Table 1. Primer pools, amplicons and probes for the URI assay.

Pool	Target	Forward	Reverse	Gene	Amplicon	A	B	C	Probes
1	B. pertussis	Bp_For_1	Bp_Rev_1	LysR TR	427	*			8
1	"	Bp_For_2	Bp_Rev_2	ABC T	476	*	*	*	18
1	"	Bp_For_3	Bp_Rev_3	ADH	769	*			14
1	"	Bp_For_4	Bp_Rev_4	LysR TR	569	*			21
1	"	Bp_For_5	Bp_Rev_5	tfdA	552	*			10
1	"	Bp_For_6	Bp_Rev_6	CAIB	534	*	*		15
1	M. pneumoniae	Mp_For_1	Mp_Rev_1	dnaK	564	*			29
1	"	Mp_For_2	Mp_Rev_2	pdhA	284	*	*	*	18
1	"	Mp_For_3	Mp_Rev_3	tuf	604	*	*		33
1	S. pyogenes	Sp_For_1	Sp_Rev_1	3-oxoacyl	510	*			19
1	"	Sp_For_2	Sp_Rev_2	23S rRNA	463	*	*		26
1	"	Sp_For_3	Sp_Rev_3	ABC T	421	*	*	*	24
1	C. pneumoniae	Cp_For_1	Cp_Rev_1	clp endop	491	*			23
1	"	Cp_For_2	Cp_Rev_2	HB-2	528	*	*	*	25
1	"	Cp_For_3	Cp_Rev_3	29 kDa lip	475	*			23
1	"	Cp_For_4	Cp_Rev_4	RNA pol S	526	*			22
1	"	Cp_For_5	Cp_Rev_5	R-Isomer	526	*	*		20
1	Adenovirus 4	Adv_For_1	Adv_Rev_1	gp 12	531	*	*		55
1	"	Adv_For_2	Adv_Rev_2	gp 12	606	*	*	*	**
2	Coronavirus 229E	CV229E_F_1	CV229E_R_1	Matrix	299	*	*		20
2	Coronavirus HK	CV HK_F_1	CV HK_R_1	HE	767	*	*		22
2	Coronavirus OC43	CVOC43_F_1	CVOC43_R_1	HE	528	*			28
2	"	CVOC43_F_2	CVOC43_R_2	N	507	*	*		33
2	Influenza A	InfA_For_1	InfA_Rev_1	Matrix	500	*	*		20
2	"	InfA_For_2	InfA_Rev_2	Matrix	339	*			13
2	Influenza B	InfB_For_1	InfB_Rev_1	NP	516	*	*		29
2	"	InfB_For_2	InfB_Rev_2	Matrix	506	*			28
2	PIV 1	PIV1_For_1	PIV1_Rev_1	Matrix	488	*	*		28
2	"	PIV1_For_2	PIV1_Rev_2	HN	532	*			23
2	PIV 2	PIV2_For_1	PIV2_Rev_1	Matrix	576	*			28
2	"	PIV2_For_2	PIV2_Rev_2	NP	592	*	*		34
2	PIV 3	PIV3_For_1	PIV3_Rev_1	Matrix	840	*	*		35
2	"	PIV3_For_2	PIV3_Rev_2	HA	517	*			24
2	RSV	RSV_For_1	RSV_Rev_1	Matrix 2	440	*			18
2	"	RSV_For_2	RSV_Rev_2	Matrix 2	496	*			22
2	"	RSV_For_3	RSV_Rev_3	Phos	412	*			23
2	"	RSV_For_4	RSV_Rev_4	Fusion	474	*	*		18
Cont.	Arabidopsis	RCA For	RCA Rev	RCA	508	*	*	*	32
Cont.	"	Cab For	Cab Rev	caB	501	*	*	*	23
Cont.	"	rbcL For	rbcL Rev	rcbL	515	*			12

^*Primer pair included in the respective sub-pool.

^**Probes used for both amplicon 1 and 2.