Molecular characterization of a unique Recombinant form of HIV-1 subtype F2/CRF02_AG identified in Guangdong, China

The human immunodeficiency virus type 1 (HIV-1) pandemic continues to pose a significant global public health challenge. Recombination between HIV-1 variants generates unique recombinant forms (URFs) and then circulating recombinant forms (CRFs) after ongoing transmission. Subtype F2 and CRF02_AG mainly spread in western Africa, but they are rarely detected in China. Here, we observed a URF composed of subtypes F2 and CRF02_AG isolated from a man (230794) in Guangdong, China.

The near full-length genome (NFLG) of HIV-1 was amplified with two overlapping segments by the near endpoint dilution method. The positive products were sequenced directly to obtain genomic sequences. The recombinant pattern and breakpoints of the NFLG were determined using the Simplot software and confirmed by maximum likelihood (ML) trees for segments using the IQtree tool. The maximum clade credibility (MCC) tree was reconstructed to trace the origin by using BEAST software. Genotypic drug resistance data were interpreted by the Stanford HIV Drug Resistance Database. The co-receptor tropism was predicted using the geno2pheno coreceptor 2.5 tool, the WebPSSM tool and the HIVcoPRED tool.

The individual (230794) was 47 years old and got infected via heterosexual contact in Guangzhou City, Guangdong Province. The NFLG sequence of strain 230794 was 8260 nucleotides (nt) in length, with two CRF02_AG segments substituting in the backbone of subtype F2 in the vif and env gene regions. The genomic recombinant mosaic structures of 230794 were different from those of the other nine issued subtype F2/CRF02_AG URFs. No drug-resistant mutation was identified, but an INSTI other mutation, L74I, was identified. Strain 230794 was predicted to be a X4/R5 dual-tropism strain. Bayesian inference indicated that strain 230794 originated approximately between 2015 and 2018.

A novel URF of subtype F2/CRF02_AG was identified from a Cantonese man, with R5/X4 dual tropism. It is necessary to strengthen the molecular surveillance of the spread of recombinant strains in regions with high HIV-1 genetic diversity in China.