Variations and evolution of HIV-1 provirus in peripheral blood under the pressure of ART

Abstract Human immunodeficiency virus type 1 (HIV-1) infection is characterized by its rapid evolution and extensive genetic diversity. This study analyzed sequence polymorphism in a longitudinal cohort of people living with HIV (PLWH) who have been on antiretroviral therapy (ART) while also comparing quasispecies heterogeneity across distinct genomic regions to reflect the evolutionary variation and selective pressures acting on HIV-1. A total of 138 follow-up time points from 31 subjects who have been on ART were included in this study. The HIV-1 Gag p17 and Env C2V3 gene regions were amplified and subjected to high-throughput sequencing to obtain the target sequences. The study results indicate that the amino acids of the HIV-1 V3 loop sequences were polymorphic, and dynamic changes in the proportion of dominant viral quasispecies were observed across different follow-up time points within the same PLWH. Genetic diversity in the p17 and C2V3 regions decreased with longer ART duration. Compared to the Gag gene, the Env gene exhibited a greater genetic distance, a higher rate of non-synonymous mutations (dN), and a larger dN/dS ratio at baseline, indicating a significant difference in the evolutionary selection pressure between the Gag and Env genes. The size of the HIV-1 reservoir tended to decrease with the extension of ART duration. In summary, viral genomic diversity and quasispecies heterogeneity are decreased under the selective pressure of ART, and the size of the HIV-1 reservoir tends to decrease. HIV-1 evades immune recognition and clearance through sequence variation. While the Env gene is subject to positive selection, the HIV-1 Gag gene is subject to purifying selection.