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Published on: November 5, 2021
Genomic evolution and epidemiological impact of SARS-CoV-2 omicron subvariants in Taiwan, 2023-2025
Li-Teh Liu1, Chao-Ju Chen2, Po-Chih Chen3
1Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung Hwa University of Medical Technology, Tainan City, Taiwan.
Background:
The continued evolution of SARS-CoV-2 Omicron sublineages requires ongoing genomic and epidemiological surveillance. This study investigated the genomic epidemiology, national trends, and clinical aspects of SARS-CoV-2 in Taiwan from November 2023 to February 2025.
Methods:
We analyzed the molecular and clinical characteristics of a local cohort (n = 22) from southern Taiwan. Case and mortality trends were evaluated using nationwide surveillance data, considering changes in case definitions. Broader genomic surveillance included 1782 Taiwanese sequences from GISAID to characterize the distribution and evolution of Omicron subvariants, considering the rollout timeline of XBB.1.5 and JN.1 vaccines.
Results:
Genomic surveillance revealed a major epidemiological shift driven by variant succession: JN.1 and its descendants (e.g., KP.2, KP.3) replaced XBB-related subvariants, coinciding with infection waves in early and mid-2024. A more stringent national case definition for "severe complicated COVID-19" implemented in September 2024, substantially altered epidemiological metrics, reducing reported cases but increasing case fatality. In the local cohort, no significant associations were observed between sex, age, Ct value, comorbidity number, or vaccination status and hospitalization or severity, likely due to limited sample size. Nationally, individuals aged ≥ 65 years were disproportionately represented among severe cases and deaths, with risk amplified in those with comorbidities and low recent XBB.1.5/JN.1 vaccination coverage.
Conclusions:
Taiwan experienced dynamic evolution of SARS-CoV-2 Omicron, dominated by JN.1 and its derivatives, which drove successive infection waves. Changes in national case definitions created substantial surveillance artifacts complicating interpretation of disease burden. Although national data reaffirm advanced age as the key risk factor for severe outcomes, these findings underscore the importance of targeted vaccination strategies and integrated surveillance systems capable of distinguishing the effects of viral evolution from policy-driven reporting changes.
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