Background: During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. Methods: We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020. Results: We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10⁻³ substitutions per year. Conclusions: Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches.

中文翻译：

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大流行初期瑞典SARS-CoV-2的时空突变谱出现。

背景：在COVID-19大流行期间，该病毒得以进化，因此我们旨在提供一个洞察力，以了解哪些遗传变体被富集以及它们如何在瑞典传播。方法：我们分析了从2020年2月7日至2020年5月14日从GISAID免费获得的348个瑞典SARS-CoV-2序列。结果：我们在人群中鉴定了频率≥5％的14个变异位点。在这些位点中，病毒穗蛋白中的D936Y取代处于正选择状态。变异位点可以区分瑞典的11个突变谱。其中九个分布图出现在2020年3月的斯德哥尔摩。随着时间的推移，包含D936Y突变的变异分布图3（B.1.1）和6（B.1）成为主要分布图，在四月和六月期间从斯德哥尔摩传播到其他瑞典地区。五月初。此外，每年^−3个替代。结论：我们的研究为大流行早期瑞典SARS-CoV-2变异的时空动态提供了新颖的知识。这些病毒变体的表征可以提供有关病毒发病机理的宝贵见解，并且对于诊断和药物开发方法可能是有价值的。