Table 1.

Viruses identified in the viral metagenomic analysis. The table displays the viruses identified in each of the 16 pigs—eight specific pathogen-free pigs (S1 to S8) and eight conventionally reared pigs from a herd with respiratory problems (R1 to R8). Green means that the pig was positive for the specific virus, and the number indicates how many individual reads mapped to each virus; the viruses with less than 10 reads per sample are marked with a lighter green. * Posavirus 1 has not been assigned to a viral family but is placed within the Picornavirales order.

		S1	S2	S3	S4	S5	S6	S7	S8	R1	R2	R3	R4	R5	R6	R7	R8
Adenoviridae	Porcine mastadenovirus A	24	8	66	50	112	4	945	245	2		124	13	14	98	69	38
	Porcine mastadenovirus B	376			2147			6619	1361	14666	7		3615	1191		230	9584
	Other mastadenovirus	609		24,010	3167		3	6561	1073	19478	5		7901	2255		206	8138
Herpesviridae	Suid herpesvirus 2			4	16		4							50			752
	Porcine lymphotrophic herpesvirus 1														30
Parvoviridae	Porcine bocavirus 1		4	2	2		2	88	2			27	4		31	1	4
	Porcine bocavirus 3				1							1					3
	Porcine parvovirus 7			1			2						14131	14
	Adeno-associated virus											2		4	2	16
	Uncharacterised parvovirus				20							3	3	1	1
Circoviridae	Porcine circovirus 2								1								1
	Unclassified circovirus																2
Anelloviridae	Torque teno sus virus 1		4	1	106			8	16								5
	Torque teno sus virus 2								1
Picornaviridae	Pasivirus A	4	30	29	31	8	30	46		34		4	1	16	125	5	8
	Teschovirus				1	8				6			2	67	5939	3385	85
	Porcine sapelovirus A											31	56
Unassigned *	Posavirus 1	1			2					17					2		3
Caliciviridae	Sapovirus											1
Astroviridae	Astrovirus			2		1	1	1		1					1	1
Retroviridae	Porcine endogenous retrovirus		80	27	47	87	120	50	80	102	128	93	59	64	88	173	133