Table 2. Amino acid substitutions that do not discriminate between the genome sequences derived from non-FIP (faecal) and FIP (tissue lesion) samples.

The positions of the substitutions are indicated as the position of the relevant mutation/substitution based upon an alignment of the six FCoV genomes analysed in this study (Supplementary Fig. S1). The amino acid positions in the nsp proteins refer to pp1ab. The consensus nucleotide constituted more than 96% of the sequence reads at a given position, unless indicated otherwise.

Nt position	Protein	65F	67F	80F	26M	27C	28O	Aa position
813	nsp2	V	I	I	I	I	V	234
1794/1795	nsp2	E	G	G	G	G	R	561
2955	nsp3	A	T*	T	T	T	A	948
3082	nsp3	R	K†	K	K	K	R	990
3797	nsp3	Q	Q	H	Q	Q	Q	1228
5218	nsp3	V	A	A	A	A	V	1702
5337	nsp3	L	M	M	M	M	L	1742
6804	nsp3	A	S	A	A	A	A	2231
8939	nsp5	K	K	N	N	N	K	2942
14 564	nsp12	A	A	P	P	P	A	4818
15 185	nsp13	I	I	L	I	I	I	5025
20 509/20 510	S	A	P‡	L	P	P	A	116
20 584	S	D	N	N	N	N	D	141
20 861	S	S	S§	N	S	S	S||	233
20 864	S	R	Q	R	Q	Q	R	234
20 866	S	I	L¶	I	I	I	L	235
21 275	S	R	R#	Q	R	R	R	371
21 467	S	I	T	T	T	T	I	435
22 151	S	R	K**	K	R	R	R	663
22332	S	I	I††	M	I	I	I	723
27273	N	L	Q	Q	Q	Q	L	185
27873	7A	H	Y‡‡	H	Y	Y	H	6

^*The consensus nucleotide constituted 71 % of the sequence reads at this position.

^†The consensus nucleotide constituted 72 % of the sequence reads at this position.

^‡The consensus nucleotide constituted 71 % of the sequence reads at this position.

^§The consensus nucleotide constituted 68 % of the sequence reads at this position.

||The consensus nucleotide constituted 85 % of the sequence reads at this position.

^¶The consensus nucleotide constituted 71 % of the sequence reads at this position.

^#The consensus nucleotide constituted 60 % of the sequence reads at this position.

^**The consensus nucleotide constituted 59 % of the sequence reads at this position.

^††The consensus nucleotide constituted 56 % of the sequence reads at this position.

^‡‡The consensus nucleotide constituted 78 % of the sequence reads at this position.