Fig. 4

A Temporally-resolved phylogenetic tree showing cases sampled from either the SNF (residents and staff, squares) or the broader community (grey circles). The putative index case is annotated. While the community-associated lineage continued to circulate and was sampled in late-January 2021, the SNF-associated clade was not detected after the end of December 2020. B Genetic divergence tree indicating cases within the community (grey tips) and in the skilled nursing facility that had the wildtype N at site 501 in Spike (square yellow tips), and the emergent clade with a Y at site 501 (square maroon tips). The nucleotide substitution yielding the amino acid substitution is annotated on the tree. Square tips represent cases among either the staff or resident population at the SNF, while circular tips represent cases within the community. Large clades of identical genomes are collapsed, with either a square or circular tip, and are annotated with the number of identical genomes that the collapsed tip represents. The staff member that was the putative index case given contact tracing information is annotated