Table 1.

List of the assays tested in the present study.

Protocol	FW (5′→3′)	Probe (5′→3′)	RV (5′→3′)	Position (M gene)	Size (bp)
Protocol 1	AGATGAGTCTTCTAACCGAGGTCG	TCAGGCCCCCTCAAAGCCGA	TGCAAAAACATCTTCAAGTCTCTG	25–124	99
Protocol 2	AGATGAGTCTTCTAACCGAGGTCG	TCAGGCCCCCTCAAAGCCGA	TGCAAARACATCTTCAAGTYTCTG	25–124	99
Protocol 3	AGATGAGYCTTCTAACCGAGGTCG	TCAGGCCCCCTCAAAGCCGA	TGCAAANACATCYTCAAGTCTCTG	25–124	99
Protocol 4	GGCCCCCTCAAAGCCGA	GTGCCCAG	CGTCTACGYTGCAGTCC	77–259	182
Commercial kit	Sequences not available. Supplier declares primers and probes target M and NP genes.

For each assay the sequences of primers and probe (5′→3′), the target regions and the amplicon size are reported. The degenerated bases introduced in the primers sequences are highlighted in bold.