Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences

Sci Data. 2018 Jul 31;5:180148. doi: 10.1038/sdata.2018.148.


Accurate classification of HIV-1 group M lineages, henceforth referred to as subtyping, is essential for understanding global HIV-1 molecular epidemiology. Because most HIV-1 sequencing is done for genotypic resistance testing pol gene, we sought to develop a set of geographically-stratified pol sequences that represent HIV-1 group M sequence diversity. Representative pol sequences differ from representative complete genome sequences because not all CRFs have pol recombination points and because complete genome sequences may not faithfully reflect HIV-1 pol diversity. We developed a software pipeline that compiled 6,034 one-per-person complete HIV-1 pol sequences annotated by country and year belonging to 11 pure subtypes and 70 CRFs and selected a set of sequences whose average distance to the remaining sequences is minimized for each subtype/CRF and country to generate a Geographically-Stratified set of 716 Pol Subtype/CRF (GSPS) reference sequences. We provide extensive data on pol diversity within each subtype/CRF and country combination. The GSPS reference set will also be useful for HIV-1 pol subtyping.

Publication types

  • Dataset
  • Research Support, N.I.H., Extramural

MeSH terms

  • Genes, pol*
  • HIV Infections / epidemiology
  • HIV Infections / virology*
  • HIV-1 / classification
  • HIV-1 / genetics*
  • Humans
  • Molecular Epidemiology
  • Recombination, Genetic

Associated data

  • Dryad/10.5061/dryad.56j2n