Full
Outline
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.
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.
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.
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.
86
38
| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
关闭全屏
No. 86 Xueyuan South Road, Haidian District, Beijing
010-62662699(Operation and Technical Support)
qkjq@cast.org.cn
Copyright © 2025 China Association for Science and Technology. All rights reserved. For all open access content, the relevant licensing terms apply.
Sponsored by the Office of the Leading Group for Cybersecurity and Informatization of CAST, and supported by Science and Technology Review Publishing House
