Studies on HIV 1 Genetic Variability in South India Tamil Nadu

Abstract

This study was carried out to determine HIV-1 subtypes circulating among four different risk groups [FSW (32%), MSM (33%), Heterosexuals (30%) and IDU (6%)] in Chennai (Urban) and Namakkal (Rural) regions of Tamil Nadu. Male and female ratio was equally distributed and 50% of study subjects were in the age group of 26-35 years. Majority of them (67%) had some formal education. FSW/MSM practice sex work as occupation while heterosexual males and IDU s work as drivers or coolie. Whole blood DNA extractions for 95/101 study subjects were carried out using QIAGEN kit. 6/101 IDU blood samples were collected on FTA filter paper (Whatman) as Dried Blood Spot (DBS). The filter paper was prepared as per manufacturer instructions for down stream PCR reactions. HIV-1 Envelope PCR was carried out with ED5/ED12 for first round PCR and ES7/ES8 for second PCR. 71 samples had amplified successfully for c2v3v5 including six samples collected on FTA filter paper. HIV-1 subtypes of the study groups were determined by Heteroduplex Mobility Assay (HMA) and confirmed by direct sequencing. HMA reveals 83% are infected with subtype C, 7% are infected with subtype A and 10% samples subtype could not be determined by HMA. Subtype A was observed among heterosexual and Female Sex Workers (FSW) categories. It is inferred from this study, non C subtypes are more among the individuals who travel extensively in heterosexual category. However, one FSW who did not travel was also infected with subtype A. Sequencing of randomly selected samples confirmed the HMA results. Further, sequencing identified 7 samples subtypes that were not determined by HMA as 6 Subtype C samples and one CRFO1. Thus HMA is a cost effective technique for screening of HIV-1 subtypes. Phylogenetic analysis reveals study subjects had bootstrap values 70-100%, with high genetic distance. This suggests that they were infected for a long period of time. Very few had bootstrap values 100% with a genetic distance. This suggests that they were infected for a long period of time.