Table 2. Primers and probes used in this study.
(F: Forward; R: Reverse; P: Probe)
| Virus | Specificity | Sequence (5’—3’) | Location Size | Target | Reference |
|---|---|---|---|---|---|
| (+/-adapted for this study) | |||||
| Hepatitis A virus | All genotypes | F—TCA CCG CCG TTT GCC TAG | 68–85 | 5’UTR | [22] |
| R—GGA GAG CCC TGG AAG AAA G | 241–223 | M14707 | [22] | ||
| P—FAM-CCT GAA CCT GCA GGA ATT AA-MGB | 169–150 | 174bp | [22] | ||
| Hepatitis E virus | All genotypes | F—CGG TGG TTT CTG GGG TGA C | 5260–5278 | ORF2/ORF3 | [35] |
| R—AGG GGT TGG TTG GAT GAA TAT AG | 5330–5308 | M73218 | [35] | ||
| P—FAM-GGG TTG ATT CTC AGC CCT TCG C-BHQ1 | 5280–5301 | 71bp | [35] | ||
| Rotavirus | Serotype A | F—ACC ATC TWC ACR TRA CCC TC | 963–982 | NSP3 (segment 7) | [36], adapted |
| R—GGT CAC ATA ACG CCC C | 1049–1034 | X81436 | [37] | ||
| P—FAM-ACA ATA GTT AAA AGC TAA CAC TGT CAA-BHQ1 | 990–1016 | 87pb | [36], adapted | ||
| Norovirus | Genogroup I | F—CGC TGG ATG CGN TTC CAT | 5291–5308 | 5' end of ORF2 | [38] |
| R—CCT TAG ACG CCA TCA TCA TTT AC | 5376–5334 | M87661 | [39] | ||
| P—FAM-TGG ACA GGA GAY CGC RAT CT-BHQ1 | 5321–5340 | 86bp | [39] | ||
| Norovirus | Genogroup II | F—ATG TTC AGR TGG ATG AGR TTC TCW GA | 5012–5037 | 5' end of ORF2 | [40] |
| R—TCG ACG CCA TCT TCA TTC ACA | 5080–5100 | X86557 | [41] | ||
| P—FAM-AGC ACG TGG GAG GGC GAT CG-BHQ1 | 5042–5061 | 89bp | [40] | ||
| Norovirus | Genogroup IV | F—GGA TGC GRT TCT CAG ACT | 4986–5003 | ORF1-ORF2 | This study |
| R—TCT TCA TTC ACA AAR TCG GGA G | 5055–5034 | JQ613567 | This study | ||
| P—FAM-TGG GAG GGG GAT CGC GAT CT-BHQ1 | 5012–5031 | 70bp | [42] | ||
| Sapovirus | GG 1, 2, 4, 5 | F—GAC CAG GCT CTC GCY ACC TAC | 5074–5094 | Polymerase / capsid junction | [43] |
| R—CCC TCC ATY TCA AAC ACT AWT TTG | 5177–5154 | NC_006269 | [43] | ||
| P—FAM-CCC ACT GGG TCA RGT ACT GTA C-BHQ1 | 5135–5114 | 104bp | This study | ||
| Aichi virus | / | F—CCA GCC TGA CGT ATC ACA GG | 268–287 | 5’ UTR | [44] |
| R—CAC AAT TGC CAC GTG AGC AGC TT | 329–307 | AB040749 | [44] | ||
| P—FAM-CTG TGT GAA GYC C-MGB | 288–300 | 62bp | [44] | ||
| Astrovirus | / | F—TCT YAT AGA CCG YAT TAT TGG | 2209–2229 | ORF 1a | [45] |
| R—TCA AAT TCT ACA TCA TCA CCA A | 2322–2301 | NC_001943 | [45] | ||
| P—FAM-CCC CAD CCA TCA TCA TCT TCA TCA-BHQ1 | 2295–2272 | 114bp | [45] | ||
| Adenovirus | 40 and 41 (serotype F) | F—CTC GAC ATG ACT TTT GAG GT | 20256–20275 | Hexon protein | [45], adapted |
| R—GTA GAC GGC CTC GAT GAC | 20375–20358 | NC_001454 | [45], adapted | ||
| P—FAM-AGG ATG AGC CCA CAC TTC TYA TGB-BHQ1 | 20290–20302 | 120bp | [45], adapted | ||
| Coronavirus (human) | 229 (α-coronaV) | F—CAT ACT ATC AAC CCA TTC AAC AAG | 25374–25397 | glycoprotein | [46] |
| R—CAC GGC AAC TGT CAT GTA TT | 25510–25491 | AF304460 | [46] | ||
| P—FAM-ATG AAC CTG AAC ACC TGA AGC CAA TCT ATG-BHQ1 | 25480–25451 | 137bp | [47] | ||
| HKU1 (β-coronaV) | F—TCC TAC TAY TCA AGA AGC TAT CC | 28775–28797 | phosphoprotein | [46] | |
| R—AAT GAA CGA TTA TTG GGT CCA C | 28921–28900 | HM034837.1 | [46] | ||
| P—FAM-TYC GCC TGG TAC GAT TTT GCC TCA-BHQ1 | 28808–28831 | 147bp | [47] | ||
| NL63 (α-coronaV) | F—GTT CTG ATA AGG CAC CAT ATA GG | 26215–26237 | phosphoprotein | [46] | |
| R—TTT AGG AGG CAA ATC AAC ACG | 26357–26337 | JX504050 | [46] | ||
| P—FAM-CGC ATA CGC CAA CGC TCT TGA ACA-BHQ1 | 26326–26303 | 143bp | [47] | ||
| OC43 (β-coronaV) | F—CAT ACY CTG ACG GTC ACA ATA ATA | 28812–28835 | glycoprotein | [46] | |
| R—ACC TTA GCA ACA GTC ATA TAA GC | 28921–28899 | JN129835.1 | [46] | ||
| P—FAM-TGC CAA AGA ATA GCC ART ACC TAG T-BHQ1 | 28889–28865 | 110bp | [47], adapted | ||
| Tick-born-encephalitis virus | European and Far-Eastern subtypes | F—GGG CGG TTC TTG TTC TCC | 11054–11071 | 3’NCR | [48], adapted |
| R—ACW CAT CAC CTC CTT GTC AGA CT | 11121–11099 | U27495 | [48], adapted | ||
| P—FAM-TGA GCC ACC ATC ACC CAG ACA CA-BHQ1 | 11073–11095 | 68bp | [48], adapted | ||
| Parvovirus | B19 | F—CCC CGG GAC CAG TTC AGG | 2241–2258 | NS | [49] |
| R—CCC CTY ACA CCR TCC CAC AC | 2393–2374 | AB550331 | [49] | ||
| P—FAM-ATC ATY TGT CGG AAG CYC AGT TTC CTC CG-BHQ1 | 2262–2290 | 153bp | [49] | ||
| Enterovirus | / | F—GCC CCT GAA TGC GGC | 334–348 | Polyprotein | [50] |
| R—GAT TGT CAC CAT AAG CAG C | 481–464 | AJ295199 | [51], adapted | ||
| P—FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT-BHQ1 | 416–441 | 148pb | [51] | ||
| Cosavirus | / | F—TTG TAG YGA TGC TGT RTG TGT GTG | 735–758 | 5’-UTR | [52], adapted |
| R—CCA YTG TGT GGG TCC TTT CG | 827–808 | NC_012800 | [52], adapted | ||
| P—FAM-CYC ACA GGC CRR AAG CCC TGT C-BHQ1 | 783–807 | 93bp | [52], adapted | ||
| Bocavirus | hBoV2 | F—TCA GAC CAA GCG ACG AAG AC | 2531–2550 | Gene NP-1 | [53] |
| R—CTC TAG CAA GYC TAG TAG AAT GCC | 2675–2652 | NC_012042 | [53] | ||
| P—FAM-AAC CCA CAC CAT CCA GGA GCA TCT G-BHQ1 | 2646–2622 | 145bp | [53] | ||
| MNV | MNV-1 | F—CCG CCA TGG TCC TGG AGA ATG-3' | 3193–3213 | Polyprotein | [54] |
| R—GCA CAA CGG CAC TAC CAA TCT TG-3' | 3330–3308 | DQ285629 | [54] | ||
| P—FAM-CGT CGT CGC CTC GGT CCT TGT CAA-BHQ1 | 3227–3250 | 138bp | [54] | ||
| Mengovirus | MC0 | F—GCG GGT CCT GCC GAA AGT | 5’NTR | [55] | |
| R—GAA GTA ACA TAT AGA CAG ACG CAC AC | / | [55] | |||
| P—FAM-ATC ACA TTA CTG GCC GAA GC-MGB | 100bp | [55] |