Genetic Diversity of HIV-1 Isolates and Anti-Retroviral Drug Resistance from Patients in Kirinyaga County, Kenya

Abstract

Background: Human Immunodeficiency Virus type 1 (HIV-1) is the prototype immunodeficiency virus; it is highly virulent and is the cause of AIDS in most parts of the world. AIDS-related deaths have drastically reduced with antiretroviral treatment, even though access to therapy is not universal especially in low-income countries. In recent times, HIV research has been augmented, but as yet, the prospects of an AIDS cure and an effective immunizing agent are still uncertain. There is a great diversity in HIV-1 strains circulating globally as evidenced by phylogenetic analyses. Detailed studies show an intricate pattern of recombination between subtypes with further proof of sub-subtypes in circulation. In Kenya, the prevalent subtype of HIV-1 in circulation is subtype A-1. With the devolution of the health docket from the national to the county government, there is the need to reorient HIV research to the county level to equip county medical staff with current and accurate data on the efficacy of antiretroviral therapy. The main focus of this research was to establish the genetic diversity and antiretroviral drug resistance of HIV-1 isolates from Kirinyaga County, Kenya. HIV-1 genetic diversity compounded with the problem of drug resistance have a great implication on treatment, spread, and HIV-1 viral evolution.

Methodology: A cross-sectional molecular epidemiological study using purposive sampling was used to select sixty HIV-positive blood samples from patients in Kerugoya County Hospital in Kirinyaga County. HIV-1 proviral DNA was extracted from genomic DNA and amplified using specific primers for the HIV genomic pol region encoding the enzyme reverse transcriptase, and the amplicons sequenced. Resistance mutations were inferred from the Stanford database on HIV drug resistance.

Results: Sequence analysis established that subtype A1 was the most predominant in the County accounting for 66.67%(22/33), followed by subtypes D at 12.12%(4/33) and C at 9.09%(3/33) each. Four of the samples were found to be recombinants accounting for 12.12% of all the samples sequenced. 12.12%(4/33) of the samples had major drug resistance mutations to reverse transcriptase inhibitor drugs. There were Minor mutations and polymorphisms in all the 33 isolates analyzed for subtypes and mutations.

Conclusions: The study has shown that HIV-1 subtype A1 dominates Kirinyaga County population while HIV drug resistance is significant (12.12%) in the population. Information on subtypes and DRMs generated from this study will help in updating the HIV surveillance data generated annually by the Kenya Medical Research Institute together with other Research Institutes carrying out HIV-1 research and monitoring. The data can also be useful in advising on policy for diagnosis and development of HIV-1 vaccines in the country.