AEGiS-15IAC: Identification of two novel HIV-1 circulating recombinant forms (CRF) and a unique inter-CRF mosaic virus in Cuba by near full-length genome characterization.

15th International AIDS Conference

Bangkok, Thailand - July 11-16, 2004

Identification of two novel HIV-1 circulating recombinant forms (CRF) and a unique inter-CRF mosaic virus in Cuba by near full-length genome characterization.

Int Conf AIDS 2004 Jul 11-16; 15:(abstract no. MoOrC1010)

Casado G, Thomson MM, Sierra M, Delgado E, Cuevas MT, Najera R
CNM Instituto de Salud Carlos III, Madrid, Spain

BACKGROUND: a high diversity of genetic forms of probable African ancestry has been identified recently in Cuba by analysis of partial pol and env sequences, including two probable circulating recombinant forms (CRFs), D[pol]/A[env ]and U(unknown)[pol]/H[env], which were detected in 21% and 7% samples, respectively. Objectives: to characterize CRFs from Cuba by analysis of near full-length genome sequences. Materials and

METHODS: We analyzed 7 samples from Cuba, originally characterized as U[pol]/H[env] (n=3) and as D[pol]/A[env ](n=4), without known epidemiological links. Near full-length viral genomes (~9 kb) were directly amplified by nested PCR in four overlapping segments from peripheral blood mononuclear cells' DNA. The phylogenetic analysis of the sequences was done by bootscanning and by neighbour-joining trees.

RESULTS: The three U[pol]/H[env] viruses were complex AFGHKU intersub type recombinants with identical structures and uniform clustering with each other along the genome. They also clustered along all the genome with a previously characterized complex recombinant from Cameroon (CM53379), and in partial segments with sequences from several viruses from Central Africa deposited in databases. Three D[pol]/A[env ]viruses were ADG intersubtype recombinant viruses with identical structures and uniform clustering with each other along the genome. One virus from Senegal clustered with these recombinants in the V3 region. A fourth D[pol]/A[env] virus was a unique ADGH intersubtype mosaic virus, recombinant between the two CRFs identified in Cuba.

CONCLUSIONS: Two novel complex CRFs of probable African origin have been identified in Cuba. One of them, an AFGHKU recombinant, is probably also circulating in Central Africa. The identification of a unique recombinant form between the two newly defined CRFs further supports that these are being transmitted among the Cuban population.

Keywords: AEGIS, HIV-1, Genes, pol, Genes, env, HIV-1 Reverse Transcriptase, Genome, Viral, Mosaic Viruses, Africa, Central, Cameroon, Senegal, Cuba, genetics

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