TABLE 1.
Oligonucleotide primers and probes designed for typing and subtyping of influenza viruses
| Influenza virus type/subtype | Primer or probea | Sequence | Coordinatesb |
|---|---|---|---|
| A | AM-151 | 5′ CATGGAATGGCTAAAGACAAGACC | 151–174 |
| AM-397 | 5′ AAGTGCACCAGCAGAATAACTGAG | 374–397 | |
| Probe AM-245 | 5′ CTGCAGCGTAGACGCTTTGTCCAAAATG | 245–272 | |
| A/H1 | HA1-583 | 5′ GGTGTTCATCACCCGTCTAACAT | 583–605 |
| HA1-895 | 5′ GTGTTTGACACTTCGCGTCACAT | 873–895 | |
| Probe HA1-783 | 5′ TGCCTCAAATATTATTGTGTCCCCGGGT | 756–783 | |
| A/H3 | HA3-115 | 5′ GCTACTGAGCTGGTTCAGAGTTC | 115–137 |
| HA3-375 | 5′ GAAGTCTTCATTGATAAACTCCAG | 352–375 | |
| Probe HA3-208 | 5′ CTATTGGGAGACCCTCATTGTGATGG | 208–233 | |
| A/N1 | NA1-1078 | 5′ ATGGTAATGGTGTTTGGATAGGAAG | 1078–1102 |
| NA1-1352 | 5′ AATGCTGCTCCCACTAGTCCAG | 1331–1352 | |
| Probe NA1-1138 | 5′ TGATTTGGGATCCTAATGGATGGACAG | 1138–1164 | |
| A/N2 | NA2-560 | 5′ AAGCATGGCTGCATGTTTGTG | 560–580 |
| NA2-858 | 5′ ACCAGGATATCGAGGATAACAGGA | 835–858 | |
| Probe NA2-821 | 5′ TGCTGAGCACTTCCTGACAATGGGCT | 796–821 | |
| B | BHA-188 | 5′ AGACCAGAGGGAAACTATGCCC | 188–209 |
| BHA-347 | 5′ CTGTCGTGCATTATAGGAAAGCAC | 324–347 | |
| Probe BHA-273 | 5′ ACCTTCGGCAAAAGCTTCAATACTCCA | 273–299 |
AM, M gene of influenza A viruses; HA1 and HA3, HA gene of influenza A viruses of subtypes H1 and H3, respectively; NA1 and NA2, NA gene of influenza A viruses of subtypes N1 and N2, respectively; BHA, HA gene of influenza B viruses.
Primer and probe positions for type A-specific primers correspond to the M gene of A/Bangkok/1/79 (GenBank accession no. Z26862), for subtyping of H1N1 viruses to A/USSR/90/77 (GenBank accession no. K01330 [HA gene] and K02018 [NA gene]), for subtyping of H3N2 viruses to A/Beijing/32/92 (GenBank accession no. Z46392 [HA gene] and U42770 [NA gene]) and for detection of influenza B viruses to the HA gene of B/Kobe/1/94 (D38646).