Phylogenetic Trees based on 4,535 trimmed full genome SARS C0V02 alignments from GISAID.
A) A basic neighbor joining tree, centered on the Wuhan reference strain, with the GISAID G clade (named for the D614G mutation, though a total of 3 base changes define the clade) are highlighted in yellow. The regions of the world where sequences were sampled are indicated by colors. By early April, G614 was more common than the original D614 form isolated from Wuhan, and rather than being restricted to Europe (red) it had begun to spread globally. B) The same tree expanded to show interesting patterns of Spike mutations that we are tracking against the backdrop of the phylogenetic tree based on the full genome. Note three distinct patterns: mutations that predominantly appear to be part of a single lineage (P1263L, orange in the UK and Australia, and also A831V, red, in Iceland); a mutation that is found in very different regions both geographically and in the phylogeny, indicating the same mutation seems to be independently arising and sampled (L5F green, rare but found in scattered locations worldwide); and a mutation in sequences from the same geographic location, but arising in very distinct lineages in the phylogeny (S943P), blue, found only in Belgium. A chart showing how GISAID sequence submissions increase daily is provided in Fig. S1. The tree shown here can be recreated with contemporary data downloaded from GISAID at www.cov.lanl.gov. The tree shown here was created using PAUP (Swofford, 2003); the trees generated for the website pipeline updates are based on parsimony (Goloboff, 2014).