Presence of CRF09_cpx and complex CRF02_AG/CRF09_cpx recombinant HIV type 1 strains in Côte d'Ivoire, West Africa

• Published in: AIDS research and human retroviruses Vol. 21; no. 7; p. 667
• Main Authors: Toni, Thomas, Adjé-Touré, Christiane, Vidal, Nicole, Minga, Albert, Huet, Charlotte, Borger, Marie-Yolande, Recordon-Pinson, Patricia, Masquelier, Bernard, Nolan, Monica, Nkengasong, John, Fleury, Hervé J, Delaporte, Eric, Peeters, Martine
• Format: Journal Article
• Language: English
• Published: United States 01.07.2005
• Subjects: Cote d'Ivoire; Gene Products, env - genetics; Gene Products, pol - genetics; HIV-1 - classification; HIV-1 - genetics; Molecular Sequence Data; Species Specificity; Cote d'Ivoire
• ISSN: 0889-2229
• DOI: 10.1089/aid.2005.21.667

Based on partial env and pol (protease and RT) subtyping, we recently documented that the majority (>80%) of the HIV-1 strains that circulate in Côte d'Ivoire were CRF02_AG and about 11% were recombinants or could not be clearly assigned to a known subtype or CRF. In order to determine in more detail the precise structure of these viruses we sequenced the full-length genomes for six such strains. Bootscan and phylogenetic tree analysis showed that four strains were complex and unique CRF02_AG/CRF09_cpx recombinants, one was a CRF02_AG/CRF06_cpx recombinant, and one was a pure CRF09_cpx. Reanalysis of the remaining recombinants asserted the predominance of CRF09_cpx within intersubtype recombinants and circulation of CRF09_cpx in Côte d'Ivoire. More detailed analysis of the CRF09_cpx strains revealed also that part of the pol gene belonged to subtype K. This is the first time that such recombinants are described.