Fig. 2

Alignment of ISAV segment 8 nucleotide sequences in the target region of the primer-probe set of the real time RT-qPCR TaqMan® assay for ISAV [36]. The ISAV sequences belonged to a 221 bp-long PCR product amplified from 50 samples in this study and 47 selected classical ISAV segment 8 sequences of different ISAV isolates in the GenBank database. The nucleotide sequences were aligned using CLUSTAL X with the default settings [58]. Green is forward primer and reverse primer sequences and red is probe sequence. The single nucleotide mutation in the probe sequence is in blue. The reverse primer sequence includes the 9-nucleotide overlap between the reverse primer sequence of the real time RT-qPCR TaqMan® assay [36] and that of the conventional RT-PCR protocol [39]