A putative HIV-1 subtype C/CRF11_cpx unique recombinant from South Africa

The HIV epidemic in South Africa is overwhelmingly driven by HIV-1 subtype C viruses. The HIV gag, pol, env (C2-V5) and nef sequences of virus 08MB26ZA, obtained from a 47 year old woman, were studied by phylogenetic analysis, REGA and the jumping Profile Hidden Markov Model (jPHMM) tools. The pol gene was further analyzed for recombination by Simplot. The pol and env sequences were examined for genetic drug resistance mutations and predicted co-receptor usage respectively. There was agreement in the assignment of the gag sequence as pure HIV-1 subtype C by phylogenetic, REGA and jPHMM analyses. The pol sequence clustered with CRF11_cpx and in the J-clade by phylogenetic analysis; and to a CRF11_cpx/subtype C recombinant by REGA. The assignment of pol to CRF11_cpx and subtype C was confirmed by Simplot. The recombinant was of the R5 biotype, with no important drug resistance mutations in the pol region. The epidemiologic and biologic significance of the virus are unknown. The finding suggests that complex viruses are being introduced into South Africa with potential implications for diagnosis. This is apparently the first report from South Africa of a putative unique recombinant involving CRF11_cpx and subtype C genomes.