title: Detection of the newly characterized HIV CRF56_cpx in Marseille, southeastern France.
abstract: OBJECTIVE
  We aimed to seek HIV sequences highly similar to CRF56-cpx, a recently described newly circulating B/CRF02/G recombinant HIV, in our local clinical microbiology laboratory sequence database.
  
  
  METHODS
  A recently implemented tool that combines a databank of all HIV nucleotide sequences obtained at our clinical microbiology laboratory with a search tool that uses BLAST was used. A comparative and phylogenetic analysis of HIV protease and reverse transcriptase fragments was performed.
  
  
  RESULTS
  We identified two sequences that were clustered with CRF56-cpx with a bootstrap value of 99% in phylogenetic analyses; these were obtained from two patients diagnosed with HIV in 2009-2011. HIV protease-reverse transcriptase sequences obtained from these two patients shared a mean identity of 98.2±0.2% with previously described CRF56-cpx sequences. Both case patients diagnosed with HIV in our centre were highly sexually active men who have sex with men.
  
  
  CONCLUSIONS
  Our findings highlight the continuous expansion of HIV diversity in France and indicate that real-time surveillance of HIV molecular epidemiology, including the comparison of sequences from laboratory, national, and international databases, might be helpful to identify the emergence, circulation, and transmission of viral strains.
authors.affiliation: Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, 27 boulevard Jean Moulin, 13385, Marseille Cedex 05, France; Fondation IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique - Hôpitaux de Marseille, 264 rue Saint-Pierre, 13385, Marseille Cedex 05, France. Electronic address: philippe.colson@univ-amu.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Colson
authors.affiliation: Fondation IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Conception, Assistance Publique - Hôpitaux de Marseille, 147 boulevard Baille, 13385, Marseille Cedex 05, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Ravaux
authors.affiliation: Fondation IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique - Hôpitaux de Marseille, 264 rue Saint-Pierre, 13385, Marseille Cedex 05, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Tourrès
authors.affiliation: Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, 27 boulevard Jean Moulin, 13385, Marseille Cedex 05, France; Fondation IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Conception, Assistance Publique - Hôpitaux de Marseille, 147 boulevard Baille, 13385, Marseille Cedex 05, France.
authors.forename: Andréas
authors.initials: A
authors.lastname: Stein
authors.affiliation: Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, 27 boulevard Jean Moulin, 13385, Marseille Cedex 05, France; Fondation IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique - Hôpitaux de Marseille, 264 rue Saint-Pierre, 13385, Marseille Cedex 05, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Tamalet
mesh_terms: D000328:Adult; D001483:Base Sequence; D005602:France; D006678:HIV / Q000235:genetics / Q000302:isolation & purification*; D015658:HIV Infections / Q000821:virology; D006801:Humans; D008297:Male; D010802:Phylogeny; D016415:Sequence Alignment; D055815:Young Adult
keywords: Circulating recombinant form; France; HIV; MSM; Molecular epidemiology; Primary HIV infection