Molecular genetic characterization of a novel HIV-1 second-generation circulating recombinant form (CRF188_0107) among men who have sex with men in Henan,China

Introduction: HIV-1 genetic diversity in China is largely driven by recombination between predominant strains such as CRF01_AE and CRF07_BC. This study reports the identification and characterization of a novel second-generation CRF, designated CRF188_0107, identified among men who have sex with men (MSM) in Henan Province, China. Methods: Near-full-length genomes (NFLGs) were amplified from plasma samples of five epidemiologically unlinked individuals using a near-endpoint dilution nested PCR approach. Phylogenetic analysis was performed using IQ-TREE under the GTR model, recombination breakpoints were identified with SimPlot v3.5.1 and Bootscan, and Bayesian evolutionary analysis was conducted in BEAST v1.10.5 to estimate the time of the most recent common ancestor (tMRCA). Drug resistance mutations were analyzed using the Stanford HIVdb program. Results: All five NFLGs formed a distinct monophyletic clade separate from known CRFs. Recombination analysis revealed a mosaic structure consisting of nine segments with eight breakpoints, characterized by four inserted CRF07_BC fragments within a CRF01_AE backbone. The tMRCA was estimated between 2019 and 2023. No major drug resistance mutations were detected against PIs, NRTIs, NNRTIs, or INSTIs. Discussion: This study identifies CRF188_0107, a novel HIV-1 recombinant derived from CRF01_AE and CRF07_BC, among MSM in Henan, China. The strain shows a complex mosaic genome and emerged around 2019–2023. Some segments suggest a previously unrecognized CRF01_AE sublineage in the region. Our findings underscore the critical need for sustained molecular surveillance among key populations like MSM to monitor the rapid evolution and potential public health impact of novel HIV-1 recombinants in China.