Sequence Notes: Genomic Characterization of Two Novel HIV-1 Recombinant Forms (B/C) Among Men Who Have Sex with Men in Hebei, China.

Abstract

The genetic diversity of HIV-1, driven by mutation and recombination, poses significant challenges to prevention and control efforts, particularly in regions like China where multiple subtypes and circulating recombinant forms co-circulate. Men who have sex with men (MSM) represent a key population for the emergence of novel recombinants. This study characterizes two novel unique recombinant forms (URFs) identified within the MSM population in Hebei, China. Viral RNA extraction, amplification, and near full-length genome (NFLG) sequencing were performed. Phylogenetic analysis based on NFLG alignments was conducted in MEGA 6 under the Kimura 2-parameter model with 1,000 bootstrap replicates. Recombination was assessed using the Recombinant Identification Program and SimPlot v3.5.1. Breakpoint-defined regions were phylogenetically analyzed, and recombination maps were generated. Phylogenetic and recombinant analysis based on NFLG sequences (designated BDL061 and BDL071) revealed that they originated from subtypes B and C. BDL061 exhibited a predominantly subtype B backbone with interspersed subtype C segments, while BDL071 displayed a predominantly subtype C backbone with subtype B segments. Phylogenetic analysis of recombinant segments strongly supported (bootstrap >90%) subtype B and C parental origins for the respective fragments. We report the identification and characterization of two phylogenetically distinct, novel HIV-1B/C URFs (BDL061 and BDL071) among MSM in Hebei, China. Their unique mosaic structures, differing predominant backbones, and confirmation as novel recombinants underscore the ongoing evolution and increasing complexity of the HIV-1 epidemic within this high-risk population in China. These findings highlight the critical need for NFLG-based surveillance to accurately track viral diversity and inform public health strategies.