Table 2.
Primers and probes used for qPCR viral detection within this study.
| Target | Reference | Primers and probe name | Primer and probe sequence (5′-3′) | Target sequence (5′-3′) |
|---|---|---|---|---|
| SARS-CoV-2 | (Centers for Disease Control and Prevention, 2020) | N1-F | GACCCCAAAATCAGCGAAAT | GTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAA ACCAGGTGGAACCTCATC AGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAA CATTTG |
| N1-R | TCTGGTTACTGCCAGTTGAATCTG | |||
| N1-P | ACCCCGCATTACGTTTGGTGGACC | |||
| Norovirus GII | (ISO, 2019) | NoVGII-F | ATGTTCAGRTGGATGAGRTTCTCWGA | ATGTTCAGATGGATGAGAT TCTCAGATCTGAGCACGTGGGAGGGCGATCGCAATCTGGCTCCCAGTTTTGTGAATGAAGATGGCGTCGA |
| NoVGII-R | TCGACGCCATCTTCATTCACA | |||
| NoVGII-P | AGCACGTGGGAGGGCGATCG | |||
| Pepper mild mottle virus | (Haramoto et al., 2013) | PMMoV-F | GAGTGGTTTGACCTTAACGTTTGA | GAGTGGTTTGACCTTAACGT TTGAGAGGCCTACCGAAGCAAATGTCGCACTTGCATTGCAACCGACAA |
| PMMoV-R | TTGTCGGTTGCAATGCAAGT | |||
| PMMoV-P | CCTACCGAAGCAAATG | |||
| CrAssphage | (Stachler et al., 2017) | CrAss-F | CAGAAGTACAAACTCCTAAAAAACGTAGAG | CAGAAGTACAAACTCCTAAAAAACGTAGAGGTAGAGGTATTAATAACGATTTACGTGATGTAACTCGTAAAAAGTTTGATGAACGTACTGATTGTAATAAAGCTAATGGCTTGTTTATTGGTC |
| CrAss-R | GATGACCAATAAACAAGCCATTAGC | |||
| CrAss-P | AATAACGATTTACGTGATGTAAC | |||
| Influenza A | (Shu et al., 2021) | Influ-A-F | CAAGACCAATCYTGTCACCTCTGAC CAAGACCAATYCTGTCACCTYTGAC | AAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTAAATGGG |
| Influ-A-R | GCATTYTGGACAAAVCGTCTACG GCATTTTGGATAAAGCGTCTACG | |||
| Influ-A-P | TGCAGTCCTCGCTCACTGGGCACG | |||
| Influenza B | (Shu et al., 2021) | Influ-B-F | TCCTCAAYTCACTCTTCGAGCG | GGATCCTCAACTCACTCTTCGAGCGTTTTGATGAAGGACATTCAAAGCCAATTCGAGCAGCTGAAACTGCGGTGGGAGTCTTATCCCAATTTGGTCAAGAGCACCGATT |
| Influ-B-R | CGGTGCTCTTGACCAAATTGG | |||
| Influ-B-P | CCAATTCGAGCAGCTGAAACTGCGGTG | |||
| Measles virus | (Hummel et al., 2006) | MeV-F | TGGCATCTGAACTCGGTATCAC | TGGCATCTGAACTCGGTATCACTGCTGAGGATGCAAGGCTTGTTTCAGAGATTGCAATGCATACTACTGAGGACA |
| MeV-R | TGTCCTCAGTAGTATGCATTGCAA | |||
| MeV-P | CCGAGGATGCAAGGCTTGTTTCAGA | |||
| Phi6 phage | (Gendron et al., 2010) | Phi6-F | TGGCGGCGGTCAAGAGC | TGGCGGCGGTCAAGAGCAACCCGGTCGTCGCAGGTCTGACACTCGCTCAGATCGGAAGCACCGGTTATGACGCCTATCAGCAGCTTCTGGAGAATCATCC |
| Phi6-R | GGATGATTCTCCAGAAGCTGCTG | |||
| Phi6-P | CGGTCGTCGCAGGTCTGACACTCGC | |||
| Adenovirus | (van Maarseveen et al., 2010) | AdV_R AdV_F |
CCGGCCGAGAAGGGTGTGCGCAGGTA CATGACTTTTGAGGTGGATC |
CATGACTTTTGAGGTGGATCCCATGGATGAGCCCACCCTGCTTTATCTTCTTTTCGAAGTCTTCGACGTGGTCAGAGTGCACCAGCCACACCGCGGCGTCATCGAGGCCGTCTACCTGCGCACACCGTTCTCGGCCGG |