Identification of a Novel HIV-1 Second-Generation Circulating Recombinant Form (CRF117_0107) in China

Under the background of the main epidemic HIV strains (CRF01_AE and CRF07_BC) co-circulation in China, more HIV second-generation recombinant (SGR) strains with CRF01_AE and CRF07_BC as the backbone were also emerging. In this study, we characterize a novel HIV-1 second-generation circulating recombinant form (CRF117_0107) consisting of CRF01_AE and CRF07_BC fragments from three epidemiologically unrelated individuals infected with HIV-1. One near full-length genome (NFLG) sequence was amplified, sequenced, and spliced in two halves using RNA extracted from the plasma of a homosexual in Shenzhen, Guangdong Province. Two other NFLG sequences were obtained from the Los Alamos HIV Sequence Database under accession numbers KY201177 and MK397789, which were isolated from men who have sex with men (MSM) in Guangdong Province and Zhejiang Province, respectively. Phylogenetic analysis revealed that these NFLG sequences formed a monophyletic cluster with a high bootstrap value of 1.0. Recombination analysis demonstrated that the genome of CRF117_0107 was separated into three segments by two breakpoints. Further subregional phylogenetic analysis was performed that showed segment I+III (790-5990nt, 8295-9412nt) of CRF117_0107 originated from the CRF07_BC cluster, and Segment I+III (5991-8294nt) originated from the CRF01_AE cluster. The appearance of CRF117_0107 further highlights that HIV-1 SGR strains containing CRF01_AE and CRF07_BC will be generated more frequently and will most likely be more conducive to accelerating the spread of HIV in China. This study suggested it's essential to monitor HIV-1 second-generation CRFs among high-risk populations such as MSM for the epidemic and evolution dynamics of HIV-1 in China.