TABLE 3.
Primers and probes used in TaqMan assays to discriminate BoHV-1.1 and BoHV-1.2 at seven SNP positions
| SNP | SNP position in BoHV-1a | Nucleotide identity
|
TaqMan probec | TaqMan primerb | |
|---|---|---|---|---|---|
| BoHV-1.1 | BoHV-1.2 | ||||
| UL44/gC | 17983 | A | C | VIC-CGCGTCCCCACGGG | GGCGTGCTGTTGGTAACG (F) |
| FAM-CGCGTCCCCCCGGG | ACGCCCGGTGCTACTAC (R) | ||||
| UL27/gB | 56095 | T | C | VIC-TGAAGCCTGCGCGGC | ACGACGACCCCTGGGA (F) |
| FAM-AAGCCCGCGCGGC | CGTCCGTCGTGTGCCA (R) | ||||
| UL11 | 84380 | G | A | VIC-ACTGGTCCGACGTCAT | GGGCGGCGAGGACAA (F) |
| FAM-ACTGGTCCAACGTCAT | GCGGCCGGTACGGTTTTA (R) | ||||
| UL0/LRT | 100561 | A | G | VIC-TCGAGCCGCAGTCG | CGAGCAGTTACTTTCGGTTTGG (F) |
| FAM-TCGAGCCGCAGCCG | CCCCAGCCTGCATACTTAACTT (R) | ||||
| US2 | 115577 | A | G | VIC-CTCGGCAAGGAAA | AGCGCCCGGCTCTG (F) |
| FAM-CTCGGCGAGGAAA | GGGCAAGCCAGACGT (R) | ||||
| US6/gD | 119103 | A | G | VIC-CTACGCGACGAGCG | GCAGCCCGTCGAGGT (F) |
| FAM-TACGCGGCGAGCG | GATCAGCGCCAGCATGTC (R) | ||||
| US8/gE | 121768 | T | C | VIC-CTACGCGACGAGCG | CTGCCGCTGCTGCTG (F) |
| FAM-TACGCGGCGAGCG | CGGCCATCAAGCCCGAAA (R) | ||||
a
BoHV-1 GenBank accession number AJ004801.
b
F, forward; R, reverse.
c
SNPs differentiating BoHV-1.1 and BoHV-1.2 are indicated in boldface type.