TABLE 1.
Virus primers and probes
| Virus | GenBank accession no. | Primer or probe name | Primer/probe final concn (nM) | Probe label | Sequencec | Product size (bp) | Product region | Reference |
|---|---|---|---|---|---|---|---|---|
| Murine norovirus | AY228235 | MNVKS1 | 400 | 5′-AGGTCATGCGAGATCAGCTT-3′ | 159 | ORF1 | Bae and Schwab (3) | |
| MNVKS2 | 400 | 5′-CCAAGCTCTCACAAGCCTTC-3′ | ||||||
| MNVKS3 | 200 | FAMa | 5′-CAGTCTGCGACGCCATTGAGAA-3′ | |||||
| Human norovirus GI | M87661 | COG1F | 1,000 | 5′-CGYTGGATGCGNTTYCATGA-3′ | 85 | ORF1-ORF2 junction | Kageyama et al. (13) | |
| COG1R | 1,000 | 5′-CTTAGACGCCATCATCATTYAC-3′ | ||||||
| RING 1A | 100 | FAMa | 5′-AGATYGCGATCYCCTGTCCA-3′ | |||||
| RING 1B | 100 | FAMa | 5′-AGATCGCGGTCTCCTGTCCA-3′ | |||||
| Human norovirus GII | AF145896 | COG2F | 1,000 | 5′-CARGARBCNATGTTYAGRTGGATGAG-3′ | 88 | ORF1-ORF2 junction | Kageyama et al. (13) | |
| COG2R | 1,000 | 5′-CGACGCCATCTTCATTCACA-3′ | ||||||
| RING2-TP | 200 | FAMa | 5′-TGGGAGGGCGATCGCAATCT-3′ | |||||
| Human adenovirus | AC_000008 | JTVXF | 400 | 5′-GGACGCCTCGGAGTACCTGAG-3′ | 96 | Hexon region | Jothikumar et al. (12) | |
| (types A to F) | JTVXR | 400 | 5′-ACIGTGGGGTTTCTGAACTTGTT-3′ | |||||
| JTVXP | 150 | FAMa | 5′-CTGGTGCAGTTCGCCCGTGCCA-3′ | |||||
| Human polyomaviruses | AB092584 | SM2 | 500 | 5′-AGTCTTTAGGGTCTTCTACCTTT-3′ | 173 (JC) 176 (BK) | Partial T antigen | McQuaig et al. (20) | |
| (JC and BK) | P6 | 500 | 5′-GGTGCCAACCTATGGAACAG-3′ | |||||
| KGJ3 | 400 | FAMb | 5′-TCATCACTGGCAAACAT-3′ | |||||
| Human enteroviruses | AJ293918 | EV1R | 700 | 5′-TGTCACCATAAGCAGCCA-3′ | 143 | 5′ untranslated region | Gregory et al. (7) | |
| EV1F | 700 | 5′-CCCTGAATGCGGCTAAT-3′ | ||||||
| EV probe | 120 | FAMa | 5′-ACGGACACCCAAAGTAGTCGGTTC-3′ | |||||
| Hepatitis G virus | U44402 | HepG-F | 400 | 5′-CGGCCAAAAGGTGGTGGATG-3′ | 185 | 5′ untranslated region | Lambertini et al. (15) | |
| (internal standard) | HepG-R | 400 | 5′-CGACGAGCCTGACGTCGGG-3′ | |||||
| HepG probe | 200 | FAMa | 5′-AGGTCCCTCTGGCGCTTGTGGCGAG-3′ | |||||
| Bovine enteroviruses | PS87 isolate | BEV-5FL | 500 | 5′-GCCGTGAATGCTGCTAATCC-3′ | 92 | 5′ noncoding region | Jimenez-Clavero et al. (11) | |
| BEV-3FL | 500 | 5′-GTAGTCTGTTCCGCCTCCACCT-3′ | ||||||
| BEV-SON | 250 | FAMa | 5′-CGCACAATCCAGTGTTGCTACGTCGTAAC-3′ | |||||
| Bovine noroviruses | AJ011099 | SW GIII forw | 400 | 5′-CGCTCCATGTTYGCBTGG-3′ | 91 | ORF1-ORF2 junction | Wolf et al. (30) | |
| SW GIII rev | 400 | 5′-TCAGTCATCTTCATTTACAAAATC-3′ | ||||||
| SW GIII probe | 200 | FAMa | 5′-TGTGGGAAGGTAGTCGCGACRYC-3′ |
a
The 6-carboxyfluorescein (FAM) quencher was BHQ-1 (black hole quencher 1).
b
The FAM quencher was MGBNFQ (minor groove binder nonfluorescent quencher).
c
Mixed bases in degenerate primers and probes were as follows: Y = C, T; R = A or G; B = C, T, or G; N = A, C, T, or G.