TABLE 2.

PCR primers used in NS5b-based in-house methods

Gene region and primer name	Polarity	Sequencea	Positionb	Reference
NS5b
PR1	Sense	5′-TGGGGATCCCGTATGATACCCGCTGCTTTGA-3′	8245-8275	14
PR2	Antisense	5′-GGCGGAATTCCTGGTCATAGCCTCCGTGAA-3′	8616-8645	14
PR3	Sense	5′-TATGAYACCCGCTGYTTTGACTC-3′	8256-8278	25
PR4	Antisense	5′-GCNGARTAYCTVGTCATAGCCTC-3′	8622-8644	25
PR5	Antisense	5′-GCTAGTCATAGCCTCCGT-3′	8619-8636	33
1203	Sense	5′-ATGGGGTTCTCGTATGATACCCGCTGCTTTGACTC-3′	8244-8278	24
1204	Antisense	5′-GGAGGGGCGGAATACCTGGTCATAGCCTCCGTCAA-3′	8616-8650	24
122	Sense	5′CTCAACCGTCACTGAGAGAGACAT-3′	7935-7958	24
123	Antisense	5′-CCTCCTGCTCGCCTTGGACTCTCG-3′	8614-8591	24
242	Antiense	5′-GGCGGAATTCCTGGTCATAGCCTCGCTGAA-3′	8275-8304	14
243	Sense	5′-TGGGGATCCCGTATGATACCCGCTGCTTTGA-3′	7904-7934	14
5′ NC
KY 80	Sense	5′-GCAGAAAGCGTCTAGCCATGGCGT-3′	−274 to −250	40
KY 78	Antisense	5′-CTCGCAAGCACCCTATCAGGCAGT-3′	−31 to −55	40
SF1	Sense	5′-GCCATGGCGTTAGTATGAGT-3′	−261 to −240	13
DOG-1	Antisense	5′-CAGGCAGTACCACAAGGC-3′	−54 to −77	13

^aY = C or T; R = A or G; V = A, C, or G; N = A, T, G, or G.

^bNumbering according to Choo et al. (10).