TABLE 1.
Primers and probes for cycling probe real-time PCR method
| Subtype | Primer or probe | Sequence (5′-3′) | Locationa |
|---|---|---|---|
| Seasonal influenza A (H1N1) virus | sH1N1-His275Tyr forward primer | 5′-CAAGATCGAAAAGGGGAAG-3′ | 768-786 |
| sH1N1-His275Tyr reverse primer | 5′-GACACCCAAGGTCGATTTG-3′ | 896-914 | |
| sH1N1-His275b | 5′-(Eclipsec)-[ATG]dAAAATTGGGTG-(FAMe)-3′ | 812-825 | |
| sH1N1-Tyr275b | 5′-(Eclipse)-[ATA]AAAATTGGGTG-(ROXe)-3′ | 812-825 | |
| Influenza A pandemic (H1N1) 2009 | H1N1pdm-His275Tyr forward primer | 5′-TGGACAGGCCTCATACAAGA-3′ | 744-763 |
| H1N1pdm-His275Tyr reverse primer | 5′-GCCAGTTATCCCTGCACACA-3′ | 870-889 | |
| H1N1pdm-His275b | 5′-(Eclipse)-CCTAATTAT[CAC]T-(FAM)-3′ | 814-826 | |
| H1N1pdm-Tyr275b | 5′-(Eclipse)-AT[TAC]TATGAGGA-(ROX)-3′ | 821-833 |
a
Location of primers and probes in the NA-coding region (total, 1,413 bp), segment 6, of influenza A (H1N1) virus. Note that both cycling probes for seasonal H1N1 were designed as reverse complements.
b
Fluorescent dye and quencher-labeled DNA/RNA chimeric probe.
c
Quenching molecule.
d
Nucleotides inside brackets indicate the codon relevant to sequences for oseltamivir sensitivity (His) and resistance (Tyr). Boldface and italicized letters indicate the nucleotide replaced by RNA.
e
Fluorescent molecules.