Table 2. Comparison of non-synonymous and non-coding mutations of California natural isolates as compared to strain NY99.

Virus strains in bold were sequenced in the current study, while others were published previously [NY99 strain 382-99 (Lanciotti et al., 1999) and strains IMP102, IMP1075 and CA-04 (Deardorff et al., 2006)]. Italics indicate the nucleotide or amino acid substitutions in the COAV997 strain that were introduced into the NY99 virus backbone by site-directed mutagenesis. Mutations marked with lower case letters indicate a change in nucleotide, upper case letters indicate a change in amino acid.

Nucleotide position	Amino acid position	Virus strain
		NY99	COAV997	IMP102	IMP116	IMP1075	CA-04	COAV689	COAV2900
19	5′ UTR	g					a
458	C-121	V							A
1442	E-159	V	A	A	A	A	A	A	A
2799	NS1-110	K	N	N	N	N		N
6263	NS3-551	V				A
6721	NS4A-85	A							T
6742	NS4A-92	F	L		L/F	L		L
6871	NS4A-135	V				M		M
6901	NS4A-145	S					G
6992	NS4B-26	N							S
8620–21	NS5-314	K				N			R
10 213	NS5-845	G			R
10 279	NS5-867	N							D
10 384	NS5-902	D							N
10 403	3′ UTR	t							c
10 435	3′ UTR	c							t
10 459	3′ UTR	t							c
10 682	3′ UTR	g							a
10 772	3′ UTR	c	t	t	t	t		t
10 851	3′ UTR	a/g	g	g	g	g	g	g	g
10 980	3′ UTR	c		a
11 009	3′ UTR	t						c