The rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of distinct viral clades, though their clinical significance remains unclear. Here, we examined the genome sequences of 88 SARS-CoV-2 viruses from COVID-19 patients in Chicago, USA and identified three distinct phylogenetic clades. Clade 1 was most closely related to clades centered in New York, and showed evidence of rapid expansion across the USA, while Clade 3 was most closely related to those in Washington. Clade 2 was localized primarily to the Chicago area with limited evidence of expansion elsewhere. Average viral loads in the airways of patients infected with the rapidly spreading Clade 1 viruses were significantly higher than those of the poorly spreading Clade 2. These results show that multiple variants of SARS-CoV-2 are circulating in the USA that differ in their relative airway viral loads and potential for expansion.

中文翻译：

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一个独特的 SARS-CoV-2 病毒进化枝与患者上呼吸道中较低的病毒载量有关。

SARS-CoV-2 是 2019 年冠状病毒病 (COVID-19) 的病原体，其迅速传播伴随着不同病毒进化枝的出现，尽管它们的临床意义仍不清楚。在这里，我们检查了来自美国芝加哥 COVID-19 患者的 88 种 SARS-CoV-2 病毒的基因组序列，并确定了三个不同的系统发育进化枝。进化枝 1 与以纽约为中心的进化枝关系最密切，并显示出在美国迅速扩张的证据，而进化枝 3 与华盛顿的进化枝关系最密切。Clade 2 主要位于芝加哥地区，其他地方扩张的证据有限。感染快速传播的进化枝 1 病毒的患者气道中的平均病毒载量显着高于传播不良的进化枝 2。