Table 1.
Oligonucleotide primers and probes used in the Flu‐6plx assay
| Assay | Oligonucleotide | Sequence (5′–3′) | Concentration (μm) | Target gene | References |
|---|---|---|---|---|---|
| Flu‐6plx | hMPV_383F | ACAAAGARGCAAGAAAAACAATGG | 0·4 | ||
| hMPV_451R | GGTGTGTCTGGTGCTGArGG | 0·4 | hMPV NP | Modified | |
| hMPV_424A | (FAM)– TCATCAGGyAATATyCCACAAAATCAGAG –(BHQ1) | 0·2 | from 17 | ||
| hMPV_424B | (FAM)– TCATCAGGTAACATCCCACAAAACCAGAG –(BHQ1) | 0·1 | |||
| RSV_F | GCAAATATGGAAACATACGTGAACA | 0·4 | |||
| RSV_R | GCACCCATATTGTWAGTGATGCA | 0·4 | RSV matrix | 18 | |
| RSV_LC610 | (LC610)– CTTCACGAAGGCTCCACATACACAGCWG –(BHQ2) | 0·1 | |||
| IfB_F | AAATACGGTGGATTAAATAAAAGCAA | 0·4 | |||
| IfB_R | CCAGCAATAGCTCCGAAGAAA | 0·4 | Influenza B HA | 18 | |
| IfB_cyan500 | (Cyan500)– CACCCATATTGGGCAATTTCCTATGGC –(BHQ1) | 0·1 | |||
| IfA_F | AAGACCAATCCTGTCACCTCTGA | 0·4 | |||
| IfA_R | CAAAGCGTCTACGCTGCAGTCC | 0·4 | Influenza A matrix | 18 | |
| IfA_VIC | (VIC)– TTTGTGTTCACGCTCACCGT –(MGB‐NFQ) | 0·1 | |||
| H1_F | ATTGCCGGTTTCATTGAAGG | 0·4 | |||
| H1_R | ATGGCATTYTGTGTGCTYTT | 0·4 | Influenza A HA | 19 | |
| Swine_H1_LC640 | (LC640)– ATGAGCAGGGGTCAGGATATGCAGCCGACC –(BHQ2) | 0·1 | |||
| Human_H1_LC670 | (LC670)– ATGAGCAAGGATCTGGCTATGCTGCAGATC –(BHQ2) | 0·1 | |||
| PIV‐6plx | PIV1 HN525 F | GATTTCTGGAGATGTCCCGTAGG | 0·4 | ||
| PIV1 HN722 R | TGACTTCCCTATATCTGCACATCC | 0·4 | PIV type 1 HA‐NM | ||
| PIV‐1 HN556 | (FAM)– TACTGAGCAACAACCC –(MGB‐NFQ) | 0·16 | |||
| PIV‐2 F | CCATTTACCTAAGTGATGGAA | 0·4 | |||
| PIV‐2 R | CGTGGCATAATCTTCTTTT | 0·4 | PIV type 2 HA‐NM | 7 | |
| PIV2 LC640 | (LC640)– AATCGCAAAAGCTGTTCAGTCAC –(BHQ2) | 0·16 | |||
| PIV3 NP300 F | CTTTCAGACAAGATGGAACAGTGC | 0·4 | |||
| PIV3 NP800 R | AGTTACCAAGCTCTGTTGAGACC | 0·4 | PIV type 3 NP | ||
| PIV3 NP766 | (LC610)– CCAATCTGATCCACTGTGTCACCGCTCA –(BHQ2) | 0·16 | |||
| PIV4 NP271 F | CAGGCCACATCAATGCAGAATC | 0·4 | |||
| PIV4 NP407 R | ATGTCATCCCAGCCAGATCTTG | 0·4 | PIV type 4 NP | ||
| PIV4 NP298 | (LC670)– ATGATTGCTGCCAGAGCCCCAGATGC –(BHQ2) | 0·16 | |||
| hRV F | TGG ACA GGG TGT GAA GAG C | 0·4 | |||
| hRV R | CAA AGT AGT CGG TCC CAT CC | 0·4 | Rhinovirus 5′ UTR | 7 | |
| hRV HEX | (VIC)– TCC TCC GGC CCC TGA ATG –(BHQ1) | 0·16 | |||
| MS2 F1 | TGG CAC TAC CCC TCT CCG TAT TCA CG | 0·2 | |||
| MS2 R1 | GTA CGG GCG ACC CCA CGA TGA C | 0·2 | MS2 phage | 20 | |
| MS2 Cyan500 | (Cyan500)– CACATCGATAGATCAAGGTGCCTACAAGC–(BHQ1) | 0·08 |
C denotes position of pdC nucleic acid bases. PIV; parainfluenza virus, NP; nucleoprotein, HA; haemagglutinin, NM; neuraminidase, UTR; untranslated region.
All oligonucleotides were purchased from Metabion Ltd, Martinsried, Germany, except MGB probes that were obtained from Applied Biosystems, Warrington, UK.