TABLE 1.
Primers used for amplification and sequencing of HCV
| Primera | Sequence (5′ to 3′) | Position | Polarity | Source or reference |
|---|---|---|---|---|
| 16† | GRGGCGACACTCCACCAT | 16-33 | Forward | This study |
| s17† | ACCATAGATCACTCCCCTGT | 29-48 | Forward | 31 |
| 953 | AGGTCTCGTAGACCGTGCATCATG | 321-344 | Forward | 24 |
| 951 | CAYGTRAGGGTATCGATGAC | 697-716 | Reverse | 24 |
| 410 | ATGTACCCCATGAGGTCGGC | 731-750 | Reverse | 24 |
| 693 | AAYTTGGGTAARGTCATCG | 693-711 | Forward | This study |
| 845 | CCYGGTTGCTCYTTYTCTAT | 849-868 | Forward | This study |
| 1298 | CTGGGAYATGATGATGAA | 1298-1315 | Forward | This study |
| 1992† | GGNTGYACVTGGATGAA | 1992-2008 | Forward | This study |
| 2085 | TTSCKGAARCARTCVGTRGG | 2085-2104 | Reverse | This study |
| 3277F‡ | ATGGAGAAGAARVTYATCAC | 3277-3296 | Forward | This study |
| 3277R† | CTRATRABYTTVDTCTCCAT | 3277-3296 | Reverse | This study |
| 3636 | TGGTCYACATTGGTRTACATYTG | 3636-3658 | Reverse | This study |
| 4039ঠ| GGCAGYGGBAARAGYAC | 4039-4955 | Forward | This study |
| 4662† | CRCCYGTRTASCCRGTCAT | 4662-4680 | Reverse | This study |
| 4863 | CCSTCNGGHATGTTYGA | 4863-4879 | Forward | This study |
| A5310 | CCCAGGTGCTAGTGACGAC | 5304-5322 | Reverse | 31 |
| 5460† | TAGMRCAYTCYTCCATCTC | 5460-5478 | Reverse | This study |
| 5930‡ | AGTSGCYTTYAARRTCATG | 5930-5948 | Forward | This study |
| 6085 | GCTATBAGYCKGTTCATCCA | 6084-6103 | Reverse | This study |
| 6800 | TCCCBTGYGARCCBGAG | 6820-6836 | Forward | This study |
| 7039 | TGGMGGCARGARATGGG | 7038-7054 | Forward | This study |
| 7100‡ | AAGMGGVTCRAARGAGT | 7102-7118 | Reverse | This study |
| 7600 | TGVCGRATKAGRGAGTTGC | 7681-7699 | Reverse | This study |
| 8170 | ATGGGRTTCTCCTAYGAYAC | 8244-8263 | Forward | This study |
| Pr1 | TGGGGATCCCGTATGATACCCGCTGCTTTGA | 8245-8275 | Forward | 32 |
| Pr3¶ | TATGAYACCCGCTGYTTTGACTC | 8256-8278 | Forward | 32 |
| Pr2‡ | GGCGGAATTCCTGGTCATAGCCTCCGTGAA | 8616-8645 | Reverse | 32 |
| Pr4 | GCNGARTAYCTVGTCATAGCCTC | 8622-8644 | Reverse | 32 |
| 8625‡ | GARTACCTRGTCATAGC | 8625-8641 | Reverse | This study |
| 9325¶ | CTACRGTAAGTAGGAGTAGGC | 9325-9345 | Reverse | This study |
| 3′UTR¶ | AAAAAAAAAAAAAAAAAA | 9418-9435 | Reverse | This study |
a
†, Primer used for amplification of cDNA fragment nucleotides 17 to 5460; ‡, primer used for amplification of cDNA fragment nucleotides 3227 to 8625; ¶, primer used for amplification of cDNA fragment nucleotides 4039 to 9435.