Abstract Since spilling over into humans, SARS-CoV-2 has rapidly spread across the globe, accumulating significant genetic diversity. The structure of this genetic diversity and whether it reveals epidemiological insights are fundamental questions for understanding the evolutionary trajectory of this virus. Here, we use a recently developed phylodynamic approach to uncover phylogenetic structures underlying the SARS-CoV-2 pandemic. We find support for three SARS-CoV-2 lineages co-circulating, each with significantly different demographic dynamics concordant with known epidemiological factors. For example, Lineage C emerged in Europe with a high growth rate in late February, just prior to the exponential increase in cases in several European countries. Non-synonymous mutations that characterize Lineage C occur in functionally important gene regions responsible for viral replication and cell entry. Even though Lineages A and B had distinct demographic patterns, they were much more difficult to distinguish. Continuous application of phylogenetic approaches to track the evolutionary epidemiology of SARS-CoV-2 lineages will be increasingly important to validate the efficacy of control efforts and monitor significant evolutionary events in the future.

中文翻译：

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新出现的 SARS-CoV-2 大流行的系统发育结构

摘要自从蔓延到人类身上，SARS-CoV-2 迅速蔓延到全球，积累了显着的遗传多样性。这种遗传多样性的结构以及它是否揭示了流行病学见解是理解这种病毒进化轨迹的基本问题。在这里，我们使用最近开发的系统动力学方法来揭示 SARS-CoV-2 大流行背后的系统发育结构。我们发现了对三个共同传播的 SARS-CoV-2 谱系的支持，每个谱系都具有与已知流行病学因素一致的显着不同的人口动态。例如，C 系于 2 月下旬以高增长率出现在欧洲，就在几个欧洲国家的病例呈指数增长之前。表征谱系 C 的非同义突变发生在负责病毒复制和细胞进入的功能重要基因区域。尽管血统 A 和 B 具有不同的人口统计模式，但要区分它们要困难得多。持续应用系统发育方法来追踪 SARS-CoV-2 谱系的进化流行病学对于验证控制工作的有效性和监测未来的重大进化事件将变得越来越重要。