Impact of unique host genetic variants in the HIV life cycle, differentiates the long-term non-progressors and rapid progressors in South Indian females

Abstract

Human immunodeficiency virus infected individuals manifest variability to resistance and susceptibility towards the progression of acquired immunodeficiency syndrome. This contrariety challenges the understanding of host genome for the disease progression and resistance. In this study, the reasons for the differential disease progression based on the immunogenetics of the individuals are explored through whole exome sequencing. A retrospective study of 19 HIV patients, clinically classified as Long-Term Non-Progressors (LTNPs = 9) and Rapid Progressors (RPs = 10), were sequenced for their coding regions using Illumina platform. The raw data of these 19 samples were analyzed for calling single nucleotide polymorphism using various bioinformatics tools like Alignment, GATK, and SnpEff. The variations in the exome were filtered based on missense pathogenicity and combined annotation dependent depletion score. The present study identified the variations in 35 host genes involved in HIV viral life cycle that differentiate the progression of AIDS in the infected individuals. Among these host genetic variants, the variations in the genes SERINC2, NUP153, PSIP1, SUPT4H1 and EP300 were found only in the LTNPs but not in RPs. Similarly the variations in the genes TRIM54, KAT2B, BICD2, FEZ, and MAP1LC3B were found only in the RPs. The variations in the genes PDCD6IP & MAP1A were observed both in LTNPs & RPs. Hence, the 5 genetic variants specifically found in the LNTPs might have a key role in the delayed progression of AIDS.