Sequencing of One Unique Recombinant CRF85_BC/CRF01_AE Genome and Two Partial Genomes from Ningxia, China

The recent emergence of new HIV-1 recombinant strains presents a new challenge to the control of HIV-1/AIDS and the development of an effective vaccine. We employed a near full-length genomic sequence analysis of a newly identified CRF85_BC recombinant strain in Ningxia, China, to determine its recombination pattern. Blood samples were collected from HIV-infected or AIDS patients in Ningxia in 2023. CRF85_BC subtype strains were detected from three samples using an in-house method, and one sample's near full-length genome sequence was also obtained. MEGA11, jpHMM, and Simplot software were used to identify subtypes and analyze recombination patterns. Neighbor-joining phylogenetic tree analysis showed that HIV-1 pol region sequences of three samples were CRF85_BC subtypes. One near full-length genome sequence of the recombinant strain was obtained, and jpHMM preliminarily judged that the recombinant strain was inserted with two subtype B fragments and two CRF01_AE fragments based on subtype C as the backbone. Further analysis using Simplot software revealed that the recombinant strain was the second-generation recombinant strain of CRF85_BC and CRF01_AE, and the recombination mode was based on the full-length genome of CRF85_BC, and CRF01_AE gene fragments that were inserted at positions 7365-8279 and 8431-9492, respectively. The results of the fragment phylogenetic tree verified its accuracy. One CRF01_AE and CRF85_BC second-generation recombinant strain was found in HIV-1 infected people in Ningxia, indicating that new HIV-1 recombinant strains continuously emerge and circulate in this region. Genomic surveillance of these recombinants should inform targeted interventions, such as prioritized contact tracing, to mitigate the formation of transmission clusters.