Table 1.
Primer and Probe Sequences Used in this Study
| Primers | Sequence | Gene target | Forward or reverse orientation | 5′ Position |
|---|---|---|---|---|
| Universal influenza A* | 5′-AGATGAGTCTTCTAACCGAGGTCG-3′ | Matrix | Forward | 25 |
| 5′-TGCAAAAACATCTTCAAGTCTCTG-3′ | Reverse | 124 | ||
| 5′-FAM-TCAGGCCCCCTCAAAGCCGA-TAMRA-3′ | Forward | 64 | ||
| Influenza A (H1 subtype)† | 5′-TGCAAAGACACTTTCCAGTCTCTG-3′§ | Hemagglutinin (H1) | Reverse | 124 |
| 5′-AACATGTTACCCAGGGCATTTCGC-3′ | Forward | 347 | ||
| 5′-GTGGTTGGGCCATGAGCTTTCTTT-3′ | Reverse | 461 | ||
| 5′-HEX-GAGGAACTGAGGGAGCAATTGAGTTCAG-TAMRA-3′ | Forward | 378 | ||
| Influenza A (H3 subtype)† | 5′-ACCCTCAGTGTGATGGCTTCCAAA-3′ | Hemagglutinin (H3) | Forward | 266 |
| 5′-TAAGGGAGGCATAATCCGGCACAT-3′ | Reverse | 373 | ||
| 5′-FAM-ACGCAGCAAAGCCTACAGCAACTGTT-TAMRA-3′ | Forward | 315 | ||
| Influenza B‡ | 5′-AAATACGGTGGATTAAACAAAAGCAA-3′ | Hemagglutinin (Influenza B) | Forward | 970 |
| 5′-CTCCGAAGAAACCCCTTTCC−3′ | Reverse | 1110 | ||
| 5′-FAM-CACCCATATTGGGCAATTTCCTATGGC-TAMRA-3′ | Forward | 1004 | ||
| Influenza A (H1N1/2009) | 5′-GGCACGGTCAGCACTCATT-3′ | Nucleoprotein (Influenza A) | Forward | 777 |
| 5′-CTTTCAAAGTCATGCCCACTT-3′ | Reverse | 858 | ||
| 5′-FAM-CTGCCTGCCTGCTTGTGTGTATGGGCT-BHQ1–3′ | Forward | 822 | ||
| 5′-AGTTCAAGTCGGAAATAGCAAT-3′ | Hemagglutinin (Influenza A) | Forward | 677 | |
| 5′-ATACCAGATCCAGCATTTCTTTC-3′ | Reverse | 823 | ||
| 5′-HEX-CCAAAGTGAGGGATCAAGAAGGGAGAAT-BHQ1–3′ | Forward | 704 |
The underlined nucleotides represent the modifications made.
*
From Spackman et al.16
†
From Krafft et al.17
‡
From Centre for Health Protection (Hong Kong) [CHP molecular diagnostic protocols for the detection of human swine influenza virus type A (subtype H1), http://www01.chp.gov.hk/files/pdf/CHP_Protocols_for_the_Detection_of_Human_Swine_Influenza.pdf, last accessed May 26, 2009].
§
Modified from Spackman et al.16