Genetic characterization of a novel unique recombinant form of HIV-1 originating from subtype A1 and C in Guangdong Province, China

The dominant human immunodeficiency virus type 1 (HIV-1) subtypes are CRF01_AE, CRF07_BC and CRF08_BC in Guangdong Province, China. In this study, we report a unique recombinant form (URF) of HIV-1 that was identified in an HIV/hepatitis B virus (HBV)/hepatitis C virus (HCV) triple-infected patient who was an intravenous drug user (IDU) in Heyuan City, Guangdong Province. The near full-length genome was amplified, and the PCR products were sequenced by Sanger's method. The Recombination Identification Program (RIP 3.0) and jpHMM online tools showed that four subtype C fragments were inserted into the A1 backbone genome in the gag, pol, vpr and nef gene regions. In the phylogenetic tree analysis, the subtype A1 and C fragments clustered with HIV-1 A1 and C reference sequences, respectively. No similar breakpoints between our strain and the other strains in the Los Alamos HIV database were observed. The results of evolutionary analysis using BEAST software showed that the subtype A1 fragment originated from Guangzhou City, China; however, the subtype C fragment originated from East Africa. This is the first report of HIV-1 URF A1C in Guangdong Province, China. The identification of this URF suggested that further dynamic surveillance of new recombinant forms is needed.