Primer and probe sequences selected from the large T region of each polyomavirus genome
| Virus oligonucleotide | Sequence (5'–3') | Nucleotide positions |
| BKV Forward | TGA CTA AGA AAC TGG TGT AGA TCA | 4361–4384 |
| BKV Reverse | YTCC TT TAAT GA AAA ATG GGA | 4505–4525 |
| BKV Probe | FAM AGT GTT GAG AAT CTG CTG TTG CTT C BHQ-1 | 4437–4461 |
| JCV Forward | ACT GAG GAA TGC ATG CAG A | 4363–4381 |
| JCV Reverse | GGT GGA ATA CAT TTA ATG AGA AGT | 4509–4532 |
| JCV Probe | Cy5 TAG GTG GGG TAG AGT GTT GGG ATC BHQ-3 | 4425–4448 |