Table 1.
Primers used for sequencing analyses
| Gene | Primer name | Sensea | Sequence (5′ to 3′)b | Position numbering in H77 | Reference |
|---|---|---|---|---|---|
| 5′ UTR | KY80 | F | GCAGAAAGCGTCTAGCCATGGCGT | 68–91 | 13 |
| KY78 | R | CTCGCAAGCACCCTATCAGGCAGT | 288–311 | ||
| Core | C954 | F | ACTGCCTGATAGGGTGCTTGCGAG | 288–311 | 14 |
| C410 | R | ATGTACCCCATGAGGATCGGC | 732–752 | ||
| NS3 | NS3-1 | F | M13,c ATGGARAAGAARRTYATYRTITGGG | 3276–3300 | 15 |
| NS3-2 | F | M13,c ATGGARAYYAAGVTYATYACITGGG | |||
| NS3-1 | R | M13,c CTYTTICCRCTICCIGTIGGIGCRTG | 4026–4051 | ||
| Nest-S3-1 | F | M13,c ATCTTICTIGGICCIGCYGA | 3369–3388 | ||
| Nest-S3-2 | F | M13,c ATACTICTIGGICCIGCIGA | |||
| Nest-S3-1 | R | M13,c GCIACYTGRTAIGTITGIGG | 3999–4018 | ||
| NS5B | HC1 | F | TGGGGATCCCGTATGATACCCGCTTTGA | 8245–8275 | 16 |
| HC2 | R | GGCGGAATTCCTGGTCATAGCCTCCGTGAA | 8616–8645 | ||
| HC3 | F | TATGAYACCCGCTGYTTTGACTC | 8256–8278 | ||
| HC5 | R | GCTAGTCATAGCCTCCGT | 8619–8636 | ||
| NA1 | F | TTCACGGAGGCTATGACYAGG | 8617–8638 | ||
| NA2 | R | CGCGCATGMGACASGCTGTGA | 9283–9304 |
a
F, forward; R, reverse.
b
Y indicates C or T, R indicates A or G, V indicates A, C, or G, I indicates deoxyinosine, used as a “universal” nucleotide replacing A, G, C, or T.
c
M13 universal primers.