TABLE 3.

The nucleotide differences within the 3′UTRs between JEV genotypes.

No.	Position of mutation	Standard strain	Genotypes
		Nakayama	I	II	III	IV	V
							Muar/Tengah	XZ0934
1	1–13	-					AGAACTCTTGAAA	-AAACTTTTGGTA*
2	24	G	–	–		A	A	A
3	25–26	GT	–	AT			TA	TA
4	28	G				A	T	T
5	36	A					G	–*
6	14–17	TGTG	–	–			ACAA	ATGA*
7	27	A					G	G
8	30–31	AA	GG				GT	GC*
9	33	A	T	T	G		A	–*
10	35	A					T	–*
11	37	A	G	G			T	T
12	38	C	T	T		T	T	T
13	39	C		T	T	G	T	T
14	41	–					G	T*
15	45–47	AAA	GTG	GTA
16	50	A				G	G	G
17	54	A	G	G		G
18	56	-	G
19	59	G	A	A		A	A	A
20	61	G				T	A	A
21	62	A					T	T
22	67	G					T	T
23	68–69	TA	–	–	CA	TG	–	–
24	71	G		A		A	A	A
25	72	C					G	A*
26	75	A	G
27	76	T					G	G
28	78	G					A	G*
29	88–89	AG					GA	GA
30	91–93	AAA				GTT	GCG	GTA*
31	96–97	CT					TC	TC
32	108–109	TA					AG	TG*
33	113	G	A				A	A
34	133	T					C	C
35	139	T					C	C
36	172	A	G			G	C	C
37	179	G	G	G	G	G	A	A
38	180	A	G				G	G
39	207	T	C			A	A	A
40	219	C					T	T
41	222	T	C	C
42	226	A				T	G	G
43	231	A		G		G	G	G
44	238–240	AAC					G-T	G-T
45	251–252	AA					G-	G-
46	253	A	T			T	–	–
47	254–256	TTT	TCT		TAT	CTT	TAA	CAA*
48	265	C					T	T
49	271	G				A	A	A
50	279	G					A	A
51	285–286	CG				TA	TA	TA
52	294	A					G	G
53	302	T					C	C
54	307	T					A	A
55	309	C	A	A		A	A	A
56	318–320	TTG					AAA	ATG*
57	338	G					A	A
58	343	G					A	A
59	348	G	A
60	360	C					T	T
61	361	G	T
62	365	T					C	C
63	400–401	AC					–	–
64	404	C					G	G
65	407	C	T	T			G	A*
66	419	G					A	A
67	421	C					T	T
68	423–424	CC				CT	TT	TT
69	438	G				A	A	A
70	440–441	AG		AA			GA	GA
71	487	-	A				A	A
72	508	A					T	T
73	515	G				A	A	A
74	528	C					A	A
75	550	T					A	A

A, adenine; G, guanine; C, cytosine; and T, thymine. “–” indicates missing nucleotides.

I–V indicate genotype I to genotype V of JEVs. * Indicates in this site the mutation were equal within the strain XZ0934, Muar and Tengah.