MOLECULAR ANALYSIS OF A COMPLETE HIV-1 Pol GENE ISOLATED IN CENTRAL JAVA, INDONESIA

Abstract

Background: HIV-1 is an infectious agent causing global health problem. Molecular analysis of HIV-1 strains is crucial due to the association with viral fitness, drug resistance, serological failure, and more importantly, for vaccine development. However, HIV-1 molecular data in Indonesia is limited, including that of the HIV pol gene. Aims: The present study performed a molecular analysis of the pol gene of HIV isolated in Central Java, Indonesia, in order to enrich HIV-1 molecular data in Indonesia, particularly in Central Java.Methods: A complete coding sequence of pol gene was cloned from 09IDSKA-6 (HIV isolated in Central Java, Indonesia), inserted into an Escherichia coli expression plasmid, and sequenced. The sequencing results of the pol gene then subjected for virus subtyping, genotyping, and phylogenetic analysis. The drug resistance, identification of the HLA binding motifs and viral epitopes, proteomic motifs, and physicochemical analysis was performed.Results: The HIV-1 isolate analyzed in this study was CRF01_AE strain. The isolate remains in low evolutionary state due to the low level of nonsynonymous to synonymous substitutions ratio (dN/dS). None of mutations identified was related to ARV drug resistance. A total of 33 CTL/CD8+ epitopes, 6 T-helper/CD4+ epitopes and 2 antibody epitopes were identified in our isolate. Six distinct proteomic domains were found. Physicochemical analysis revealed the molecular weight (Mw), estimated half-life, instability index, aliphatic index, and hydrophilicity of each proteins encoded by the complete HIV-1 pol gene.