Short Communication: Evidence of HIV Type 1 Complex and Second Generation Recombinant Strains Among Patients Infected in 1997–2007 in France: ANRS CO06 PRIMO Cohort

Abstract Although subtype B strains are still predominant in France, non-B viruses have been isolated from 26% of patients with a primary HIV-1 infection in 2005–2006. The objective of this study was to characterize recombinant-HIV-1 strains by a subtyping based on the phylogenetic analysis of both pol and env sequences. We studied 591 patients who were part of the French PRIMO-Cohort between 1997 and 2007. The RT and V3 regions were sequenced and phylogenetic analyses were performed. Phylogenetic analyses showed concordant subtype results for 91.7% of viruses: 71.6% of the viruses were subtype B and 28.4% belonged to non-B subtypes or circulating recombinant forms (CRFs). Forty-nine strains showed different phylogenies between the two genes (pol and env), indicating that recombinations were observed in 8.3% of the cases. These recombinants were observed in patients from sub-Saharan Africa (28.3%) and in white patients (6.3%). Moreover, among the 49 recombinant viruses, 15 (30.6%) contained a B sequence i...