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. Mutations that characterize Lineage C in particular are non-synonymous and 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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SARS-CoV-2大流行的新兴系统发育结构

自传播到人类以来，SARS-CoV-2已在全球迅速传播，积累了重要的遗传多样性。这种遗传多样性的结构及其是否揭示流行病学见识，是理解该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大流行的基础系统发育结构。我们发现了三个共同传播的SARS-CoV-2谱系的支持，每个谱系具有与已知的流行病学因素一致的人口统计学差异。例如，血统C在2月下旬出现在欧洲，增长率很高，就在几个欧洲国家的病例呈指数级增长之前。特别是表征谱系C的突变是非同义的，发生在负责病毒复制和细胞进入的功能重要的基因区域中。即使宗族A和B具有不同的人口统计模式，但要区分它们却要困难得多。持续应用系统进化方法来追踪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重大的进化事件将越来越重要。