Genetic and Molecular Characterization of Gag Gene of Human Immunodeficiency Virus

Abstract

Human Immunodeficiency Virus (HIV) which is the major cause of a condition called Acquired Immunodeficiency Syndrome (AIDS). It is a single-stranded RNA virus from Retroviridae family and genus Lentivirus. Global burden of HI V has been increasing and World Health Organization (WHO) recently (as of 2019) revealed a staggering increase as 1.7 million new cases and 0.69 million deaths have been reported. Pakistan is among those countries where HIV prevalence is increasing. In this current study, we isolated blood samples from high-risk behavior individuals of HIV infection referred to some cities of Pakistan like Islamabad, Lahore, Peshawar and Kohat. The HIV positive individuals were confinued by Real Time-Polymerase Chain Reaction (RT PCR). The Real Time PCR based positive samples were further processed for Gag gene amplification following nucleotide sequencing through Sanger method. The evolutionary history was inferred by using the Jukes-Cantor model and Neighbor-Joining method. Sequences analyzed in the current study (isolates QAU-HIVI-AHI and QAU- HIVI -AH2) clustered with a previously reported reference sequence (accession No. KX232595). In the present study, we report several amino acid substitutions in functionally important domains of Gag gene. Key substitutions in the isolate QAU-HIVI-AHI are W212M, P328Q, N392S, E474K, D479T, and Q480R. Whereas, amino acid substitutions found in isolate QAU-HIVI-AH2 are L321M, L322Q, V323I, N325I, A326V, N327R, N374Y, K413Q and S477C position of the latterly analyzed reference sequence (KX232595). On the basis of current results, we suggest that the mentioned substitutions are linked with structural variation in the protein and could alter protein's function(s). The Gag gene of the viral isolates from Pakistani patients need to be further explored for possible drug resistance associated substitutions