Table 3.

List of single nucleotide variations (SNV) uniquely identified for clades I and II.

Genomic Positiona	Reference base	Altered base	Substitution type	aab change	Clade	Genomic region	aac position	Frequencyd
3208	C	T	S	D>D	1	nsP2	509	1.00
3217	T	C	S	Y>Y	1	nsP2	512	1.00
3277	C	T	S	S>S	1	nsP2	532	1.00
3295	G	A	S	P>P	1	nsP2	538	1.00
3314	G	T	NS	A>S	1	nsP2	544	1.00
7328	G	A	NS	V>I	1	nsP4	555	1.00
7787	A	G	NS	Q>R	1	capsid	74	1.00
7788	G	A	NS	Q>R	1	capsid	74	1.00
8641	C	T	S	L>L	1	E2	34	0.68
9283	C	T	NS	L>F	1	E2	248	0.22
9285	C	T	S	L>L	1	E2	248	0.73
9936	T	C	S	C>C	1	6K	42	1.00
9970	A	G	NS	I>V	1	6K	54	1.00
1754	T	C	S	L>L	2	NSP2	25	1.00
1759	T	A	S	V>V	2	NSP2	26	1.00
1783	T	G	S	R>R	2	NSP2	34	1.00
1789	A	G	S	Q>Q	2	NSP2	36	1.00
1795	T	C	S	L>L	2	NSP2	38	1.00
2735	C	G	NS	P>A	2	NSP2	352	1.00
2767	A	G	S	G>G	2	NSP2	362	1.00
2887	T	C	S	L>L	2	NSP2	402	1.00
3403	T	C	S	F>F	2	NSP2	574	1.00
3901	A	G	S	V>V	2	NSP2	740	1.00
3916	T	C	S	F>F	2	NSP2	745	1.00
4711	T	C	S	D>D	2	NSP3	212	1.00
4837	A	G	S	S>S	2	NSP3	254	1.00
4843	C	T	S	P>P	2	NSP3	256	1.00
4939	T	C	S	S>S	2	NSP3	288	1.00
5783	C	T	S	L>L	2	NSP4	40	1.00
5793	C	T	NS	A>V	2	NSP4	43	1.00
5807	C	T	S	L>L	2	NSP4	48	1.00
5857	T	C	S	Y>Y	2	NSP4	64	1.00
5921	T	C	S	L>L	2	NSP4	86	1.00
5956	C	T	S	T>T	2	NSP4	97	1.00
6994	T	C	S	N>N	2	NSP4	443	1.00
7213	A	G	S	T>T	2	NSP4	516	1.00
9153	T	C	S	G>G	2	E2	204	0.89
9642	T	A	S	T>T	2	E2	367	0.80
10856	C	T	NS	T>I	2	E1	288	0.86
11241	T	C	S	G>G	2	E1	416	0.81

^aGenomic position according to the reference sequence NC_004162.2.

^bAmino acid change.

^cAmino acid position in the respective peptide.

^dFrequency of the substitution in the dataset from the respective clade. Non-synonymous substitutions are highlighted in bold.