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Rafaqat W, Tariq U, Farooqui N, Zaidi M, Raees A, Zuberi M, Batool A, Abidi SH. Analysis of temporal changes in HIV-1 CRF01_AE gag genetic variability and CD8 T-cell epitope evolution. PLoS One 2022; 17:e0267130. [PMID: 35536783 PMCID: PMC9089901 DOI: 10.1371/journal.pone.0267130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/02/2022] [Indexed: 11/19/2022] Open
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.
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Wang C, Liu D, Zuo T, Hora B, Cai F, Ding H, Kappes J, Ochsenbauer C, Kong W, Yu X, Bhattacharya T, Perelson AS, Gao F. Accumulated mutations by 6 months of infection collectively render transmitted/founder HIV-1 significantly less fit. J Infect 2019; 80:210-218. [PMID: 31812703 DOI: 10.1016/j.jinf.2019.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/22/2019] [Accepted: 12/01/2019] [Indexed: 01/16/2023]
Abstract
OBJECTIVE Viral fitness plays an important role in HIV-1 evolution, transmission and pathogenesis. However, how mutations accumulated during early infection affect viral fitness has not been well studied. METHODS Paired infectious molecular clones (IMCs) for transmitted/founder (T/F) and 6-month (6-mo) viruses post infection were generated from 10 infected individuals to investigate the impact of accumulated mutations on viral fitness by comparing 6-mo viruses to their cognate T/F viruses. RESULTS All ten 6-mo viruses were less fit than their cognate T/F viruses. Moreover, the fitness losses of the 6-mo viruses correlated with the decrease in viral loads from the peak of viremia. CONCLUSION These results show that the mutations accumulated during half a year post infection collectively reduce viral fitness and thereby contribute to lowering viral loads.
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Affiliation(s)
- Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Donglai Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Division of the Second in Vitro Diagnostic, National Institute for Food and Drug Control, Beijing 100050, China
| | - Tao Zuo
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Bhavna Hora
- Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Fangping Cai
- Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - John Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Alan S Perelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.
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