Fig. 6: Epidemiologically linked MPXV cases in NYC.

The symbols on the branches were colored by putative groups of epidemiologically linked cases. The outer ring (Sequence Type) in the figure was colored by the genome sequences that belonged to the same or different individual of epidemiologically linked cases in a particular group. The middle ring (Phylogenomic Category) is colored by the phylogenetic placement of the genome sequences of epidemiologically linked cases within a group. Epidemiologically linked cases in groups with sequences placed on the same or sister branches were designated as “monophyletic”. Epidemiologically linked cases in groups for which genome sequences were in the same clade in the phylogeny and shared a common ancestor with other NYC sequences in this clade were designated as “Shared Ancestor”. Epidemiologically linked cases in groups for which most of the genome sequences were placed in the basal part of the phylogenetic tree were designated as “inconclusive”. Epidemiologically linked cases in groups for which genome sequences were in different clades in the phylogeny were designated as “Not-linked”. The inner ring (Intra-host category) was colored by the categories that were assigned using the phylogenetic placement of the genome sequences from the same individual (See multiple infection result section: Fig. 4 and Supplementary Fig. 7). The source data files for Fig. 6 are available in the following GitHub repository: https://github.com/sakther-NYCDOHMH/nyc_mpox_genomic_epidemiology/.