Table 1. Amino acid substitutions that partially or fully 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 on alignment of the six FCoV genomes analysed in this study (Supplementary Fig. S1). The amino acid positions in the non-structural replicase proteins (nsps) 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
1758	nsp2	I	I	I	V	V	I	549
1794	nsp2	G	G	G	G	G	R	561
6553	nsp3	D	D	D	G	G	D	2147
14 727	nsp12	Y	Y	Y	F*	F*	Y	4872
17 883	nsp14	T	T	T	I	I	T	5924
19 277	nsp16	N	N†	N	H	H	N	6389
21 370	S	S	S	S	A	S	S	403
21 377	S	I	I	I	I	I	T	405
22 291	S	F	F	F	F	F	L	710
22 361	S	S	S	S	I	I	S	733
22 528	S	R	R	R	G	G	R	789
22 539	S	R	R	R	R	R	S	792
22 757	S	S	S	S	F	F	S	865
23 302	S	M	M	M	L	L	L	1047
23 486	S	I	I	I	T	T	T‡	1108
23 589	S	K	K	K	N	N	K	1142
24 190	S	P	P	P	P	P	S	1343
24 298	S	E	E	E	Q	Q	E	1379
25 447	3C	T	T	T	T	T	M	165
25 580–25 589§	3C	(−)	(−)	(−)	(+)	(+)	(−)	Deletion
27 228	N	S	S	S	L	L	S	170
28 759	7B	L	L	L	F	L	L||	198

^*The consensus nucleotide constituted 83 % (26M) and 55 % (27C) of the sequence reads at this position.

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

^‡The consensus nucleotide constituted 75 % of the sequence reads at this position.

^§(−), 3c protein gene was complete; (+), 3c protein gene had a deletion. The deletions were: 26M and 27C, nt 25584–25593 (10 nt, AGGAGTTTAC).

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