Table 1.

RT-qPCR Ct value results obtained from viral samples extracted from NS at different time points and from the lung, BALF, and NT.

Group	Pig ID	Nasal Swab						Euthanized Day		Tissue Samples
		1 dpi	2 dpi	3 dpi	5 dpi	7 dpi	10 dpi		BALF	LUNG	NT
Vaccinated Group	1	35.8	38.7	†	†	†	†	2 dpi	30.2	25.7 *	35.2
	2	Neg.	39.4	†	†	†	†		30.4	23.3 *	Neg.
	3	Neg.	37	†	†	†	†		33,9	Neg.	Neg.
	4	Neg.	Neg.	34.14 *	Neg.	†	†	5 dpi	36.7	35.1	Neg.
	5	Neg.	Neg.	33.8	Neg.	†	†		35.4	32.31 *	Neg.
	6	Neg.	Neg.	37	36.5	†	†		Neg.	Neg.	Neg.
	7	38.4	30.7	34	Neg.	Neg.	Neg.	10 dpi	Neg.	Neg.	Neg.
	8	Neg.	35.72 *	33.2	34.11 *	Neg.	Neg.		Neg.	Neg.	Neg.
Nonvaccinated Group	9	34.8	31.3	†	†	†	†	2 dpi	28.4	21.4	28.8
	10	36.1	34.79 *	†	†	†	†		22.8	24.9	Neg.
	11	Neg.	33.42 *	†	†	†	†		29	21.8	Neg.
	12	30.1	28.9	32.8	33.8	†	†	5 dpi	29.8	26.3	39.2
	13	26.9	28	29.3	Neg.	†	†		29.7	30.4	Neg.
	14	32.9	29.9	32.8	Neg.	†	†		28.6	30.2	Neg.
	15	39.67	36.7	35.25	35.28	33.18	33.72	10 dpi	Neg.	Neg.	Neg.

Neg.: negative; highlighted in grey: sequenced samples; *: sequenced samples with low coverage; bold: negative whole genome influenza amplification; †: euthanized animal. Cells shaded in blue and green indicate vaccinated and nonvaccinated animals, respectively.