P25.09
Background: Cameroon has one of the most genetically diverse HIV epidemics in the world. The country is home to virtually every known HIV subtypes, plus a vast array of CRFs and URFs. In the analysis we performed in a previous study (Tongo et al., 2013), many of the Cameroonian CRFs and URFs showed up as having less evidence of recombination than many of the “pure” subtype sequences. This is exactly as would be expected if these Cameroonian sequences were extant examples of early diverging lineages or rare pre-epidemic HIV-1 group M lineages.
Methods: Nine potential candidate “ancient” viruses were selected from our previous study and their full length sequences were generated. A maximum likelihood phylogenetic tree was constructed with 100 boostrap replicates with these sequences and a representative selection of the sequences from the rest of the world and all other published sequences from west central African countries. A blinded fully exploratory screen for recombination will be performed using RDP4. In addition, we wish to better understand the pathogenicity of these viruses by studying the function of nef and other accessory proteins.
Results: Preliminary analyses revealed that the full genome sequence of one sample (BS13) was an outlier of all the CRF02_AG sequences sampled to date. Two full length sequences, BS11 and BS55, were both too divergent to be placed within any existing subtype or CRF grouping and therefore remained unclassified. They may in fact belong to a novel CRF or subtype, since they clustered with three other previously characterised Cameroonian sequences. The full length viral genome of BS72 was also too divergent to be placed within any existing subtype or CRF grouping. Analyses are underway for more phylogenetic and pathogenicity characterization.
Conclusions: These preliminary results suggest that there is unquestionably a far more diverse pool of HIV sequences circulating amongst humans than presently accounted for in the current HIV-1 group M classification.
