Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.
Faculty of Science and Technology, Institute of Technology, University of Tartu, Tartu, Estonia.
PLoS One. 2024 May 10;19(5):e0303176. doi: 10.1371/journal.pone.0303176. eCollection 2024.
BACKGROUND: The COVID-19 pandemic was characterised by rapid waves of disease, carried by the emergence of new and more infectious SARS-CoV-2 virus variants. How the pandemic unfolded in various locations during its first two years has yet to be sufficiently covered. To this end, here we are looking at the circulating SARS-CoV-2 variants, their diversity, and hospitalisation rates in Estonia in the period from March 2000 to March 2022. METHODS: We sequenced a total of 27,550 SARS-CoV-2 samples in Estonia between March 2020 and March 2022. High-quality sequences were genotyped and assigned to Nextstrain clades and Pango lineages. We used regression analysis to determine the dynamics of lineage diversity and the probability of clade-specific hospitalisation stratified by age and sex. RESULTS: We successfully sequenced a total of 25,375 SARS-CoV-2 genomes (or 92%), identifying 19 Nextstrain clades and 199 Pango lineages. In 2020 the most prevalent clades were 20B and 20A. The various subsequent waves of infection were driven by 20I (Alpha), 21J (Delta) and Omicron clades 21K and 21L. Lineage diversity via the Shannon index was at its highest during the Delta wave. About 3% of sequenced SARS-CoV-2 samples came from hospitalised individuals. Hospitalisation increased markedly with age in the over-forties, and was negligible in the under-forties. Vaccination decreased the odds of hospitalisation in over-forties. The effect of vaccination on hospitalisation rates was strongly dependent upon age but was clade-independent. People who were infected with Omicron clades had a lower hospitalisation likelihood in age groups of forty and over than was the case with pre-Omicron clades regardless of vaccination status. CONCLUSIONS: COVID-19 disease waves in Estonia were driven by the Alpha, Delta, and Omicron clades. Omicron clades were associated with a substantially lower hospitalisation probability than pre-Omicron clades. The protective effect of vaccination in reducing hospitalisation likelihood was independent of the involved clade.
背景：COVID-19 大流行的特点是疾病的快速传播，这是由新的、更具传染性的 SARS-CoV-2 病毒变异引起的。在大流行的头两年，它在不同地点的发展情况尚未得到充分的报道。为此，我们正在研究 2000 年 3 月至 2022 年 3 月期间在爱沙尼亚流行的 SARS-CoV-2 变异株、其多样性以及住院率。
方法：我们在 2020 年 3 月至 2022 年 3 月期间对爱沙尼亚的 27550 个 SARS-CoV-2 样本进行了测序。对高质量的序列进行了基因分型，并分配到 Nextstrain 进化枝和 Pango 谱系。我们使用回归分析来确定谱系多样性的动态以及按年龄和性别分层的特定进化枝住院的概率。
结果：我们成功地对总共 25375 个 SARS-CoV-2 基因组（或 92%）进行了测序，鉴定出 19 个 Nextstrain 进化枝和 199 个 Pango 谱系。在 2020 年，最流行的进化枝是 20B 和 20A。随后的几次感染浪潮是由 20I（Alpha）、21J（Delta）和 Omicron 进化枝 21K 和 21L 驱动的。在 Delta 波期间，通过 Shannon 指数表示的谱系多样性达到了最高水平。大约 3%的测序 SARS-CoV-2 样本来自住院患者。在四十多岁以上的人群中，住院率随年龄显著增加，而在四十岁以下的人群中则微不足道。疫苗接种降低了四十多岁以上人群的住院几率。疫苗接种对住院率的影响强烈依赖于年龄，但与进化枝无关。感染 Omicron 进化枝的人比感染前 Omicron 进化枝的人在四十岁及以上的年龄组中住院的可能性要低。
结论：爱沙尼亚的 COVID-19 疾病浪潮是由 Alpha、Delta 和 Omicron 进化枝驱动的。与前 Omicron 进化枝相比，Omicron 进化枝与住院概率显著降低有关。疫苗接种在降低住院几率方面的保护作用与所涉及的进化枝无关。
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