Table 1

Nucleotide sequences of primers and probes used for real-time TaqMan PCRa

AssayForward primer (5′ to 3′)Reverse primer (5′ to 3′)TaqMan probe (5′ to 3′)Gene target
AdvGCC ACG GTG GGG TTT CTA AAC TTGCC CCA GTG GTC TTA CAT GCA CAT C(FAM)-TGC ACC AGA CCC GGG CTC AGG TAC TCC GA-(TAMRA)Hexon
RSV AAGA TCA ACT TCT GTC ATC CAG CAATTC TGC ACA TCA TAA TTA GGA GTA TCA AT(FAM)-CAC CAT CCA ACG GAG CAC AGG AGA T-(TAMRA)N
RSV BAAG ATG CAA ATC ATA AAT TCA CAG GATGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG(VIC)-TTC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T-(TAMRA)N
IV ACAT GGA RTG GCT AAA GAC AAG ACCAGG GCA TTT TGG ACA AAK CGT CTA(FAM)-TGC AGT CCT CGC TCA CTG GGC ACG-(TAMRA)Matrix
IV A H1ACT ACT GGA CTC TGC TKG AAAAG CCT CTA CTC AGT GCG AA(FAM)-TTG AGG CAA ATG GAA ATC TAA TAG C-(TAMRA)HA
IV A H3TGC TAC TGA GCT GGT TCA GAG TAGG GTA ACA GTT GCT GTR GGC(FAM)-AGA T+GC +TC+T A+TT +GG+G AGA CC-(BHQ-1)HA
IV A 2009 H1N1TAG AGC CGG GAG ACA AAACGT GGA CTG GTG TAT CTG AA(FAM)-TCT AGT GGT ACC GAG ATA TGC ATT CGC-(TAMRA)HA
IV BTCC TCA ACT CAC TCT TCG AGC GCGG TGC TCT TGA CCA AAT TGG(VIC)-CCA ATT CGA GCA GCT GAA ACT GCG GTG-(TAMRA)NSP
PIV type 1ATT GGG CGC CTC ACA AAGCTC TCG GAC ATT TGT TGA ACC A(FAM)-CCT GTC ACG ACC AGG AAA CCC AGA CT-(TAMRA)HN
PIV type 2AGT CAT ATC TCT TCC GAA CAC AAC AGAGA TGA TAG ATC CCG CTT CCA A(FAM)-CAA TGG GCC ACA ATC AAT CCT GCA-(TAMRA)HN
PIV type 3CAG ACA AAT CCA AAT YCG AGA TGYGT YTC CAG CTC ATT ACC AGC AT(FAM)-AAT ACT GGA AGC AYA CCA ATC ACG GGA A-(TAMRA)HN
MPVCAT ATA AGC ATG CTA TAT TAA AAG AGT CTCCCT ATT TCT GCA GCA TAT TTG TAA TCA G(FAM)-TGY AAT GAT GAG GGT GTC ACT GCG GTT G-(TAMRA)NP
RhVCY+A GCC +TGC GTG GCGAA ACA CGG ACA CCC AAA GTA(FAM)-TCC TCC GGC CCC TGA ATG YGG C-(TAMRA)5′ NCR
BocavirusTGC AGA CAA CGC YTA GTT GTT TCTG TCC CGC CCA AGA TAC A(FAM)-CCA GGA TTG GGT GGA ACC TGC AAA-(TAMRA)NS-1
AGA GGC TCG GGC TCA TAT CACAC TTG GTC TGA GGT CTT CGA A(FAM)-AGG AAC ACC CAA TCA RCC ACC TAT CGT CT-(TAMRA)NP-1
B. pertussisCCC ATA AGC ATG CCC GAT TGA CCGC ACA GTC GGC GCG GTG AC(JOE)-TGC CTG AAG CGG CCC GCG C-(BHQ-1)IS481
M. pneumoniaeCCA ACC AAA CAA CAA CGT TCAACC TTG ACT GGA GGC CGT TA(JOE)-TCA ACT CGA ATA ACG GTG ACT TCT TAC CAC TG-(BHQ-1)P1 AP
Internal controlGCT GTC ATC TCT TGT GGG CTG TAAA CTC ATG GGA GCT GCT GGT T(FAM)-CCT GTC ATG CCC ACA CAA ATC TCT CC-(BHQ-1)Albumin
  • a Abbreviations: Adv, adenovirus; RSV, respiratory syncytial virus; IV, influenza virus; PIV, parainfluenza virus; MPV, metapneumovirus; RhV, rhinovirus; FAM, 6-carboxyfluorescein; VIC, proprietary formulation, Applied Biosystems; JOE, 6-carboxy-4′,5′-dichloro-2′,7′dimethoxyfluorescein; TAMRA, 6-carboxytetramethylrhodamine; BHQ-1, black hole quencher 1; N, nucleocapsid; HA, hemagglutinin; NSP, nonstructural protein; HN, hemagglutinin-neuraminidase; NP, nucleoprotein; NCR, noncoding region; NS, nonstructural; IS, insertion sequence; AP, adhesion protein. International Union of Biochemistry base codes: Y = C or T, K = G or T, R = A or G. A plus sign in front of a base indicates a locked nucleic acid.