Characterization of the near full-length genome of a novel HIV-1 CRF01-AE/CRF07-BC recombinant in an injection drug user from Southern Taiwan

HIV-1 CRF07-BC became prevalent in Taiwan after the epidemic among injection drug users (IDUs). We describe a unique recombinant form (URF) consisting of CRF01-AE and CRF07-BC (named URF-0107-H8) genes detected from an IDU. The 8.8 kb near full-length genome of URF-0107-H8 had a CRF01-AE backbone with two CRF07-BC fragments in the reverse transcriptase and integrase region [RT-Int; HXB2 nucleotide (nt) positions 2942-4709] and within the envelop (nt 8467-8722) gene. Phylogenetic analyses revealed that its 1.8 kb RT-Int sequence clustered with those of CRF07-BC strains from Taiwan, while sequences of CRF01-AE portions were more similar to those of Central African origin than contemporaneous CRF01-AE isolates in Taiwan or prevalent in East or Southeast Asia. Recombination breakpoints and phylogenetic relationships of URF-0107-H8 were different from those of CRF01-AE/CRF07-BC URFs previously reported from China. This highlighted the importance of continual monitoring of genetic evolution of HIV strains and the emergence of new recombinants.