TABLE 1.
Oligonucleotide primers for amplification and sequencing of the 3′ UTR, NTD, S1/S2, and S2′
| Name | Specificity | Sense | Sequence (5′ to 3′) | Product size (bp) |
|---|---|---|---|---|
| CCV 1-1 | Type 1 S1/S2 cleavage site | + | CTGCTCAAGCTGCTGTAATT | 244 |
| − | TACTACTGTGTTGGTGGTGA | |||
| CCV 1-2 | Type 1 S2′ cleavage site | + | ATGTAATGACAGAAGTACA | 261 |
| − | TACATTGCCATCTTATTATCA | |||
| CCV 2-1 | Type 2 S1/S2 cleavage site | + | GCCATAGTTGGAGCTATGAC | 203 |
| − | CCTATTTACAAAGAATGGCC | |||
| CCV 2-2 | Type 2 S2′ cleavage site | + | ATGCCATTGTAATATTGTGC | 225 |
| − | CCATCAGAATGTGTGACGTTA | |||
| CCV-IIa | Type IIa NTD | + | ATGATTGTGATCGTAACTTG | 200 |
| − | TTGTACCACACCTCTGTAGG | |||
| CCV-IIb | Type IIb NTD | + | GAACTATAGGCAACCATTGG | 138 |
| − | TACAATGCTTTAAGATTTTC | |||
| 20179a | Type I NTD | + | GGCTCTATCACATAACTCAGTCCTAG | 163 |
| CCV-IIc | − | TACATACTAGCTTCAAATC |
a
Previously described oligonucleotide (20).