eron JJ., et al. HIV-1 Protease, Reverse Transcriptase, and Integrase Variation. J Virol. 2016; 90(13):6058-70. doi:10.1128/jvi.00495-16
47. Miura T, Brumme ZL, Brockman MA, Rosato P, Sela J, Brumme CJ., et al. Impaired replication capacity of acute/early viruses in persons who become HIV controllers. J Virol. 2010; 84(15):7581-91. doi:10.1128/jvi.00286-10
48. Pernas M, Casado C, Arcones C, Llano A, Sánchez-Merino V, Mothe B., et al. Low-replicating viruses and strong anti-viral immune response associated with prolonged disease control in a superinfected HIV-1 LTNP elite controller. PLoS One. 2012; 7(2):e31928. doi:10.1371/journal.pone.0031928
49. Mellet J, Tshabalala M, Agbedare O, Meyer P, Gray CM, Pepper MS. Human leukocyte antigen (HLA) diversity and clinical applications in South Africa. S Afr Med J. 2019; 109:29-34. doi:10.7196/SAMJ.2019.v109i8b.13825
50. Goulder PJ, Walker BD. HIV and HLA class I: an evolving relationship. Immunity. 2012; 37:426-40. doi:10.1016/j.immuni.2012.09.005
51. Payne R, Muenchhoff M, Mann J, Roberts HE, Matthews P, Adland E., et al. Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence. Proc Natl Acad Sci U S A. 2014; 111(50):E5393-400. doi:10.1073/pnas.1413339111
52. Adland E, Hill M, Lavandier N, Csala A, Edwards A, Chen F., et al. Differential Immunodominance Hierarchy of CD8(+) T-Cell Responses in HLA-B*27:05- and -B*27:02-Mediated Control of HIV-1 Infection. J Virol. 2018; 92 doi:10.1128/jvi.01685-17
53. Liu Y, McNevin J, Rolland M, Zhao H, Deng W, Maenza J., et al. Conserved HIV-1 epitopes continuously elicit subdominant cytotoxic T-lymphocyte responses. J Infect Dis. 2009; 200(12):1825-33. doi:10.1086/648401
54. Tebit DM, Arts EJ. Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease. Lancet Infect Dis. 2011; 11:45-56. doi:10.1016/S1473-3099(10)70186-9
55. Friedrich TC, Valentine LE, Yant LJ, Rakasz EG, Piaskowski SM, Furlott JR., et al. Subdominant CD8+ T-cell responses are involved in durable control of AIDS virus replication. J Virol. 2007; 81(7):3465-76. doi:10.1128/jvi.02392-06
56. Ahmed T, Borthwick NJ, Gilmour J, Hayes P, Dorrell L, Hanke T. Control of HIV-1 replication in vitro by vaccine-induced human CD8(+) T cells through conserved subdominant Pol epitopes. Vaccine. 2016; 34(9):1215-24. doi:10.1016/j.vaccine.2015.12.021
57. Liu Y, McNevin J, Zhao H, Tebit DM, Troyer RM, McSweyn M., et al. Evolution of human immunodeficiency virus type 1 cytotoxic T-lymphocyte epitopes: fitness-balanced escape. J Virol. 2007; 81:12179-88. doi:10.1128/jvi.01277-07
58. Yokomaku Y, Miura H, Tomiyama H, Kawana-Tachikawa A, Takiguchi M, Kojima A., et al. Impaired processing and presentation of cytotoxic-T-lymphocyte (CTL) epitopes are major escape mechanisms from CTL immune pressure in human immunodeficiency virus type 1 infection. J Virol. 2004; 78(3):1324-32. doi:10.1128/jvi.78.3.1324-1332.2004
59. Sun J, Zhao Y, Peng Y, Han Z, Liu G, Qin L., et al. Multiple T-cell responses are associated with better control of acute HIV-1 infection: An observational study. Medicine 2016; 95:e4429. doi:10.1097/md.0000000000004429
60. Koibuchi T, Allen TM, Lichterfeld M, Mui SK, O'Sullivan KM, Trocha A., et al. Limited sequence evolution within persistently targeted CD8 epitopes in chronic human immunodeficiency virus type 1 infection. J Virol. 2005; 79(13):8171-81. doi:10.1128/jvi.79.13.8171-8181.2005
61. Mohamed YS, Borthwick NJ, Moyo N, Murakoshi H, Akahoshi T, Siliquini F., et al. Specificity of CD8+ T-Cell responses following vaccination with conserved regions of HIV-1 in Nairobi, Kenya. Vaccine. 2020; 8:260. doi:10.3390/vaccines8020260
62. Zou C, Murakoshi H, Kuse N, Akahoshi T, Chikata T, Gatanaga H., et al. Effective Suppression of HIV-1 Replication by Cytotoxic T Lymphocytes Specific for Pol Epitopes in Conserved Mosaic Vaccine Immunogens. J Virol. 2019; 93(7) doi:10.1128/jvi.02142-18