Background:  Non-B subtypes increased in France from 10% in 1998 to 1999 to 28% in 2006 in patients diagnosed at the time of primary HIV-1 infection and enrolled in the PRIMO Cohort. Our objective was to characterize more in detail non-B strains which remained “undetermined” in RT phylogenetic analysis.

Methods:  Since 1996, 745 patients have been enrolled in the PRIMO Cohort, 176 (23.6%) were infected with non-B strains. Whereas the majority (57%) were CRF02_AG viruses, 16 (9.1%) could not be classified into the known HIV-1 subtypes or circulating recombinant form. The V3-V5 env region was sequenced in 15 “undetermined” strains and 3 strains (04FR-KZS, 06FR-CRN, 04FR-AUK) were full-length sequenced. Phylogenetic analysis using neighbor-joining method and “bootscan” approach were used to determine their mosaic structure.

Results:  Phylogenetic analysis of the 15 V3-V5 sequences was as follows:  6 divergent A, 2 distantly related to env subtype E or D, 2 C, 1 B, and 4 undetermined. Of 15 persons, 8 were born in France, and the majority were heterosexual contaminations. 04FR-KZS, isolated in a Congolese woman infected in France, clustered with 2 previously described viruses from the Democratic Republic of Congo which were env subtype E, but with a recombinant structure different from CRF01_AE. Since the 3 viruses were epidemiologically unlinked and shared the same recombinant structure, they represented a circulating recombinant form, designated as CRF27_cpx and involving A/E/G/H/J/K/U subtypes. 04FR-AUK, isolated in a Congolese patient infected in France, was a A/K/CRF09/U recombinant strain, which clustered in gag, pol, vif, and vpr with HIV-1 MAL, one of the oldest African HIV-1 strains. 06FR-CRN, isolated in a homosexual Caucasian patient in 2006, was a B/C/U recombinant involving a Brazilian C strain. Moreover, 2 other seroconversions were observed in 2007 with KZS and CRN like viruses, suggesting their further spread in France.

Conclusions:  This study illustrates the increasing HIV-1 diversity in France, with description of 3 new complex mosaic strains, 1 new CRF and 2 URF. CRF27 and MAL-like sequences are old HIV-1 strains which are rare in their region of origin but may have a founder effect in France. Our results strengthen the French guidelines recommending genotypic resistance tests in patients with primary HIV-1 infection for the surveillance of the frequency of resistant strains, but also for surveillance of HIV-1 diversity.