Genomic Characterization of Dengue Virus in the Ningxia Hui Autonomous Region, China (2019 and 2023)

Dengue virus (DENV) transmission has risen across China in recent years, but genomic data from inland regions remain scarce. We screened 9 clinical samples collected in Ningxia in 2019 and 2023, obtaining 5 near-complete DENV-1 genomes, and performed phylogenetic reconstruction and molecular clock analyses using a global dataset of 452 DENV-1 sequences to infer spatiotemporal origins; epitope divergence relative to vaccine strains and human monoclonal antibodies was also assessed. The 2019 Ningxia strains clustered within DENV-1 genotype I, clade E, and were closely related to viruses from Hebei Province, whereas the 2023 strain fell within genotype I, clade K, showing the highest similarity to sequences from Yunnan and Guangdong. The most recent common ancestor of the Ningxia strains was estimated to have existed around 1989 (95% highest posterior density: 1985-1993) and is shared with strains from Guangdong, Yunnan, and Southeast Asia. Comparative analysis of prM-E proteins identified 16 (2019) and 11 (2023) amino acid substitutions relative to the vaccine strain, and E-protein epitope mutation (N52D) is predicted to alter binding to the neutralizing antibody 1F4. These findings establish a molecular baseline for origin tracing and proactive surveillance in northwestern China.