Genome-scale analysis of evolutionary rate and selection in a fast-expanding Spanish cluster of HIV-1 subtype F1

Infect Genet Evol. 2018 Dec:66:43-47. doi: 10.1016/j.meegid.2018.09.008. Epub 2018 Sep 13.

Abstract

This work is aimed at assessing the presence of positive selection and/or shifts of the evolutionary rate in a fast-expanding HIV-1 subtype F1 transmission cluster affecting men who have sex with men in Spain. We applied Bayesian coalescent phylogenetics and selection analyses to 23 full-coding region sequences from patients belonging to that cluster, along with other 19 F1 epidemiologically-unrelated sequences. A shift in the overall evolutionary rate of the virus, explained by positively selected sites in the cluster, was detected. We also found one substitution in Nef (H89F) that was specific to the cluster and experienced positive selection. These results suggest that fast transmission could have been facilitated by some inherent genetic properties of this HIV-1 variant.

Keywords: HIV-1; Men who have sex with men; Selection; Subtype F1; Transmission cluster.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigens, Viral / immunology
  • Databases, Genetic
  • Epitopes, T-Lymphocyte / immunology
  • Evolution, Molecular*
  • Genome, Viral*
  • Genomics* / methods
  • Genotype*
  • HIV Infections / epidemiology*
  • HIV Infections / immunology
  • HIV Infections / transmission
  • HIV Infections / virology*
  • HIV-1 / genetics*
  • HIV-1 / immunology
  • Humans
  • Phylogeny
  • Recombination, Genetic
  • Selection, Genetic
  • Sex Factors
  • Spain / epidemiology

Substances

  • Antigens, Viral
  • Epitopes, T-Lymphocyte