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

Authors

Wardah Rafaqat, Aga Khan UniversityFollow
Uroosa Tariq, Aga Khan UniversityFollow
Nida Farooqui, Aga Khan UniversityFollow
Maheen Zaidi, Aga Khan UniversityFollow
Aanish Raees, Cincinnati Children's Hospital Medical Center, Cincinnati
Maaz Zuberi, Aga Khan University
Amna Batool, Aga Khan University
Syed Hani Abidi, Aga Khan UniversityFollow

Document Type

Article

Department

Medical College Pakistan; Biological and Biomedical Sciences

Abstract

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.

Comments

Pagination are not provided by the author/publisher.

Publication (Name of Journal)

PLOS One

Recommended Citation

Rafaqat, W., Tariq, U., Farooqui, N., Zaidi, M., Raees, A., Zuberi, M., Batool, A., Abidi, S. H. (2022). Analysis of temporal changes in HIV-1 CRF01_AE gag genetic variability and CD8 T-cell epitope evolution. PLOS One, 17(5).
Available at: https://ecommons.aku.edu/pakistan_fhs_mc_mc/284

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This work is licensed under a Creative Commons Attribution 4.0 International License.