Identification of a novel HIV-1 circulating ADG intersubtype recombinant form (CRF19_cpx) in Cuba

J Acquir Immune Defic Syndr. 2005 Dec 15;40(5):532-7. doi: 10.1097/01.qai.0000186363.27587.c0.

Abstract

Circulating recombinant forms (CRFs) represent a substantial proportion of HIV-1 isolates in the global pandemic. Characterization of HIV-1 genetic forms, including CRFs, may be relevant to studies on molecular epidemiology, recombination, superinfection, vaccine development, and antiretroviral therapy. This study analyzes near complete genomes of 4 epidemiologically unlinked viruses from Cuba, originally characterized as D/A intersubtype recombinants in pol and env segments. The genomes of 3 viruses exhibited virtually coincident mosaic structures, with multiple segments of subtypes A, D, and G and uniform phylogenetic clustering with each other along the genome. These results allow us to define a new CRF (CRF19_cpx). The 4th analyzed Cuban virus was recombinant between CRF19_cpx and CRF18_cpx (which also circulates in Cuba). CRF19_cpx exhibited homology to an AG intersubtype recombinant virus from Cameroon (CM53392) along approximately 5 kb and clustered with a subtype D virus from Gabon (G109) in gag. Four other viruses from central or west Africa were also phylogenetically related to CRF19_cpx in env fragments. These results allow us to define CRF19_cpx as a second novel CRF of African origin circulating in Cuba, to identify putative representative viruses of its parental strains, and to characterize a unique CRF18/CRF19 recombinant virus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Africa / epidemiology
  • Cuba / epidemiology
  • Female
  • Genes, env
  • Genes, pol
  • HIV Infections / epidemiology
  • HIV Infections / virology*
  • HIV-1 / classification*
  • HIV-1 / genetics
  • Humans
  • Male
  • Molecular Sequence Data
  • Phylogeny
  • Recombination, Genetic*
  • Sequence Analysis, DNA

Associated data

  • GENBANK/AY588970
  • GENBANK/AY588971
  • GENBANK/AY884994
  • GENBANK/AY894995