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We analyzed the near full-length genome (NFLG) of an HIV-1-positive sample(027A) with an undetermined subtype to determine the recombinant characteristics and possible source of the parental virus. 027A is a novel HIV-1 second-generation recombinant form composed of CRF01_AE and subtype B, detected from a married HIV-1-positive male subject who was infected through homosexual transmission in Baoding, Hebei province, China. The NFLG phylogenetic tree analysis suggested that the strain was close to circulation recombinant forms' (CRFs') reference sequences involved with CRF01_AE, but formed a distinct monophyletic cluster separately from them. This indicated that the strain might be a unique CRF01_AE-related recombinant from. Furthermore, the results of RIP and jpHMM further demonstrated that the NFLG sequence of the strain was composed of CRF01_AE and subtype B. The strain was two CRF01_AE fragments inserted into B backbone. Phylogenetic analysis illustrated that the CRF01_AE subregions were from the previously identified CRF01_AE cluster 4, and the B subregions were correlated with the B strains originated from Europe and America. They were all the lineages widely prevalent in men who have sex with men (MSM) population in China. In recent years, a large number of recombinant originated from CRF01_AE and B strains are constantly emerging in MSM population in China. This continual and recurrent recombination between CRF01_AE and B in high-risk group people deserves more attention and further monitoring.

Background Human immunodeficiency virus type 1 (HIV-1) genetic diversity and pre-treatment drug resistance (PDR) are major barriers to successful antiretroviral therapy (ART). In China, sexual intercourse is the most frequent route of HIV-1 transmission. However, few studies have analyzed PDR and transmission networks in detail among individuals in China with acute HIV-1 infection and their sexual contacts. Methods A cross-sectional study was conducted in Baoding City, Hebei Province, China from 2019–2020. CD4 T cell counts and viral loads were assessed and a HIV-1 genotypic PDR assay was developed in-house. Transmission networks were visualized using Cytoscape with a threshold genetic distance of 0.015 among HIV-1 subtypes. Results From 139 newly diagnosed and drug-naïve individuals with HIV-1, 132 pol gene sequences were obtained and revealed eight HIV-1 subtypes. Circulating recombinant form (CRF)01_AE was the most frequent subtype (53.0%, 70/132) followed by CRF07_BC (26.5%, 35/132), B (13.6%, 18/132), unique recombinant forms (2.3%, 3/132), CRF55_01B (1.5%, 2/132), CRF103_01B (1.5%, 2/132), CRF65_cpx (0.8%, 1/132), and C (0.8%, 1/132). A total of 47 pol gene sequences were used to generate 10 molecular transmission networks. The overall prevalence of PDR was 7.6% and that of PDR to non-nucleotide reverse transcriptase inhibitors was 6.1%. Of three transmission networks for PDR, two were closely associated with Beijing and Tianjin, while another was restricted to sequences determined in this study. Conclusions These results demonstrate that during acute HIV-1 infection, PDR is transmitted in dynamic networks. This suggests that early detection, diagnosis, surveillance, and treatment are critical to effectively control HIV-1 spread.