FIGURE 3 | All major clades were represented in the United States at the start of the epidemic. A phylogenetic tree of 110 reference SARS-CoV-2 genomes (unlabeled tips) and 79 SARS-CoV-2 genomes from Abbott (labeled tips). Branches are color-coded by clade (which was corroborated by analysis of the hallmark clade-defining SNPs) and their lengths are calibrated to the average number of substitutions per site. The tree is rooted on the midpoint and specimens bearing the spike Q677R mutation are specifically denoted. Nodes with branching support > 60% for Ultrafast Bootstrap and > 60% for Shimodaira-Hasegawa approximate likelihood ratio test are denoted with black dots. All bootstrapping values can be found in Supplementary Figure 1