Table 1.
Details of primer sequences used for PCR-amplifications and sequencing of the AIV genes.
| Primer names | Gene targets/virus subtypes | Sequence 5′ to 3′ | References |
|---|---|---|---|
| Primers for PCR amplification of the full-length gene fragments | |||
| Ba-PB2-1F | PB2/all | TATTGGTCTCAGGGAGCGAAAGCAGGTC | Hoffmann et al. (2001) |
| Ba-PB2-2341R | ATATGGTCTCGTATTAGTAGAAACAAGGTCGTTT | ||
| Bm-PB-1F | PB1/all | TATTCGTCTCAGGGAGCGAAAGCAGGCA | |
| Bm-PB1-2341R | ATATCGTCTCGTATTAGTAGAAACAAGGCATTT | ||
| Bm-PA-1F | PA/all | TATTCGTCTCAGGGAGCGAAAGCAGGTAC | |
| Bm-PA-2233R | ATATCGTCTCGTATTAGTAGAAACAAGGTACTT | ||
| Bm-HA-1F | HA/all | TATTCGTCTCAGGGAGCAAAAGCAGGGG | |
| Bm-NS-890R | ATATCGTCTCGTATTAGTAGAAACAAGGGTGTTTT | ||
| Bm-NP-1F | NP/all | TATTCGTCTCAGGGAGCAAAAGCAGGGTA | |
| Bm-NP1565R | ATATCGTCTCGTATTAGTAGAAACAAGGGTATTTTT | ||
| Ba-NA-1F | NA/N1 and N2 | TATTGGTCTCAGGGAGCAAAAGCAGGAGT | |
| Ba-NA-1413R | ATATGGTCTCGTATTAGTAGAAACAAGGAGTTTTTT | ||
| Bm-N3-1F | NA/N3 | TATTCGTCTCAGGGAGCAAAAGCAGGTGC | |
| Bm-N3-1420R | ATATCGTCTCGTATTAGTAGAAACAAGGTGCTTTTT | ||
| Bm-M-1 | M/all | TATTCGTCTCAGGGAGCGAAAGCAGGTAG | |
| Bm-M-1027R | ATACGTCTCGTATTAGTAGAAACAAGGTAGTTTTT | ||
| Bm-NS1 | NS/all | TATTCGTCTCAGGGAGCGAAAGCAGGGTG | |
| Bm-NS-890R | ATATCGTCTCGTATTAGTAGAAACAAGGGTGTTTT | ||
| Primers for sequencing | |||
| H5N2_PB2_225F | PB2/H5N2 | TCCCTGAAAGGAATGAGCAAGGC | In-house |
| H5N2-PB2-1020R | GAGCTGATTCTTAGACCCATTG | ||
| H5N2_PB2_1370F | GGGGAATTGAACCCATCGACAA | ||
| H5N2-PB2-1480R | CTCTCTCAGTACTGGAATATTCATC | ||
| H5N2-PB2-1800R | TTGGCCTCGGGCAGCCTTAG | ||
| H5N2-PB1-580F | PB1/H5N2 | GGAGAGTAAGGGACAACATGACC | |
| H5N2-PB1-1850R | GTCTACCCTGGTAATCTTCATCC | ||
| N3-PB1-740R | PB1/H5N2 and 3 | CATTCCAGGTGTTGCAATTGCCC | |
| N3-PB1-1550R | ATCCCAGATACTCCGAAGCTGGG | ||
| H5N2-PA-475F | PA/H5N2 | ACCGGAGAGGAAATGGCCACC | |
| H5N2-PA-1800R | GGACTCAGCTTCAATCATGCTCTC | ||
| N3-PA-620R | PA/H5N2 and 3 | TCTCTTCGCCTCTCTCGGACTGA | |
| N3-PA-1280R | CCGTCAATTCGCATGCCTTGTTG | ||
| HA5-896F | HA/H5 | ACTCCAATGGGGGCGATAAAC | Poddar (2002) |
| FluN2-779F | NA/N2 | GGAAATCGTTCATATTAGCCCATTG | |
| N3_internalF | NA/H5N3 | AGATATGTGTTGCTTGGTCAAGT | In-house |
| H5N2-NP-320F | NP/H5N2 | CTGGAGGTCCAATTTACCGAAGG | |
Nt position for each primer designed in-house is relative to the gene target from H5N2 subtype (A/duck/Malaysia/F118/08/04) or H5N3 subtype (A/duck/Singapore/F119/3/97), and the accession numbers are described in Section 2. F denotes primer in the forward or positive strand, and R denotes primer in the reverse or negative strand of each gene.