Table 1.
Primer and probe oligonucleotides used for RT-qPCR
| Primer or probe | Target genotype(s) | Sequence (5′→3′)a | Polarityb | Location |
|---|---|---|---|---|
| Primers | ||||
| AiV-AB-F | A and B | GTCTCCACHGACACYAAYTGGAC | + | 1882–1904d |
| AiV-AB-R | A and B | GTTGTACATRGCAGCCCAGG | − | 1970–1989d |
| Probesc | ||||
| AiV-AB-TPc | A and B | FAM-TTYTCCTTYGTGCGTGC-MGB-NFQ | + | 1939–1955d |
| AiV-A-TPc | A | FAM-ACCTCCAGTCCTACYGCA-MGB-NFQ | + | 1909–1926d |
| AiV-B-TPc | B | VIC-TCYACAAAYTCTCCCACCGC-MGB-NFQ | + | 1892–1911e |
a
Mixed bases in degenerate primers and probes are as follows: H represents A, C, or T, R represents A or G, and Y represents C or T.
b
+, sense; −, antisense.
c
Probes are labeled with 6-carboxyfluorescein (FAM) or 6-carboxyrhodamine (VIC) reporter dye at the 5′ end and with minor groove binder (MGB) and nonfluorescent quencher (NFQ) at the 3′ end of the oligonucleotide.
d
Corresponding nucleotide position of the prototype Aichi virus A846/88 strain complete genome (accession no. AB040749).
e
Corresponding nucleotide position of Goiania/GO/03/01/Brazil, a genotype B strain (accession no. DQ028632).