title: New and old complex recombinant HIV-1 strains among patients with primary infection in 1996-2006 in France: the French ANRS CO06 primo cohort study.
abstract: BACKGROUND
  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).
  
  
  METHODS
  Among 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.
  
  
  RESULTS
  Among 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: EA 3620, Université Paris - Descartes, Laboratoire de Virologie, Hôpital Necker - Enfants Malades, AP-HP, Paris, France. pierre.frange@nck.aphp.fr
authors.forename: Pierre
authors.initials: P
authors.lastname: Frange
authors.forename: Julie
authors.initials: J
authors.lastname: Galimand
authors.forename: Nicole
authors.initials: N
authors.lastname: Vidal
authors.forename: Cécile
authors.initials: C
authors.lastname: Goujard
authors.forename: Christiane
authors.initials: C
authors.lastname: Deveau
authors.forename: Faouzi
authors.initials: F
authors.lastname: Souala
authors.forename: Martine
authors.initials: M
authors.lastname: Peeters
authors.forename: Laurence
authors.initials: L
authors.lastname: Meyer
authors.forename: Christine
authors.initials: C
authors.lastname: Rouzioux
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Chaix
mesh_terms: D000328:Adult; D005260:Female; D005602:France / Q000453:epidemiology; D014644:Genetic Variation; D016679:Genome, Viral; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014759:Viral Envelope Proteins / Q000235:genetics
chemical_list: D014759:Viral Envelope Proteins