Genetic characteristics of a novel HIV-1 circulating recombinant form (CRF128_07B) identified among MSM in Guangdong Province, China

To obtain and investigate the genetic characteristics of four HIV-1 near full-length genome sequences (NFLGs), aiming at a description of a novel circulating recombinant form (CRF) in Guangdong China. Plasma samples were collected from HIV-1 infected MSM patients in Guangdong Province who had no epidemiological association with each other. The NFLGs were amplified with two overlapping halves and phylogenetic analyses were performed using Mega V11.0.1. Recombination analyses were comprehensively screened with the jpHMM, RIP, and BootScan analyses. Finally, the Bayesian phylogenetic analyses were performed using Beast V1.10.4 to estimate the origin time. Phylogenetic analyses revealed the four NFLGs formed a distinct monophyletic cluster distinguished from other known subtypes in the Neighbor-joining tree. Recombinant analyses revealed they shared a highly similar recombinant pattern, with the CRF07_BC backbone substituted by three subtype B segments. Subregion phylogenetic analyses confirmed them to be a novel CRF composed of CRF07_BC and subtype B, therefore, designed as CRF128_07B. According to the Bayesian phylogenetic analyses, CRF128_07B was inferred to approximately originated around 2005–2006. These findings described a novel HIV-1 CRF identified from MSM in Guangdong Province. This is the first detection of a CRF comprising CRF07_BC and subtype B. The present finding highlights the urgent need for continuous molecular screening and the epidemic surveillance within the MSM populations.