Table 2.
Primers and probes used at laboratory 2b
| Pathogen identified and primer/probe namea | Primer or probe | Sequence | Fragment length (bp) | Probe typec | Labeld |
|
|---|---|---|---|---|---|---|
| 5′ | 3′ | |||||
| PIV-1 | ||||||
| 609PIV1-TQ-YAK | Probe | CAAACGATGGCTGAAAAAGGGA | 164 | TQ | YAK | BHQ-1 |
| 1101PIV1s | Sense primer | AAAAACTTAGGGTTAAAGACAATCCA | ||||
| 1102PIV1as | Antisense primer | GCCAGATGTRTGTCYTTCCTGCTGGT | ||||
| PIV-2 | ||||||
| 621PIV2-TQ-TEXAS RED | Probe | AATCGCAAAAGCTGTTCAGTCAC | 113 | TQ | TXR | BHQ-2 |
| 231PIV2s | Sense primer | CCATTTACCTAAGTGATGGAA | ||||
| 232PIV2as | Antisense primer | CGTGGCATAATCTTCTTTTT | ||||
| 1065PIV2as | Antisense primer | TGTGGCATAATCTTCTTTCT | ||||
| PIV-3 | ||||||
| 566PIV3-TQ-FAM | Probe | ACCCAGTCATAACTTACTCAACAGCAAC | 154 | TQ | FAM | BHQ-1 |
| 1106PIV3s | Sense primer | CAGGAAGCATTGTRTCATCTGT | ||||
| 1107PIV3as | Antisense primer | ATAGTGTGTAATGCAGCTYGT | ||||
| PIV-4 | ||||||
| 675PIV4-TQ-CY5 | Probe | GTCTCAAAATTTGTTGATCAAGAYAATACAATT | 200 | TQ | Cy5 | BHQ-2 |
| 264PIV4 | Sense primer | CCTGGAGTCCCATCAAAAGT | ||||
| 1071PIV4as | Antisense primer | GCATCTATACGAACRCCTGCT | ||||
| INF A | ||||||
| 1815FLUA-TQ-FAM | Probe | CCTCGCTCACTGGGCACGGT | 119 | TQ | FAM | BHQ-1 |
| 1233FluAs | Sense primer | CATGGARTGGCTAAAGACAAG | ||||
| 1234FluAas | Antisense primer | TYTGGACAAAGCGTCTACG | ||||
| INF B | ||||||
| 681FLUB-TQ-TEXAS-RED | Probe | GCAAACACTGGGCTGCARCT | 145 | TQ | TXR | BHQ-2 |
| 220FluBs | Sense primer | GTCCATCAAGCTCCAGTTTT | ||||
| 221FluBas | Antisense primer | TCTTCTTACAGCTTGCTTGC | ||||
| RSV | ||||||
| 654RSV-TQ-HEX | Probe | CCATGTGAATTCCCTGCATCAAT | 155 | TQ | HEX | BHQ-1 |
| 674RSV-TQ-HEX | Probe | CCTGcGAATTCCCTGCcTCAAT | 155 | TQ | HEX | BHQ-1 |
| 1070RSVs | Sense primer | TTTCCACAATATTTAAGTGTtAA | ||||
| 412RSVs | Sense primer | TTTCCACAATATYTAAGTGTCAA | ||||
| 413RSVas | Antisense primer | TCATCWCCATACTTTTCTGTTA | ||||
| hMPV | ||||||
| 567MPV-TQ-YAK | Probe | GCATGYCAYTGGTGTGGGATATT | 170 | TQ | YAK | BHQ-1 |
| 342MPVs | Sense primer | CATGCCCACTATAAAAGGTCAG | ||||
| 343MPVas | Antisense primer | CACCCCAGTCTTTCTTGAAA | ||||
| 1068MPVs | Sense primer | TATGCCTACCATAAAAGGTCAA | ||||
| 1069MPVas | Antisense primer | CACCCCAGTCTTTCCTAAAG | ||||
| EAV | ||||||
| 615EAV-TQ-CY5 | Probe | CGCTGTCAGAACAACATTATTGCCCAC | 134 | TQ | Cy5 | BHQ-2 |
| 417EAVs | Sense primer | CATCTCTTGCTTTGCTCCTTAG | ||||
| 418EAVas | Antisense primer | AGCCGCACCTTCACATTG | ||||
| HRV | ||||||
| 606HRV-TQ-FAM | Probe | TCCTCCGGCCCCTGAATGYGGCTAA | 142 | TQ | FAM | BHQ-1 |
| 777HRV_1s | Sense primer | GACAGGGTGTGAAGAGCC | ||||
| 778HRV_2s | Sense primer | GACATGGTGTGAAGACCC | ||||
| 779HRV_3S | Sense primer | GACAAGGTGTGAAGAGCC | ||||
| 780HRV_4s | Sense primer | GACATGGTGTGAAGACTC | ||||
| 1039HRVs | Sense primer | GACATGGTGTGAAGATCT | ||||
| 1037HRVas | Antisense primer | ACACGGACACCCAAAGTAGT | ||||
| HCOV-NL63 | ||||||
| 599HCOV-NL63-TQ-TXR | Probe | CGCATACGCCAACGCTCTTGAACA | 143 | TQ | TXR | BHQ-2 |
| 750HCOV-NL63s | Sense primer | GTTCTGATAAGGCACCATATAGG | ||||
| 751HCOV-NL63as | Antisense primer | TTTAGGAGGCAAATCAACACG | ||||
| HCOV-229E | ||||||
| 598HCOV-229E-TQ-FAM | Probe | ATGAACCTGAACACCTGAAGCCAATCTATG | 137 | TQ | FAM | BHQ-1 |
| 741HCOV-229Es | Sense primer | CATACTATCAACCCATTCAACAAG | ||||
| 742HCOV-229Eas | Antisense primer | CACGGCAACTGTCATGTATT | ||||
| HCOV-OC43 | ||||||
| 587HCOV-43-TQ-YAK | Probe | TGCCCAAGAATAGCCAGTACCTAGT | 110 | TQ | YAK | BHQ1 |
| 484HCOV43s | Sense primer | CATACTCTGACGGTCACAATAATA | ||||
| 485HCOV43as | Antisense primer | ACCTTAGCAACAGTCATATAAGC | ||||
| HCOV-HKU1 | ||||||
| 677HCOV-HKU1-TQ-CY5 | Probe | TYCGCCTGGTACGATTTTGCCTCA | 147 | TQ | Cy5 | BHQ-2 |
| 864HCOV-HKU1s | Sense primer | TCCTACTAYTCAAGAAGCTATCC | ||||
| 865HCOV-HKU1as | Antisense primer | AATGAACGATTATTGGGTCCAC | ||||
| HADV | ||||||
| 692ADV-XS-FAM | Probe | AGCCCACCCTKCTTTAT | 139 | TQ | FAM | BHQ-1 |
| 658ADV4-TQ-YAK | Probe | GAGTCYACCCTTCTCTATGT | YAK | BHQ-1 | ||
| 372ADVs | Sense primer | CATGACTTTTGAGGTGGATC | ||||
| 346ADVas | Antisense primer | CCGGCCGAGAAGGGTGTGCGCAGGTA | ||||
| 423ADV4s | Sense primer | CATGAATTTCGAAGTCGACC | ||||
| 424ADV31s | Sense primer | TATGACATTTGAAGTTGACC | ||||
| M. pneumoniae | ||||||
| 612MYCPN-TQ-YAK | Probe | CAAAGCCACCCTGATCACCC | 151 | TQ | YAK | BHQ-1 |
| 224MYCPNs | Sense primer | ATTCCCGAACAAAATAATG | ||||
| 225MYCPNas | Antisense primer | GTTTGACAAAGTCCGTGAAG | ||||
| C. pneumoniae | ||||||
| 611CPN-TQ-FAM | Probe | GGGATCTTCGGACCTTTCGG | 154 | TQ | FAM | BHQ-1 |
| 214CPN16Ss | Sense primer | GCGGAAGGGTTAGTAGTACA | ||||
| 215CPN16Sas | Antisense primer | ATCGCATAAACTCTTCCTCA | ||||
| Legionella spp. | ||||||
| 539LEGSP-MB-FAM | Probe | CCGAGCGGTGAGTAACGCGTAGGAATATGGCTCGG | 212 | MB | FAM | Dabcyl |
| 156LegSPs | Sense primer | AGGCTAATCTTAAAGCGCC | ||||
| 157LegSPas | Antisense primer | CCTGGCTCAGATTGAACG | ||||
| L. pneumophila | ||||||
| 593LEGPN-TQ-YAK | Probe | GCATTGGTGCCGATTTGGGA | 124 | TQ | YAK | BHQ-1 |
| 269LGPNs | Sense primer | TGGTGACTGCAGCTGTTATG | ||||
| 270LGPNas | Antisense primer | CATTGCTTCCGGATTAACAT | ||||
a
PIV, parainfluenza virus; INF, influenza virus; RSV, respiratory syncytial virus; hMPV human metapneumovirus; EAV, equine arteritis virus; HRV, human rhinovirus;; HCOV, human coronavirus; HADV, human adenovirus.
b
YAK, Yakima Yellow; TXR, Texas Red; HEX, hexachlorofluorescein; R = (AG); Y = (CT); K = (GT); W = (AT).
c
MB, molecular beacon; TQ, TaqMan.
d
BHQ, black hole quencher.