Molecular analysis of HIV mutations and determination Of subtypes circulating in gem, western Kenya

Abstract

As the HIV pandemic becomes increasingly complex and devastating in Africa, there is need to come up with better management strategies in terms of treatment, vaccine and better testing methods. However, this is getting hampered by the high diversity of Human Immunodeficiency Virus type 1 (HIV -I), which is brought about by high rate of replication and mutation. Such mutations may cause antiretroviral drug resistance if they occur in the gene regions coding for molecular drug targets. The high rate of mutation also leads to many viruses which are genetically related but distinguishable variants and subtypes. In this study, molecular analysis of the protease and reverse transcriptase gene sequences of the HIV -I in plasma samples collected from Gem in western Kenya was done. Sequencing of these genes was done with the aim of identifying mutations and analyzing each for antiretroviral drug resistance. Also, determination of the subtypes based on these sequences was done. A total of 30 samples were taken for sequencing, however, 9 of them had primer failures and therefore did not successfully sequence, leaving only 21 samples for molecular analysis. The results showed several mutations in these gene sequences, and analysis of each of the mutation for drug resistance showed none to be causing resistance to any of the known classes of ARV drugs. For the phylogenetic analysis, 16 (76.2%) of the isolates were found to be subtype A, subtype D were 4 (19.0%), and the remaining I (4.8%) was circulating recombinant form, CRF _AD. To verify the results, control sample was analyzed by both TruGene and ill-house methods and both gave the same results. Since this study revealed three different HIV-I subtypes in Gem, it would be necessary to conduct a future study to find out the effect of these subtypes on the transmission, pathogenicity and the rate of HIV-I disease progression in Gem, western Kenya.