Localization of primers and probes. Localization of primers and probes as mentioned in table 1 along the HA gene is depicted. Two target regions (P1, P2) were chosen. Primers and probes were selected with specificity for the HA of Egyptian HPAIV H5N1 viruses either of lineage 2.2.1p (proper) or 2.2.1v (variant). Triangles (2.2.1p) and squares (2.2.1v) distinguish nucleotide positions specific for either lineage. Labelling of hydrolysis probes was with FAM (F, 2.2.1v), HEX (H, 2.2.1p) or ROX (2.2.1p+v).