Medical Microbiology and Immunology

, Volume 203, Issue 1, pp 57–63 | Cite as

HIV-1 progression links with viral genetic variability and subtype, and patient’s HLA type: analysis of a Nairobi-Kenyan cohort

  • Syed Hani Abidi
  • Aniqa Shahid
  • Laila S. Lakhani
  • Reena Shah
  • Nancy Okinda
  • Peter Ojwang
  • Farhat Abbas
  • Sarah Rowland-Jones
  • Syed Ali
Original Investigation


In a Nairobi-Kenyan cohort of 50 HIV-1 positive patients, we analysed the prevalence of HIV-1 subtypes and human leucocyte antigen (HLA) alleles. From this cohort, 33 patients were selected for the analysis of HIV-1 infection progression markers (i.e. CD4 cell counts and viral loads) and their association with HIV-1 genetic variability and subtype, and patient’s HLA type. HIV-1 gag genetic variability, analysed using bioinformatics tools, showed an inverse relationship with CD4 cell count whereas with viral load that relationship was direct. Certain HLA types and viral subtypes were also found to associate with patients’ viral load. Associations between disease parameters and the genetic makeup of the host and virus may be crucial in determining the outcome of HIV-1 infection.


HIV Kenya Progression markers Subtype HLA Genetic variability 



For this study, Syed Hani Abidi’s training was funded by HIV Research Trust (Scholarship No. HIVRT 10-059).

Conflict of interest

Authors declare no conflict of interest.

Supplementary material

430_2013_314_MOESM1_ESM.doc (56 kb)
Supplementary material 1 (DOC 56 kb)


  1. 1.
    Hewitt EW (2003) The MHC class I antigen presentation pathway: strategies for viral immune evasion. Immunology 110(2):163–169PubMedCrossRefGoogle Scholar
  2. 2.
    Arien KK, Vanham G, Arts EJ (2007) Is HIV-1 evolving to a less virulent form in humans? Nat Rev Microbiol 5(2):141–151PubMedCrossRefGoogle Scholar
  3. 3.
    Haynes BF, Pantaleo G, Fauci AS (1996) Toward an understanding of the correlates of protective immunity to HIV infection. Science 271(5247):324–328PubMedCrossRefGoogle Scholar
  4. 4.
    Kaur G, Mehra N (2009) Genetic determinants of HIV-1 infection and progression to AIDS: immune response genes. Tissue Antigens 74(5):373–385PubMedCrossRefGoogle Scholar
  5. 5.
    Khoja S, Ojwang P, Khan S, Okinda N, Harania R, Ali S (2008) Genetic analysis of HIV-1 subtypes in Nairobi, Kenya. PLoS One 3(9):e3191PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Reekie J, Gatell JM, Yust I, Bakowska E, Rakhmanova A, Losso M et al (2011) Fatal and nonfatal AIDS and non-AIDS events in HIV-1-positive individuals with high CD4 cell counts according to viral load strata. AIDS 25(18):2259–2268PubMedCrossRefGoogle Scholar
  7. 7.
    Bettinotti MP, Mitsuishi Y, Bibee K, Lau M, Terasaki PI (1997) Comprehensive method for the typing of HLA-A, B, and C alleles by direct sequencing of PCR products obtained from genomic DNA. J Immunother 20(6):425–430PubMedCrossRefGoogle Scholar
  8. 8.
    Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SG (2011) The IMGT/HLA database. Nucleic Acids Res 39(Database issue):D1171–D1176Google Scholar
  9. 9.
    Rose PP, Korber BT (2000) Detecting hypermutations in viral sequences with an emphasis on G → A hypermutation. Bioinformatics 16(4):400–401PubMedCrossRefGoogle Scholar
  10. 10.
    Yang OO (2009) Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation. PLoS One 4(10):e7388PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Cao K, Moormann AM, Lyke KE, Masaberg C, Sumba OP, Doumbo OK et al (2004) Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci. Tissue Antigens 63(4):293–325PubMedCrossRefGoogle Scholar
  12. 12.
    Bird TG, Kaul R, Rostron T, Kimani J, Embree J, Dunn PP et al (2002) HLA typing in a Kenyan cohort identifies novel class I alleles that restrict cytotoxic T-cell responses to local HIV-1 clades. AIDS 16(14):1899–1904PubMedCrossRefGoogle Scholar
  13. 13.
    Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD et al (2010) The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 330(6010):1551–1557PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Carrington M, Nelson GW, Martin MP, Kissner T, Vlahov D, Goedert JJ et al (1999) HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science 283(5408):1748–1752PubMedCrossRefGoogle Scholar
  15. 15.
    Tang J, Tang S, Lobashevsky E, Myracle AD, Fideli U, Aldrovandi G et al (2002) Favorable and unfavorable HLA class I alleles and haplotypes in Zambians predominantly infected with clade C human immunodeficiency virus type 1. J Virol 76(16):8276–8284PubMedCentralPubMedCrossRefGoogle Scholar
  16. 16.
    Trachtenberg E, Korber B, Sollars C, Kepler TB, Hraber PT, Hayes E et al (2003) Advantage of rare HLA supertype in HIV disease progression. Nat Med 9(7):928–935PubMedCrossRefGoogle Scholar
  17. 17.
    Kiwanuka N, Robb M, Laeyendecker O, Kigozi G, Wabwire-Mangen F, Makumbi FE et al (2009) HIV-1 viral subtype differences in the rate of CD4+ T-cell decline among HIV seroincident antiretroviral naive persons in Rakai district, Uganda. J Acquir Immune Defic Syndr 54(2):180–184Google Scholar
  18. 18.
    Baeten JM, Chohan B, Lavreys L, Chohan V, McClelland RS, Certain L et al (2007) 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 195(8):1177–1180PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Syed Hani Abidi
    • 1
  • Aniqa Shahid
    • 1
  • Laila S. Lakhani
    • 2
  • Reena Shah
    • 3
  • Nancy Okinda
    • 4
  • Peter Ojwang
    • 4
  • Farhat Abbas
    • 5
  • Sarah Rowland-Jones
    • 6
  • Syed Ali
    • 1
  1. 1.Department of Biological and Biomedical SciencesAga Khan UniversityKarachiPakistan
  2. 2.Medical CollegeAga Khan UniversityKarachiPakistan
  3. 3.Department of MedicineAga Khan University HospitalNairobiKenya
  4. 4.Department of PathologyAga Khan University HospitalNairobiKenya
  5. 5.Department of SurgeryAga Khan UniversityKarachiPakistan
  6. 6.MRC Human Immunology UnitOxford UniversityOxfordUK

Personalised recommendations