GENETIC CHARACTERISTICS OF THE HYPER-VARIABLE REGION (V3-V5) OF env GENE OF HIV-1 DISTINGUISHING SUBTYPE C FROM SUBTYPE B

Aim: Carry out molecular characterization of subtype B a nd C sequences encompassing the hyper-variable region (V3V5) of envelope (env) gene of HIV-1 to determine the genetic characters that distinguish and may possi bly account for differential pathogenicity of the two subtypes. Experimental Design: Blood samples were collected from 25 HIV-1 sero-positive patients from India. Hyper-variable r egion (V3-V5) of env gene was amplified and sequenced. 173 sequences belonging to subtypes B and C were retrie ved from Los Alamos database. Co-receptor prediction, antigenic loop, co-receptor variability in CCR5 and CXCR4 utilizing subtype B and C sequences, N glycosylation s ite, signature sequence and phylogenetic analysis was carried out. Results: Loss of N glycosylation sites in CXCR4 co-receptor utilizing sequences were observed in 37% of subtype B and 23% of subtype C sequences. Antigenic tip in majority of the subtype C isolates was GPGQTFY. Significant entropy differences were observed in CCR5 and CXCR4 coreceptor utilizing sequences of subtypes B and C. W e observed several signature amino acid residues wh ich occurred in high frequencies in Subtype C CCR5/CXCR4) co-receptor utilizing sequences. Conclusions: In conclusion, the determined molecular characteristics of subtypes B and C may partially be involved in the high pathoge nicity of subtype C.