Detection of the newly characterized HIV CRF56_cpx in Marseille, southeastern France

Abstract

Objectives: 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.

Keywords

• HIV
• Circulating recombinant form
• Primary HIV infection
• Molecular epidemiology
• MSM
• France