Fig. 2. Human-to-deer transmission of SARS-CoV-2 in Ohio.

a MCC tree inferred for 786 B.1.1.7 viruses collected from humans and WTD. Branches shaded by host species and location. The two Ohio WTD clusters are labeled. b AY.25 subtree (entire delta MCC tree shown in Fig. S4, n = 1094 delta viruses). Ohio WTD virus transmission clusters are shaded similarly to Fig. 3, with the addition of black branches indicating Ohio WTD singleton detections from this study and dark gray branches indicating non-Ohio WTD singletons. c The number of bi-weekly COVID-19 cases in humans in Ohio from January 2021 to February 2022, shaded by the proportion of human SARS-CoV-2 sequences from Ohio that belong to one of four Pango lineages (or ‘other’). Red box delineates the B.1.1.7 wave in humans. Below, green bars show the estimated number of human-to-deer transmission events of B.1.1.7 viruses, per 20-week increments, based on “Markov jump” counts inferred on the alpha MCC tree (n = 786 B.1.1.7 viruses). Green circles indicate the collection dates of 9 B.1.1.7 viruses in Ohio WTD. d Similar to c, but inferred on the delta MCC tree (n = 1094). e The detection lag (months) is the time difference between a human-to-deer transmission event (estimated) and the first observed sequence from a WTD transmission cluster, shown for 14 delta and 2 alpha WTD transmission clusters, inferred from the MCC trees. Red lines represent the two time points of the two nodes defining the branch on the phylogenetic tree on which the human-to-deer transition occurred; thick black bar represents the mean time of the branch. f Estimated number of human-to-deer transmission events in Ohio and North America and long-distance deer-to-deer transmission events that span Ohio counties, inferred from the MCC trees. Data for North America does not include Ohio.