Table 1.
Primer/probe sequences for HRSV real-time RT-PCR assays.
| HRSV rRT-PCR Assay | Gene target | Genome location a | Name | Primer or Probe | Sequence (5’-3’) |
|---|---|---|---|---|---|
| Duplex | Nucleocapsid | 1141-1162 | HRSV-F | Forward primer | ATGGCTCTTAGCAAAGTCAAGT |
| 1239-1262 | HRSV-R | Reverse primer | TGCACATCATAATTRGGAGTRTCA | ||
| 1171-1204 | HRSV A-Pb | Probe | ACACTCAACAAAGA"T"CAACTTCTRTCATCCAGCA | ||
| 1171-1204 | HRSV B-Pc | Probe | ACATTAAATAAGGA"T"CAGCTGCTGTCATCCAGCA | ||
| Pan (Fry et al., 2010) |
Matrix | 3255-3278 | HRSV-pan-F | Forward primer | GGCAAATATGGAAACATACGTGAA |
| 3311-3338 | HRSV-pan-R | Reverse primer | TCTTTTTCTAGGACATTGTAYTGAACAG | ||
| 3281-3307 | HRSV-pan-Pd | Probe | CTGTGTATGTGGAGCCTTCGTGAAGCT | ||
a
Primer nucleotide numbering was based on human RSV A2 strain. Probe nucleotide numbering was based on human RSV A2 and B1 strains (GenBank accession numbers KT992094 and AF013254, respectively).
b
Probe labeled with 5′ reporter molecule 6-carboxyfluorescein (FAM) and quenched internally at a modified “T” residue with Black Hole Quencher (BHQ) 1. A terminal 3′ phosphate is added to prevent probe extension by Taq polymerase.
c
Probe labeled with 5′ CAL Fluor Red 610 and quenched internally at a modified “T” residue with BHQ2. A terminal 3′ phosphate is added as above.
d
Probe labeled with 5′-FAM and 3′-BHQ1.