Table 1.
Primers and probes used to identify respiratory viruses in clinical specimens
| Virus | Virus gene target | Oligonucleotide name | Oligonucleotide sequence | Reference |
|---|---|---|---|---|
| Influenza A | Matrix | FAM1 | 5′-CAG AGA CTT GAA GAT GTC TTT GC-3′ | 17 |
| FAM2 | 5′-GCT CTG TCC ATG TTA TTT GRA T-3′ | 17 | ||
| AH2 (probe) | 5′-TCC TGT CAC CTC TGA CTA AGG GGA TTT TG-3′ | 17 | ||
| Matrix | INFA-1a | 5′-GGA CTG CAG CGT AGA CGC TT-3′ | 21 | |
| INFA-2a | 5′-CAT YCT GTT GTA TAT GAG GCC CAT | 21 | ||
| INFA probea | 5′-FAM-CTC AGT TAT TCT GCT GGT GCA CTT GCC A-TAMRA | 21 | ||
| Influenza B | Matrix | B1 | 5′-GAA AAA TTA CAC TGT TGG TTC GGT G | 16 |
| B2B | 5′-AGC GTT CCT AGT TTT ACT TGC ATT GA | 16 | ||
| HYB365 | 5′-TTC TAG CTG AGA GAA AAA TGA GAA GAT GT | 16 | ||
| INFB1a | 5′-AAA TAC GGT GGA TTA AAT AAA AGC AA | 21 | ||
| INFB2a | 5′-CCA GCA ATA GCT CCG AAG AAA | 21 | ||
| INFB probea | 5′-FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC TAMRA | 21 | ||
| Parainfluenza virus type 1 | Matrix | PF526 | 5′-ATT TCT GGA GAT GTC CCG TAG GAG AAC | 19 |
| PR678 | 5′-CAC ATC CTT GAG TGA TTA AGT TTG ATG A | 19 | ||
| P640 (probe) | 5′-TAC CTT CAT TAT CAA TTG GTA AGT CAA | 19 | ||
| Parainfluenza virus type 2 | Matrix | P2 upstream | 5′-CAT GTA CTA TAC TGA TGG TGG | 18 |
| P2 downstream | 5′-GTT AGT AAC TTA AAT AGG GTA AC | 18 | ||
| P2 probe | 5′-AAT GGA ACA TGC AAC ATC ACC | 18 | ||
| Parainfluenza virus type 3 | Matrix | P3HN1 | 5′-CTC GAG GTT GTC AGG ATA TAG | 40 |
| P3HN2 | 5′-CTT TGG GAG TTG AAC ACA GTT | 40 | ||
| P3 (probe) | 5′-CAT CTG TAT TTA GGA GTG CTA G | 40 | ||
| HCoV OC43 | Nucleoprotein | CVP3 | 5′-IIA AAT TGC TII TCT TGT TCT GGC | 13, 41 |
| CVP4 | 5′-CCA AAA TTC TGA TTA GGG CCT CTC | 13, 41 | ||
| CVPP | 5′-AAG CAI AIT GCC AAA IAA GTC AGI CAG AAA ATT TT | 13, 41 | ||
| Nucleoprotein | O1.1a | 5′-CAT CAG GAG GGA ATG TTG TAC C | 42 | |
| O3.1a | 5′-TAC TGG TCT TTA GCA TGC GGT C | 42 | ||
| Probea | 5′-FAM-CAG CAG TTG ACG CTG GTT GCC ATC TAMRA | This study | ||
| HCoV 229E | Nucleoprotein | E7 | 5′-TCT GCC AAG AGT CTT GCT CG | 42 |
| E9 | 5′-AGC ATA GCA GCT GTT GAC GG | 42 | ||
| E8 (probe) | 5′-GGA AGT GCA GGT GTT GTG GC | 42 | ||
| E7a | 5′-TCT GCC AAG AGT CTT GCT CG | 42 | ||
| E9a | 5′-AGC ATA GCA GCT GTT GAC GG | 42 | ||
| Probea | 5′-VIC-TGG CCA CAA CAC CTG CAC TTC C-TAMRA | This study | ||
| Picornavirus | 5′ Non-coding region | R1 | 5′-ACG GAC ACC CAA AGT A | 13 |
| R2 | 5′-AGC ACT TCT GTT TCC C | 13 | ||
| R4 | 5′-TCC TCC GGC CCC TGA ATG | 13 | ||
| RSV A and B | Fusion | Forward primer | 5′-ATT GGC ATT AAG CCT ACA AAG CA-3′ | 20 |
| Rev primer | 5′-CTT GAC TTT GCT AAG AGC CAT CT-3′ | 20 | ||
| Probe A | 5′-TAG YCC AAA TGG AGC CWG AAA ATT ATA GTA-3′ | 20 | ||
| Probe B | 5′-CRG TTA AGA AGG AGC TAA TCC ATT TTA GTA-3′ | 20 | ||
| Adenovirus | Hexon | Hex1deg | 5′-GCC SCA RTG GKC WTA CAT GCA CAT C-3′ | 43 |
| Hex2deg | 5′-CAG CAC SCC ICG RAT GTC AAA-3′ | 43 | ||
| AD2 (probe) | 5′-GCC ACC GAG ACG TAC TTC AGC CTG-3′ | 44 | ||
| Human metapneumo-virus | Nucleoprotein | N3F | 5′GTC TCT TCA AGG GAT TCA CC-3′ | This study |
| N479R | 5′-ATT ATI GGT GTGTCT GGT GC-3′ | This study | ||
| N101F | 5′-CAG TGA CAC CYT CAT CAT TG-3′ | This study |
a
For real-time PCR assay.