FIG 2.

Nucleotide sequence alignments between the M genes of the A(H1N1)pdm09 and A(H3N2) viruses and the primer and probe sequences of the three real-time RT-PCR assays. The M gene sequence of the A/New Caledonia/20/1999 strain was used as a reference, and the identical nucleotide bases of the other viruses and the primer/probe sequences are indicated by dashed lines. Different nucleotide bases, compared to the reference, are directly indicated. Positions that contain modified nucleotide bases in the primer-probe sequences of the At assay established in this study, including positions 153, 154, 163, 189, 225, 228, and 238, are indicated by gray shading. Reference viruses of either A(H1N1)pdm09 or A(H3N2) subtypes included in the alignments are shown in bold along with their sequence accession numbers. The evolutionary clades (based on the HA sequences) of the viruses are also shown in parentheses in the nomenclature.