Table A1.

Rare and very rare, shared SNPs between companion animal sequences of this study and other companion animal sequences in GISAID. The percentage in which the SNP is found in all human, animal, and companion animal sequences in GISAID is calculated together with its 95% binomial proportion confidence interval using the Wilson method. Very rare mutations for the lineages in the study samples are indicated in bold.

	SNP	Aa Mutation	Samples	% Human Sequences GISAID	% Animal Sequences GISAID	% Companion Animal Sequences GISAID
1	A10323G	ORF1a:K3353R	22.2, 22.1	1.41 (1.4, 1.42)	0.93 (0.61, 1.42)	2.62 (1.28, 5.31)
2	A929G	ORF1a:I222V	36.1	0.06 (0.06, 0.06)	0.13 (0.05, 0.39)	0.75 (0.21, 2.69)
3	C15952A	ORF1b:L829I	39.1, 39.2	2.36 (2.35, 2.36)	0.44 (0.24, 0.81)	0.75 (0.21, 2.69)
4	C20844T	-	36.1	0.17 (0.17, 0.17)	0.88 (0.57, 1.36)	1.12 (0.38, 3.25)
5	C22792T	-	39.1, 39.2	5.66 (5.65, 5.68)	0.97 (0.64, 1.47)	1.12 (0.38, 3.25)
6	C6026T	ORF1a:P1921S	29.1	0.15 (0.15, 0.15)	0.13 (0.05, 0.39)	1.12 (0.38, 3.25)
7	C9286T	-	39.1, 39.2	0.2 (0.2, 0.2)	0.97 (0.64, 1.47)	1.87 (0.8, 4.31)
8	G2272A	-	29.1	0.03 (0.03, 0.04)	0.13 (0.05, 0.39)	0.37 (0.02, 2.09)
9	G25244T	S:V1228L	29.1	0.12 (0.12, 0.12)	0.44 (0.24, 0.81)	1.12 (0.38, 3.25)
10	G487A	-	36.1	0.04 (0.04, 0.04)	0.13 (0.05, 0.39)	0.75 (0.21, 2.69)
11	T27534C	-	38.2	0.03 (0.02, 0.03)	0.35 (0.18, 0.7)	1.5 (0.58, 3.79)
12	T29867A	-	36.1, 38.2, 39.1	0.12 (0.12, 0.13)	0.18 (0.07, 0.45)	1.12 (0.38, 3.25)