Table 1. Oligonucleotides used for retrotranscription (RT) reactions and PCR amplifications.
| Primer | Sequence (5′-3′) | Position in the genome |
| Npro region | ||
| PR S1 | GCCCACTGTATTGCTAC | 344–360 |
| PR AS1 | CCCCTTTCTAGTCTGTCG | 937–954 |
| Erns region | ||
| PR S2 | AGGAATCACGCAAGAAACTG | 1,116–1,135 |
| PR AS2 | GTCACTAGCCCTATCATACC | 1,539–1,558 |
| PR S3 | TTGAACCCTGGATTCTAGTC | 1,455–1,474 |
| PR AS3 | AATTTCCCAGGGCCGAC | 1,970–1,986 |
| NS2-NS3 region | ||
| RT1 | CTTCCCCTTCCTTATAGAGAG | 8,261–8,281 |
| PR S4 | AATACTGGTTTGACCTGGAG | 3,435–3,454 |
| PR AS4 | CGCCAGTTCTTTCAGTTCAGT | 7,646–7,666 |
| SR S5 | CGCTGAGTCCATATTAGTGGT | 3,481–3,501 |
| SR AS5 | ACTGAACTTATCCCGCCT | 5,605–5,622 |
| SR S6 | CTGCCGTGTGTAAGAAGAT | 5,427–5,445 |
| SR AS6 | GTCTTCTAGTCTCTGGTCCT | 7,575–7,594 |
| NS4A-NS4B region | ||
| RT2 | GTAGTGTTAGCTTGAGGTAGATA | 12,477–12,498 |
| PR S7 | TAGACTGGCCTGATCCTG | 7,401–7,418 |
| PR AS7 | GTTGGCAATCTGATCCTCT | 8,826–8,844 |
| NS5A-NS5B region | ||
| RT2 | GTAGTGTTAGCTTGAGGTAGATA | 12,477–12,498 |
| PR S8 | CTGTATGGGGTTTACTACAAAGG | 8,567–8,589 |
| PR AS8 | TCTTCTTGAGGTGGACGG | 12,417–12,434 |
| SR S9 | CTGTATGGGGTTTACTACAAAGG | 8,567–8,589 |
| SR AS9 | TTGGTAAGCTGATGCCATGTG | 10,295–10,315 |
| SR S10 | AGGAGATGTTGGAGAGGTAA | 10,090–10,109 |
| SR AS10 | TCTTCTTGAGGTGGACGG | 12,417–12,434 |
Sequences and positions in the genome of BVDV NADL of the oligonucleotides designed and used for RT reactions and PCR amplifications of Npro, glycoprotein Erns and non-structural proteins coding region. Positions in the BVDV genome are according to BVDV NADL genome sequence GenBank accession no AJ133738.1.