Objective To understand the epidemiological trends of SARS-CoV-2 Omicron variants and evolutionary variations of the spike protein in Quzhou city of Zhejiang province from 2023 to 2024.

Methods Respiratory specimens (including nasopharyngeal swabs and sputum specimens) were collected from COVID-19 cases at sentinel surveillance sites for SARS-CoV-2 variants and influenza in Quzhou between January 2023 and September 2024. The whole genome sequences of SARS-CoV-2 from 267 cases were obtained by nanopore sequencing. The genotypes and amino acid variations were analyzed through Pangolin v4.3 and Nextclade v3.13.1 platforms. Heatmaps of amino acid mutations in the key domains of the spike protein were generated by TBtools-Ⅱ v2.222, while the impact of amino acid mutations on viral adaptability was assessed by the VarEPS system.

Results All the 246 sequences were Omicron variants of SARS-CoV-2, showing the turnover of BA.5-XBB-BA.2 lineages. These variants were classified into ten sub-lineages, with JN.1 and its sub-lineages showing the highest prevalence (42.28%, 104/246). This classification was consistent with the results of the phylogenetic analysis. The distribution of SARS-CoV-2 genotypes across different age groups showed differences (P < 0.001). Amino acid mutation analysis revealed frequent mutations in the spike protein, with the number of mutation sites gradually increasing over time and involving substitutions, insertions, and deletions. JN.1, XDV.1, and their sub-lineages exhibited higher mutation frequency in the spike protein, accumulating novel mutations (K356T, R403K, N450D, N481K, E544K, A570V, P621S, etc.) in key domains. Functional assessments indicated that multiple spike protein mutations (R346T, S371F, S373P, T376A, D405N, R408S, K417N, G446S, F456L, Y505H, etc.) may reduce the binding stability between the spike protein with neutralizing antibodies.

Conclusion The Omicron variants were the predominant circulating variants in Quzhou during 2023–2024, exhibiting diverse genotypes. Monitoring and analyzing amino acid mutations in the spike protein facilitate timely understanding of the evolutionary characteristics of SARS-CoV-2, providing a theoretical basis for risk assessment of COVID-19 variant prevalence and the implementation of epidemic prevention and control measures.