Analysis of temporal changes in HIV-1 CRF01_AE gag genetic variability and CD8 T-cell epitope evolution

• Published in: PloS one 2022-05, Vol.17 (5), p.e0267130-e0267130
• Main Authors: Rafaqat, Wardah, Tariq, Uroosa, Farooqui, Nida, Zaidi, Maheen, Raees, Aanish, Zuberi, Maaz, Batool, Amna, Abidi, Syed Hani
• Format: Article
• Language: English
• Subjects: Analysis; Antigenic determinants; Antigens; Bayes Theorem; Bayesian analysis; Biology and Life Sciences; CD8 antigen; CD8-Positive T-Lymphocytes; China; Comparative analysis; Complications and side effects; Computer and Information Sciences; Cytotoxicity; Diagnosis; Dynamic tests; Engineering and Technology; Entropy; Entropy (Information theory); Epidemics; Epitopes; Epitopes, T-Lymphocyte - genetics; Evolution; Gag protein; Genetic variability; Health aspects; Histocompatibility antigen HLA; HIV; HIV (Viruses); HIV Infections; HIV-1; Human immunodeficiency virus; Humans; Immunodominance; Immunogenetics; Leukocytes; Lymphocytes; Lymphocytes T; Medicine and Health Sciences; Mutation; Peptides; Phylogenetics; Phylogeny; Physical Sciences; Population; Population number; Proteasomes; Proteins; T cells; Time dependence; Vaccines; Variability; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0267130

Currently, little is known about the time-dependent evolution of human immunodeficiency virus-1 (HIV-1) circulating recombinant forms (CRF) 01_AE, a dominant recombinant form associated with HIV-1 epidemics worldwide. Since gag is a highly immunodominant HIV-1 protein, we performed a comparative analysis of the CRF01_AE gag protein's time-dependent changes and evolution. A total of 3105 HIV-1 CRF01_AE gag sequences representing 17 countries from the timeline 1990-2017 were obtained. The sequences' phylogenetic relationship and epidemic dynamics were analyzed through a Maximum Likelihood tree and Bayesian Skyline plot, respectively. Genomic variability was measured through Shannon entropy and time-dependent immunoevolution was analyzed using changes in proteasomal degradation pattern, cytotoxic T lymphocytes (CTL) epitopes, and Human leukocyte antigens (HLA) restriction profile. The most recent common ancestor of the HIV CRF01_AE epidemic was estimated to be 1974±1. A period of exponential growth in effective population size began in 1982, fluctuated, and then stabilized in 1999. Genetic variability (entropy) consistently increased, however, epitope variability remained comparable; the highest number of novel CTL epitopes were present in 1995-1999, which were lost over time. The spread of the HIV-1 CRF01_AE epidemic is predominant in countries within Asia. Population immunogenetic pressures in the region may have contributed to the initial changes and following adaptation/stabilization of epitope diversity within gag sequences.