Fig. 3: SARS-CoV-2 collected from wildlife in comparison to human samples.

a Color ribbons show the proportion of each lineage circulating in humans in sampling region at the time of data collection⁸³. Circles represent each individual animal sampled (n = 789). A positive sample has a value of 1 and a negative sample has a value of 0. Circles outlined in red represent a positive sample with lineage assignment (n = 9, Supplementary Figs. 2–9; Table 3). The fill color within each red circle represents the lineage it was assigned. b A phylogenetic tree was generated using maximum likelihood analysis and GTR + G4 substitution models to visualize the relatedness of the nine whole genome sequences obtained from wild animals (n = 9) to SARS-CoV-2 sequences derived from human hosts (n = 90) representing different PANGO lineages. Additional phylogenetic analyses show the placement of the SARS-CoV-2 sequences from each individual wild animal within individual lineages in more detail (Supplementary Figs. 2–9). c Suspected transmission origin for each individual is represented by a human silhouette or a question mark (“?”) if the origin is suspected to be either a human-to-animal or animal-to-animal transmission. Inferences about transmission were determined by phylogenetic analysis using related human host sequences and our sequences collected from wild animals as shown in Supplementary Figs. 2–9 and in Supplementary Table 2. We also considered any unique mutations not described from a human host, as those mutations may have come from the originating hosts’ virus. The arrow color indicates the lineage assignment and silhouettes indicate the species from which the sample was collected. Across all panels color indicates the same lineage of SARS-CoV-2.