Abstract
BackgroundPrevalence of HIV-1 non-B subtypes has increased overtime in patients diagnosed at the time of primary infection (PHI) in France. Our objective was to characterize in detail non-B strains which could not be genetically classified into the known subtypes/Circulating Recombinant Forms (CRFs).MethodsAmong 744 patients enrolled in the ANRS PRIMO Cohort since 1996, 176 (23.7%) were infected with HIV-1 non-B strains. The subtype/CRF could not be identified in RT for 15 (2%). The V3-V5 env region was sequenced and 3 strains (04FR-KZS, 06FR-CRN, 04FR-AUK) were full-length sequenced. Phylogenetic and bootscan analyses were used to characterize the mosaic structures.ResultsAmong V3-V5 sequences, 6 were divergent A, 2 distantly related to E or D, 2 C, 1 B and 2 remained unclassified. 04FR-KZS, isolated in a Congolese woman infected in France, clustered with 2 previously described viruses from the Democratic Republic of Congo. They represent CRF27_cpx involving A/E/G/H/J/K/U subtypes. 06FR-CRN, isolated in a homosexual Caucasian patient, was a B/C/U recombinant involving a Brazilian C strain. 04FR-AUK, isolated in a Congolese patient infected in France, was a A/K/CRF09/U recombinant clustering from gag to vif with HIV-1 MAL. Others PHI were further observed in 2006–2007 with 1 KZS and 5 CRN-like viruses, suggesting their spread in France.ConclusionThis study illustrates the increasing HIV-1 diversity in France associating new (06FR-CRN) and old (CRF27_cpx and "MAL-like" 04FR-AUK) strains, which are rare in their region of origin but may have a possible founder effect in France. Our results strengthen the French guidelines recommending viro-epidemiological surveillance of HIV-1 diversity.
Highlights
Prevalence of Human Immunodeficiency Virus type 1 (HIV-1) non-B subtypes has increased overtime in patients diagnosed at the time of primary infection (PHI) in France
The distribution of HIV-1 strains circulating in France is particular, as successive migratory flows from African countries with French language have led to an exceptional viral diversity, higher than in other countries where subtype B epidemic is predominant
Characteristics of the study population From 1996 to October 2006, 744 strains have been genetically characterized among the 768 patients recruited in the PRIMO cohort
Summary
Prevalence of HIV-1 non-B subtypes has increased overtime in patients diagnosed at the time of primary infection (PHI) in France. Our objective was to characterize in detail non-B strains which could not be genetically classified into the known subtypes/Circulating Recombinant Forms (CRFs). In France, subtype B predominates, like in other European countries and in North America, but the overall prevalence of non-B strains is increasing, among French Caucasian individuals [8,9]. The distribution of HIV-1 strains circulating in France is particular, as successive migratory flows from African countries with French language have led to an exceptional viral diversity, higher than in other countries where subtype B epidemic is predominant. The increasing diversity may have implications for HIV-1 diagnosis, treatment, drug resistance, vaccine development, transmission and pathogenesis
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