Table I.

Primer Sequences Used in the 5 Multiplex PCR/RT‐PCR

Virus	Assay	Primer designation	Primer sequences (5′–3′)	Expected amplicon size (bp)	Refs.
Multiplex 1
IAV	RT‐PCR	A1 (For)	CAG AGA CTT GAA GAT GTC TTT GCT (A)G	212	Adapted from Bellau‐Pujol et al. 2005
		A2 (Rev)	GCT CTG TCC ATG TTA TTT GG(A) ATC		Adapted from Bellau‐Pujol et al. 2005
	Hemi nested	MIA3 (For)	CTC TGA CTA AGG GGA TTT TG	130	Bellau‐Pujol et al. 2005
		A2 (Rev)	GCT CTG TCC ATG TTA TTT GG(A) ATC		Bellau‐Pujol et al. 2005
IBV	RT‐PCR	B1 (For)	GAA AAA TTA CAC TGT TGG TTC GGT G	365	Adapted from Bellau‐Pujol et al. 2005
		B2B (Rev)	AGC GTT CCT AGT TTT ACT TGC ATT GA		Adapted from Bellau‐Pujol et al. 2005
	Hemi nested	MIB3 (Rev)	CAT GAA ARC TCA CAC ATC T	260	Bellau‐Pujol et al. 2005
		B1 (For)	GAA AAA TTA CAC TGT TGG TTC GGT G		Bellau‐Pujol et al. 2005
RSV	RT‐PCR	Cane P1 (For)	GGA ACA AGT TGT TGA GGT TTA TGA ATA TGC	278	Adapted from Bellau‐Pujol et al. 2005
		Cane P2 (Rev)	CTG CTG TCA AGT CTA GTA CAC TGT AGT		Adapted from Bellau‐Pujol et al. 2005
	Hemi nested	VRSi (Rev)	GGT GTA CCT CTG TAC TCT C	180	Bellau‐Pujol et al. 2005
		Cane P1 (For)	GGA ACA AGT TGT TGA GGT TTA TGA ATA TGC		Bellau‐Pujol et al. 2005
HMPV	RT‐PCR	MPV M1a (For)	GGA GTC CTA CCT AGT AGA C	537	Freymuth F [unpublished work]
		MPV M2 (Rev)	GCA GCT TCA ACA GTA GCT G		Bellau‐Pujol et al. 2005
	Hemi nested	MPV M3 (For)	AGG CCA ACA CAC CAC CAG	410	Bellau‐Pujol et al. 2005
		MPV M2 (Rev)	GCA GCT TCA ACA GTA GCT G		Bellau‐Pujol et al. 2005
Multiplex 2
PIV‐1	RT‐PCR	PiS1+ (For)	CCG GTA ATT TCT CAT ACC TAT G	317	Echevarria et al. 1998
		PiS1‐(Rev)	CTT TGG AGC GGA GTT GTT AAG		Echevarria et al. 1998
	Hemi nested	piS1i (For)	AGC TGC AGG AAC AAG GGG	261	Bellau‐Pujol et al. 2005
		PiS1‐(Rev)	CTT TGG AGC GGA GTT GTT AAG		Bellau‐Pujol et al. 2005
PIV‐2	RT‐PCR	PiP2+ (For)	AAC AAT CTG CTG CAG CAT TT	507	Echevarria et al. 1998
		PiP2‐ (Rev)	ATG TCA GAC AAT GGG CAA AT		Echevarria et al. 1998
	Hemi nested	PARA2i (For)	CTA GCT GAA CTG AGA CTT G	340	Bellau‐Pujol et al. 2005
		PiP2‐ (Rev)	ATG TCA GAC AAT GGG CAA AT		Bellau‐Pujol et al. 2005
PIV‐3	RT‐PCR	P3‐1 (For)	CTC GAG GTT GTC AGG ATA TAG	189	Karron et al. 1994
		P3‐2 (Rev)	CTT TGG GAG TTG AAC ACA GTT		Karron et al. 1994
	Hemi nested	PARA3i (Rev)	GCT AGA GAA CAT GAC TTC C	145	Bellau‐Pujol et al. 2005
		P3‐1 (For)	CTC GAG GTT GTC AGG ATA TAG		Bellau‐Pujol et al. 2005
PIV‐4	RT‐PCR	Pi4S+ (For)	CTG AAC GGT TGC ATT CAG GT	451	Aguilar et al. [2000]
		Pi4S‐ (Rev)	TTG CAT CAA GAA TGA GTC CT		Aguilar et al. [2000]
	Hemi nested	Pi4i (Rev)	GTC TGA TCC CAT AAG CAG C	390	Bellau‐Pujol et al. 2005
		Pi4S+ (For)	CTG AAC GGT TGC ATT CAG GT		Bellau‐Pujol et al. 2005
Multiplex 3
ICV	RT‐PCR	CHAA (For)	ACA CTT CCA ACC CAA TTT GG	485	Zhang and Evans 1991
		CHAD (Rev)	CCT GAC AGC AAC TCC C TC AT		Zhang and Evans 1991
	Hemi nested	MICi (For)	GAG GAT GTG GCA ACT ACT	391	Bellau‐Pujol et al. 2005
		CHAD (Rev)	CCT GAC AGC AAC TCC C TC AT		Bellau‐Pujol et al. 2005
HRhV	RT‐PCR	SRHI 1 (For)	GCA TCI GGY ARY TTC CAC CAC CAN CC	549	Savolainen et al. 2002
		SRHI 2 (Rev)	GGG ACC AAC TAC TTT GGG TGT CCG TGT		Savolainen et al. 2002
	Hemi nested	NESTRHI1 (Rev)	ATG GGN GCW CAN GTN TCH ANH CA	450	Bellau‐Pujol et al. 2005
		SRHI 1 (For)	GCA TCI GGY ARY TTC CAC CAC CAN CC		Bellau‐Pujol et al. 2005
SARS‐CoV	RT‐PCR	SARS‐Bin out‐AS (For)	CAT AAC CAG TCG GTA CAG CTA	195	Drosten et al. 2003
		SARS‐Bin out‐S2 (Rev)	RTG AAT TAC CAA GTC AAT GGT		Drosten et al. 2003
	Nested	SARS‐Bni/ in‐AS (For)	CTG TAG AAA ATC CTA GCT GGA	110	Drosten et al. 2003
		SARS‐Bni/in‐S (Rev)	GAA GCT ATT CGT CAC GTT CG		Drosten et al. 2003
Multiplex 4
HCoV‐OC43	RT‐PCR	MF 1 (For)	GGC TTA TGT GGC CCC TTA CT	334	Vabret et al. 2001
		MF3 (Rev)	GGC AAA TCT GCC CAA GAA TA		Vabret et al. 2001
	Hemi nested	MF2i (Rev)	CTC CAA AAA CTT CCA GTT C	170	Bellau‐Pujol et al. 2005
		MF 1 (For)	GGC TTA TGT GGC CCC TTA CT		Bellau‐Pujol et al. 2005
HCoV‐229E	RT‐PCR	MD1 (For)	TGG CCC CAT TAA AAA TGT GT	574	Vabret et al. 2001
		MD3 (Rev)	CCT GAA CAC CTG AAG CCA AT		Vabret et al. 2001
	Hemi nested	MD2i (Rev)	CCG TAT CAA CAC TCG TTA TGT GG	230	Bellau‐Pujol et al. 2005
		MD1 (For)	TGG CCC CAT TAA AAA TGT GT		Bellau‐Pujol et al. 2005
HCoV‐HKU1	RT‐PCR	HKU‐N‐sens3 (For)	ATC TGA GCG AAA TTA CCA AAC	443	Woo et al. 2005
		HKU1 antisense (Rev)	CGG AAA CCT AGT AGG GAT AGC TT		Woo et al. 2005
HCoV‐NL63	RT‐PCR	NL63 sens (For)	GAT AAC CAG TGG AAG TCA CCT AGT TC	255	Vabret et al. 2005
		NL63 antisense (Rev)	ATT AGG AAT CAA TTC AGC AAG CTG TG		Vabret et al. 2005
Multiplex 5
AdV	PCR	ADHEX1F (For)	CAA CAC CTA YGA STA CAT GAA	270	Avellon et al. 2001
		ADHEX2R (Rev)	ACA TCC TTB CKG AAG TTC CA		Palacious et al. [2003]
HBoV	PCR	188F (For)	GAS CTC TGT AAG TAC TAT TAC	354	Allander et al. 2005
		542R (Rev)	CTC TGT GTT GAC TGA ATA CAG		Allander et al. 2005