Table 4. Comparative analyses of amino acid substitutions among 4 clades of genotype I, genotype V and Indian isolate, 1979 to corresponding residues in the reference strain, H241 (AY947539, Philippines 1956) of clade A.

Sr No.	Genomic region	Polyprotein position	Gene position	Reference strain (H241)	Genotype I				JQ922559(India, 1979)	Genotype V(India, 1961–62)
					Clade A	Clade B	Clade C	Clade D(Pune 2016)
1	prM (114–279,166aa)	269	156	V	*	I	I	I	I	*
2		271	158	M	*	*	*	I	*	*
3	Env (280–774, 495aa)	409	130	V	*	*	I	*	*	*
4		411	132	I	*	*	*	V	*	*
5		479	200	K	*	*	*	T	*	*
6		481	202	K	*	*	N	*	*	*
7		512	233	Y	*	H	H	H	*	*
8		645	366	N	*	*	*	S	*	*
9	NS1 (775–1126, 352aa)	776	2	T	*	M	M	M	M	M
10		903	129	K	*	R	R	R	R	R
11		945	171	F	*	*	*	L	*	*
12	NS2A (1127–1344, 218aa)	1219	93	R	*	*	*	K!	*	*
13		1262	136	V	*	*	*	A	*	*
14		1281	155	R	*	K	K	K	K	*
15		1310	184	C	*	*	*	R	*	*
16	NS2B (1345–1474, 130aa)	1433	89	I	*	V	V	V	V	V
17	NS3(1475–2092, 618aa)	1536	62	T	*	S	S	S	S	*
18		1645	171	T	*	I	I	I	I	I
19		1795	321	A	*	T	T	T	T	*
20		1857	383	I	*	*	V	*	*	*
21		1954	480	K	*	R	R	R	R	*
22		2079	605	M	*	*	V	V	*	*
23	NS4A (2093–2219, 127aa)	2209	117	V	*	*	A	A!!	*	A
24	2K peptide (2220–2242, 23aa)	2240	21	I	*	V	V	V	V	*
25	NS4B(2243–2487, 245aa)	2440	198	V	*	I	I	I	I	I
26	NS5(2488–3387, 900aa)	2733	246	R	*	*	*	K	K	*
27		2734	247	H	*	*	Y∉	Y	*	*
28		2743	256	V	*	A	A	A	A	*
29		2762	275	T	*	*	A∉	A	*	*

*—sequence similar to reference strain Philippines, 1956

Bold–amino acid substitution unique to clade D

!—amino acid substitution unique to clade D except MG272272 (1028)

!! - amino acid substitution unique to clade D except MG272273 (S41)

Italics—amino acid substitution unique to clade C

∉—amino acid substitution unique to clade C except KU509287