Table 1.

ConsHMM conservation state assignment, sequence constraint scores, geographic area, and period of time of mutation hotspots.

	Conservation states		Geographic area		Time period
Locus	Learned from the Sarbecovirus alignment	Learned from the vertebrate CoV alignment	Asia / Oceania	Europe / North America	Jan	Feb	March
1397	S13	V20
2891	S19	V15
3036	S17	V22
8782	S26	V25
11083	S7	V9
14408	S17	V3
17746	S17	V7
17857	S17	V27
18060	S12	V8
23403	S17	V21
26143	S17	V21
28144	S9	V30
28881	S17	V13

Each row corresponds to a mutation hotspot reported by Pachetti et al¹⁸. First column contains the genomic position of the mutation. Second and third columns contain the ConsHMM conservation state learned from the Sarbecovirus alignment and the vertebrate CoV alignment, respectively, assigned to each mutation. The next two columns correspond to whether each mutation was observed in Asia or Oceania and whether each mutation was observed in Europe or North America, respectively, where grey is shown if the row’s mutation was observed in the area and white otherwise. The last three columns correspond to whether each mutation was observed in a particular month, where grey is shown if the row’s mutation was observed during the period and white otherwise.