Table 1. Primers and probes used in this study.

Target and GenBank accession No.	#	Name	Sequence (base positions in the reference sequence)	Used for:
JEV strain Nakayama EF571853.1	1	JE3-1357-1379-F	5’-GGAGAACAATCCAGCCAGAAAAC-3’	qRT-PCR
			(bases 1357 to 1379)
	2	JE3en-1470-1494-R	5’-CATTGGGTGTTACTGTAAACTTTGC-3’	qRT-PCR
			(complementary to bases 1470 to 1494)
	3	JE3-1427-1457-Taq	5’-[FAM]-AAACCATGGGAATTATTCAGCGCAAGTTGGG-[TAMRA]-3’	qRT-PCR
			(bases 1427 to 1457)
	4	JE2491-R23	5’-GCACATCCAGTGTCAGCATGCAC -3’	cDNA amplification
			(complementary to bases 2469 to 2491)
	5	JE962-F24	5’-CGCTCCGGCTTACAGTTTCAACTG-3’	cDNA amplification
			(bases 962 to 985)
Human GAPDH NM_002046.3	6	Cs_GAPDH-F	5’-AGGTCGGAGTCAACGGATTTG-3’	qRT-PCR
			(bases 116 to 136)
	7	Cs_GAPDH-R	5’-GGTCATTGATGGCAACAATATCCA-3’	qRT-PCR
			(complementary to bases 195 to 208)-
	8	Cs_GAPDH-P	5’-[FAM]-TGGTCACCAGGGCTGCTTTAACTCTGG-[TAMRA]-3’	qRT-PCR
			(bases 152 to 179)
	9	GAPDH-HA-IF1	5’-TGGCGGCCGCGAATTCACCATGGGGAAGGTGAAG-3’	cDNA amplification
			(bases 100 to 133)
	10	GAPDH-HA-IF2	5’-CATATGGGTAAGATCTCTCCTTGGAGGCCATGTG-3’	cDNA amplification
			(complementary to bases 1074 to 1107)
Human RIG-I AF038963.1	11	Sumpter F	5’-GTCCGGCCTCATTTCCTCGGAAAATC-3’	cDNA amplification [16]
			(bases 34 to 69)
	12	Sumpter R	5’-GGTACAAGCGATCCATGATTATACCCACTATGTTTG-3’	cDNA amplification [16]
			(complementary to bases 2992 to 3027)
	13	216_F21	5’-TGGACCCTACCTACATCCTGA-3’	Sequencing
			(bases 216 to 236)
	14	439_R21	5’-GAAATCCCAACTTTCAATGGC-3’	Sequencing
			(complementary to bases 419 to 439)
	15	601_F23	5’-GATGGCAGGTGCAGAGAAATTGG-3’	Sequencing
			(bases 601 to 623)
	16	1390_F23	5’-GGTTGGTGTTGGGGATGCCA-3’	Sequencing
			(bases 1390 to 1412)
	17	160_R21	5’-GTGTCCCTCATCAGCTGAGC-3’	Sequencing
			(complementary to bases 1582 to 1602)
	18	1978_R20	5’-CTCATTGCTGGGATCCCTGG-3’	Sequencing
			(complementary to bases 1959 to 1978)
	19	2129_F22	5’-CCTGGCATATTGACTGGACGTG-3’	Sequencing
			(bases 2129 to 2150)
	20	2989_R22	5’-TCTTCTCCACTCAAAGTTACTC-3’	Sequencing
			(complementary to bases 2968 to 2989)