HIV-1 subtype A gag variability and epitope evolution

Syed Hani Abidi, Marcia L. Kalish, Farhat Abbas, Sarah Rowland-Jones, Syed Ali

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Objective: The aim of this study was to examine the course of time-dependent evolution of HIV-1 subtype A on a global level, especially with respect to the dynamics of immunogenic HIV gag epitopes. Methods: We used a total of 1,893 HIV-1 subtype A gag sequences representing a timeline from 1985 through 2010, and 19 different countries in Africa, Europe and Asia. The phylogenetic relationship of subtype A gag and its epidemic dynamics was analysed through a Maximum Likelihood tree and Bayesian Skyline plot, genomic variability was measured in terms of G→A substitutions and Shannon entropy, and the time-dependent evolution of HIV subtype A gag epitopes was examined. Finally, to confirm observations on globally reported HIV subtype A sequences, we analysed the gag epitope data from our Kenyan, Pakistani, and Afghan cohorts, where both cohort-specific gene epitope variability and HLA restriction profiles of gag epitopes were examined. Results: The most recent common ancestor of the HIV subtype A epidemic was estimated to be 1956±1. A period of exponential growth began about 1980 and lasted for approximately 7 years, stabilized for 15 years, declined for 2-3 years, then stabilized again from about 2004. During the course of evolution, a gradual increase in genomic variability was observed that peaked in 2005-2010. We observed that the number of point mutations and novel epitopes in gag also peaked concurrently during 2005-2010. Conclusion: It appears that as the HIV subtype A epidemic spread globally, changing population immunogenetic pressures may have played a role in steering immune-evolution of this subtype in new directions. This trend is apparent in the genomic variability and epitope diversity of HIV-1 subtype A gag sequences.

Original languageEnglish
Article numbere93415
JournalPLoS One
Volume9
Issue number6
DOIs
Publication statusPublished - Jun 3 2014
Externally publishedYes

Fingerprint

Human immunodeficiency virus 1
epitopes
HIV-1
Epitopes
HIV
genomics
immunogenetics
Immunogenetics
Population Dynamics
Entropy
point mutation
entropy
Point Mutation
Maximum likelihood
ancestry
Substitution reactions
Genes
phylogeny
Growth
genes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Abidi, S. H., Kalish, M. L., Abbas, F., Rowland-Jones, S., & Ali, S. (2014). HIV-1 subtype A gag variability and epitope evolution. PLoS One, 9(6), [e93415]. https://doi.org/10.1371/journal.pone.0093415

HIV-1 subtype A gag variability and epitope evolution. / Abidi, Syed Hani; Kalish, Marcia L.; Abbas, Farhat; Rowland-Jones, Sarah; Ali, Syed.

In: PLoS One, Vol. 9, No. 6, e93415, 03.06.2014.

Research output: Contribution to journalArticle

Abidi, SH, Kalish, ML, Abbas, F, Rowland-Jones, S & Ali, S 2014, 'HIV-1 subtype A gag variability and epitope evolution', PLoS One, vol. 9, no. 6, e93415. https://doi.org/10.1371/journal.pone.0093415
Abidi SH, Kalish ML, Abbas F, Rowland-Jones S, Ali S. HIV-1 subtype A gag variability and epitope evolution. PLoS One. 2014 Jun 3;9(6). e93415. https://doi.org/10.1371/journal.pone.0093415
Abidi, Syed Hani ; Kalish, Marcia L. ; Abbas, Farhat ; Rowland-Jones, Sarah ; Ali, Syed. / HIV-1 subtype A gag variability and epitope evolution. In: PLoS One. 2014 ; Vol. 9, No. 6.
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