Population-specific evolution of HIV Gag epitopes in genetically diverged patients

Syed H. Abidi, Aniqa Shahid, Laila S. Lakhani, Muhammad R. Khanani, Peter Ojwang, Nancy Okinda, Reena Shah, Farhat Abbas, Sarah Rowland-Jones, Syed Ali

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Background: Under the host selection pressure HIV evolves rapidly to override crucial steps in the antigen presentation pathway. This allows the virus to escape binding and recognition by cytotoxic T lymphocytes. Selection pressures on HIV can be unique depending on the immunogenetics of host populations. It is therefore logical to hypothesize that the virus evolving in a given population will carry signature mutations that will allow it to survive in that particular host milieu. Objectives: The aim of this study was to perform a comparative analysis of HIV-1 Gag subtype A sequences from two genetically diverged populations, namely, Kenyan and Pakistani. We analyzed unique mutations that could intercept the antigen processing pathway and potentially change the repertoire of Gag epitopes in each study group. Methods: Twenty-nine Kenyan and 56 Pakistani samples from HIV-1 subtype A-infected patients were used in this study. The HIV-1 gag region p24 and p2p7p1p6 was sequenced and mutations affecting proteasomal degradation, TAP binding, HLA binding and CTL epitope generation, were analyzed using the in silico softwares NetChop and MAPPP, TAPPred, nHLAPred and CTLPred, respectively. Results: Certain mutations unique to either Pakistani or Kenyan patients were observed to affect sites for proteasomal degradation, TAP binding, and HLA binding. As a consequence of these mutations, epitope pattern in these populations was altered. Conclusion: Unique selection pressures can steer the direction of viral epitope evolution in the host populations. Population-specific HIV epitopes have to be taken into account while designing treatment as well as vaccine for HIV.

Original languageEnglish
Pages (from-to)78-86
Number of pages9
JournalInfection, Genetics and Evolution
Volume16
DOIs
Publication statusPublished - Jun 2013
Externally publishedYes

Fingerprint

human immunodeficiency virus
epitopes
Epitopes
HIV
mutation
Mutation
Human immunodeficiency virus 1
Population
HIV-1
Antigen Presentation
Pressure
antigen
immunogenetics
virus
Viruses
Immunogenetics
AIDS Vaccines
antigen presentation
viruses
cytotoxic T-lymphocytes

Keywords

  • Epitope
  • HIV
  • Kenya
  • Pakistan

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Molecular Biology
  • Microbiology
  • Infectious Diseases
  • Microbiology (medical)

Cite this

Population-specific evolution of HIV Gag epitopes in genetically diverged patients. / Abidi, Syed H.; Shahid, Aniqa; Lakhani, Laila S.; Khanani, Muhammad R.; Ojwang, Peter; Okinda, Nancy; Shah, Reena; Abbas, Farhat; Rowland-Jones, Sarah; Ali, Syed.

In: Infection, Genetics and Evolution, Vol. 16, 06.2013, p. 78-86.

Research output: Contribution to journalArticle

Abidi, SH, Shahid, A, Lakhani, LS, Khanani, MR, Ojwang, P, Okinda, N, Shah, R, Abbas, F, Rowland-Jones, S & Ali, S 2013, 'Population-specific evolution of HIV Gag epitopes in genetically diverged patients', Infection, Genetics and Evolution, vol. 16, pp. 78-86. https://doi.org/10.1016/j.meegid.2013.02.003
Abidi, Syed H. ; Shahid, Aniqa ; Lakhani, Laila S. ; Khanani, Muhammad R. ; Ojwang, Peter ; Okinda, Nancy ; Shah, Reena ; Abbas, Farhat ; Rowland-Jones, Sarah ; Ali, Syed. / Population-specific evolution of HIV Gag epitopes in genetically diverged patients. In: Infection, Genetics and Evolution. 2013 ; Vol. 16. pp. 78-86.
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