Table 2.

Sequence of the SARS-CoV-2 viruses recovered in second passage in Vero E6 cells. The full-length coding regions of the viruses were obtained by NGS. Only non-synonymous SNPs with frequencies >20% are shown. The sequences were compared to Wuhan reference sequence (NC_045512) but only the polymorphism P323L is reported in the table.

Position	Protein	Reference Base	Alternative Base	Patient	WT Clone	nsp12 L323P	nsp12 A97V	nsp12 N491S	nsp12 F480L	nsp12 V557L	nsp12 F480L/V557L	Amino Acid Change #
1,597	nsp2	A	T	-	-	-	-	-	-	43.7	-	E264D
1,877	nsp2	T	A	-	-	-	-	-	-	-	55.5	S358T
2,337	nsp2	A	C	-	-	-	-	59.2	-	-	-	D511A
3,790	nsp3	A	T	-	-	99.5	-	-	-	-	-	L357F
6,063	nsp3	A	G	-	-	39.3	-	-	-	-	-	D1115G
11,075	nsp6	T	C	-	-	-	-	-	20.8	-	-	F35L
11,186	nsp6	T	G	-	-	-	-	-	-	41.2	-	L72V
13,730	nsp12	C	T	-	-	-	99.2	-	-	-	-	A97V
14,408	nsp12	C	T	99.8	99.7	-	99.4	99.8	99.7	99.8	99.7	P323L
14,878	nsp12	T	C	-	-	-	-	-	99.6	-	99.7	F480L
14,880	nsp12	T	A	-	-	-	-	-	99.8	-	99.8	F480L
14,912	nsp12	A	G	-	-	-	-	99.6	-	-	-	N491S
15,109	nsp12	G	C	-	-	-	-	-	-	99.2	99.1	V557L
21,784	S	T	A	-	-	-	-	-	21.0	-	0.7	N74K
22,301	S	A	C	-	42.7	0.8	-	-	-	-	-	S247R
23,525	S	C	T	-	0.3	-	8.5	4.7	-	-	-	H655Y
23,606	S	C	T	-	3.1	33.5	17.5	1.3	-	-	-	R682W
23,615	S	C	A	-	-	-	-	-	99.4	-	-	R685S
26,261	E	C	T	-	1.7	-	45.1	8.0	-	2.5	-	S6L
26,333	E	C	T	-	-	-	0.5	66.6	-	-	1.0	T30I
26,435	E	A	C	-	-	-	-	-	-	81.0	-	N64T
27,224	ORF6	A	C	-	-	-	-	-	-	-	94.3	Q8P

WT: wild-type. #: numbers refer to protein specific residues. -: not detected. Mutations marked in bold green were engineered. Mutation marked in bold red occurred randomly during cloning, but it was outside the target region of study.