Near-full-length genomic characterization and phylogenetic analysis of an HIV-1 CRF02_AG/G second-generation recombinant in Ningxia, China

With the rapid evolution of global HIV-1 recombinant strains, existing diagnostic and therapeutic strategies are under threat. This study aims to conduct molecular characterization and origin tracing of a CRF02_AG-derived second-generation recombinant detected in Ningxia, China. In 2024, during genotyping screening of the pol region in HIV-1-infected individuals from Ningxia, preliminary evidence of CRF02_AG-related signals was identified in one sample. Subsequently, the near-full-length genome sequence of this strain (designated A01) was successfully obtained. Phylogenetic analysis revealed that its gag, pol, and env gene regions clustered within the A1 and G subtypes, respectively. Recombination analysis using jpHMM and Simplot software confirmed that this strain utilizes the CRF02_AG (A1/G primary recombinant) as its genomic backbone, with two G subtype fragments inserted into the env region (HXB2 sites: 6194–7137 and 7788–8532). Consequently, this strain was defined as a novel CRF02_AG/G second-generation recombinant. Bayesian phylogeographic analysis further revealed that this Ningxia strain shares close genetic relationships with CRF02_AG strains prevalent in the United Kingdom and South Korea. This study marks the first identification of an HIV-1 CRF02_AG/G second-generation recombinant in Ningxia (singular case), underscoring the importance of sustained high-resolution molecular surveillance in populations with mobility for early warning of imported and locally transmitted novel recombinant strains.