Investigation of intra-subtype recombination in Zimbabwean HIV 1 subtype C using bioinformatics. (December 2019)

Intra-subtype recombination is a common phenomenon among HIV strains which involves transfer of genetic information between two viral strains belonging to the same HIV subtype. However, more research has been done on inter-subtype recombination which is the transfer of genetic information between two strains belonging to different HIV subtypes. In this study HIV 1 subtype C env sequences from Zimbabwean nucleotide sequences (n=2 915) downloaded from Los Alamos HIV databases were used to investigate intra-subtype recombination. Using the GENECUTTER tool, ∼44.4% of whole genomes were selected to have informative env regions (n = 1 295). Clustal was used for Multiple Sequence Alignment and RDP 4 was used for analysis and detection of Intra-subtype recombination. Apparently, GENECONV included in RDP 4 detected 47 recombination events. One of the most informative recombination events was further analysed using UPGMA phylogenetic tree to understand the extent of the intra-subtype recombination.