Molecular Characterization of Pol Gene of HIV in Pakistan

Abstract

Human Immunodeficiency Virus (HIV) is a single stranded RNA virus belong to family Retroviridae and genus Lentivirus. HIV is the major causative agent of a lethal condition called Acquired-Immunodeficiency-Syndrome (AIDS). World Health Organization (WHO) reported 38 million HIV infected people globally. By the end of 2021, 1.7 million new HIV cases and 0.69 million deaths were reported. Pakistan is among those countries where HIV prevalence is increasing rapidly and a remarkable increase of 57% new HIV cases have been reported in the last decade. In current study, blood samples were taken from high-risk behavior individuals from different cities of Pakistan. The HIV positive samples were confirmed by Real Time Polymerase Chain Reaction. The Real Time-PCR based positive samples were further processed for pol gene amplification followed by nucleotide sequencing through Sanger method. Phylogenic analysis was performed through Maximum likelihood method using Hasegawa-Kishino-Yano + Gamma with Invariant-sites (HKY+G+I) model. Moreover, amino acid substitutions were also identified. The amplified pol gene sequence of our isolates QAU AZ1 and QAU-AZ3 clustered with a previously reported sequence from China (Accession no. MN908916), while isolate QAU-AZ2 clustered with a Pakistani sequence (Accession no. JQ011662). Moreover, amino acid substitutions were identified in all three isolates. The positions of these substitutions were analyzed with reference sequence (GenBank Accession No. AHF27452). The 2D and 3D structure of all isolates and reference protein revealed no change in structure of protein as the substituted amino acids are involved in function of proteins. Further studies are required to investigate the pol gene of the viral isolates from Pakistani patients to identify possible drug resistance associated with amino acid substitutions. Keywords: HIV, pol gene, pol protein, Phylogenetic analysis, Mutational analysis.