TABLE 1.
Primer and probe sequences
| Assay and gene target | Primer or probe | Amplicon size (bp) | Primer or probe sequence (5′-3′)b | nt positions or accession no.a |
|---|---|---|---|---|
| Inf A/H1 | FJ966082 | |||
| HA | H1SWS | 78 | CATTTGAAAGGTTTGAGATATTCCC | 380-404 |
| HA | H1SWAs | ATGCTGCCGTTACACCTTTGT | 457-437 | |
| HA | H1SWP | FAM-ACAAGTTCATGGCCCAATCATGACTCG-BBQ | 409-435 | |
| Inf A/M2c | CY038773 | |||
| MA | M_InfA_F | 95 | AAGACCAATCCTGTCACCTCTGA | 175-197 |
| MA | M_InfA_R | CAAAGCGTCTACGCTGCAGTCC | 269-248 | |
| MA | M_InfA_TM | FAM-TTTGTGTTCACGCTCACCGT-BBQ | 215-234 | |
| Sequencing | ||||
| HA | HAH1-58F | 1,619 | TTATGTATAGGTTATCATGCGAA | 58-80 |
| HA | HAH1-1657R | GACCCATTAGAGCACATCCA | 1676-1657 | |
| HA | HAH1-149F | 717 | TAGAAGACAAGCATAACGGGAAA | 149-171 |
| HA | HAH1-865R | CTGGTGTATCTGAAATGATAATA | 865-843 | |
| HA | S1910F | 828 | CATTTCAGATACACCAGTCCACGA | 849-872 |
| HA | HAH1-1657R | GACCCATTAGAGCACATCCA | 1676-1657 |
a
nt, nucleotide. Reference sequence accession numbers are for the GenBank/EMBL/DDBJ databases.
b
Hydrolysis probes were labeled with 6-carboxyfluorescein (FAM) at the 5′ end and a BlackBerry (BBQ) quencher at the 3′ end.
c
Primers and probes reported in reference 18.