Since the beginning of the pandemic, two mutations across the genome have become consensus: P4715L in ORF1ab (nucleotide 14,143, C to T) and D614G in S (nucleotide 23,403, A to G) (Fig. 1B) (a third consensus mutation, at nucleotide 3,037, is not reported as the site was masked during our sequence-filtering procedure). These mutations were found in 69.3% and 69.4% of sequences, respectively, and are in linkage (Fig. 2B). Given the importance of S for virus entry and as a target of the host neutralizing response, the biologic implications of the D614G mutation are under intense scrutiny (24–28). This mutation was first observed in a sequence from China dated January 24, with seven more sequences sampled until February 8. Then, the D614G mutation was not observed in China until March 13. In contrast, the D614G mutation was introduced in Europe at the end of January (first sequence identified in Germany, dated January 28), and it rapidly became dominant on that continent and at every location where the virus subsequently spread (Fig. 2A). The phylogenetic tree (Fig. 2B) and the distribution of sequences (Fig. 2C) are suggestive of a founder effect. The rapid spread of sequences carrying the D614G mutation implies that the growing viral population should become more homogeneous, that is, the frequency of sequences with shared polymorphisms will increase. We found a median of seven substitutions (based on a comparison of 18,514 sequences) between two independent SARS-CoV-2 genomes (SI Appendix, Fig. S2). Yet, genomes with the D614G mutation showed a median of five substitutions, whereas those with D at position 614 differed by eight substitutions (Fig. 2D).