COVID-19 is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any homoplasies observed in SARS-CoV-2 to date are significantly associated with increased viral transmission. To do so, we develop a phylogenetic index to quantify the relative number of descendants in sister clades with and without a specific allele. We apply this index to a curated set of recurrent mutations identified within a dataset of 46,723 SARS-CoV-2 genomes isolated from patients worldwide. We do not identify a single recurrent mutation in this set convincingly associated with increased viral transmission. Instead, recurrent mutations currently in circulation appear to be evolutionary neutral and primarily induced by the human immune system via RNA editing, rather than being signatures of adaptation. At this stage we find no evidence for significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations.

COVID-19 是由冠状病毒 SARS-CoV-2 引起的，该病毒于 2019 年底从目前未知的动物宿主传播到人类群体中。由于最近与人类的联系，SARS-CoV-2 可能尚未完全适应其人类宿主。这引发了人们的猜测：SARS-CoV-2 可能正在向更高的传播能力进化。在假定的自然选择下，最可能的突变是那些重复且独立出现的突变（同质性）。在这里，我们正式测试了迄今为止在 SARS-CoV-2 中观察到的任何同质性是否与病毒传播增加显着相关。为此，我们开发了一个系统发育指数来量化具有和不具有特定等位基因的姐妹进化枝中后代的相对数量。我们将该指数应用于从全球患者中分离出的 46,723 个 SARS-CoV-2 基因组数据集中确定的一组精选的复发突变。我们没有在这组突变中发现任何一个与病毒传播增加令人信服地相关的突变。相反，目前流行的反复突变似乎是进化中性的，主要是由人类免疫系统通过 RNA 编辑诱导的，而不是适应的特征。现阶段，我们没有发现任何证据表明 SARS-CoV-2 由于反复突变而具有明显更多的传播谱系。