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

Syed Hani Abidi, Aga Khan University
Aniqa Shahid, Aga Khan University
Laila S. Lakhani, Aga Khan University
Reena Shah, Aga Khan University
Nancy Okinda, Aga Khan University
Peter Ojwang, Aga Khan University
Farhat Abbas, Aga Khan University
Sarah Rowland-Jones, Oxford University
Syed Ali, Aga Khan University


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.