Abstract
The rapid expansion of CRF07_BC is primarily driven by the CRF07_BC_N (07BC_N) lineage, with its proportion surpassing that of CRF01_AE in China. However, the intra-host evolution and clinical characteristics of CRF07_BC remain poorly understood. In this study, we conducted systematic surveillance of newly diagnosed HIV-1 patients in Shanghai from 2017 to 2023. A total of 2508 pol sequences of CRF07_BC were obtained, and an additional 130 near-full-length CRF07_BC genomes were generated using next-generation sequencing (NGS) for further analysis. The prevalence of 07BC_N in Shanghai consistently exceeded that of CRF07_BC_O (07BC_O). At baseline, individuals infected with 07BC_N exhibited lower viral loads and higher CD4+ T cell counts. 07BC_N primarily circulated among men who have sex with men (MSM) in Eastern China, while 07BC_O was prevalent in southern provinces among people who inject drugs (PWID) and heterosexual populations. The rapid transmission of 07BC_N in MSM gradually replaced 07BC_O. Moreover, the intra-host single nucleotide variant (iSNV) count was significantly higher in 07BC_O than in 07BC_N, both overall and across most genes except for gag. The prevalence of transmitted drug resistance (TDR) mutations in CRF07_BC was 5.7% (130/2,286). This study provides valuable insights into the evolution, transmission dynamics, and clinical characteristics of CRF07_BC, highlighting the distinctive features of 07BC_N and its potential impact on public health strategies for HIV-1 management in China.