Table 2. Ct value differences in WGS confirmed lineages with S-gene amplification.

Lineage Category	Total Samples with S-gene Present	Mean Ct Value Difference (S-gene Ct value–AVG Ct value (N: ORF1ab-genes))	Median Ct Value Difference (S-gene Ct value–AVG Ct value (N: ORF1ab-genes))	Mean Ct Value Difference (N gene Ct value–ORF1ab gene Ct value)	Median Ct Value Difference (N gene Ct value–ORF1ab gene Ct value)
Alpha	6,493	5.08	5.31	-0.23	-0.17
Delta	224,943	0.36	0.28	0.25	0.30
Omicron B.1.1.529/BA.1/BA.1.1	6,243	6.01	6.07	0.16	0.24
Omicron BA.2	3,726	0.49	0.42	0.05	0.16
Other	33,103	0.23	0.19	0.38	0.39