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.

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 in the pol or in the env gene compared to 34 (69.4%), which contained non-B or CRF sequences. Twenty-six different recombination patterns involving subtypes, CRFs, or undetermined strains were observed. We have reported the occurrence of new recombinant forms between the two major viral types of strains circulating in France: subtype B and CRF02_AG. Our study confirms a high HIV-1 diversity among patients infected in France within the past 10 years, with a high proportion of non-B strains and the circulation of complex recombinant strains among both sub-Saharan patients and French patients.