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Table 3 Primer sequences, gene targets and expected product sizes for viruses on the molecular strip.

From: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections

Name

Sequence (5' to 3')

Gene Target

1st/2nd

Size (bp)

PF1 1A

CCT TAA ATT CAG ATA TGT AT

HN1

1

478

PF1 1B

GAT AAA TAA TTA TTG ATA CG

   

PF1 1C

CCG GTA ATT TCT CAT ACC TAT G

 

2

317

PF1 1D

CCT TGG AGC CGA GTT GTT AAG

   

PF2 1A

AAC AAT CTG CTG CAG CAT TT

HN1

1

508

PF2 1B

ATG TCA GAC AAT GGG CAA AT

   

PF2 1C

CCA TTT ACC TAA GTG ATG GAA T

 

2

204

PF2 1D

GCC CTG TTG TAT TTG GAA GAG A

   

PF3 2A

CTTG TAA ACT CAG ACT TGG TA

HN1

1

478

PF3 2B

TTT AAG CCC TTG TCA ACA AC

   

PF3 2C

ACT CCC AAA GTT GAT GAA AGA T

 

2

103

PF3 2D

TAA ATC TTG TTG TTG AGA TTG

   

hMPV 1A

GCG GCA ATT TTC AGA CAA CG

Fusion

1

696

hMPV 1B

ACA TGC TGT TCG CCT TCA AC

   

hMPV 1C

CAG CAG CAG GAA TCA ATG TT

 

2

288

hMPV 1D

TCG CCT TCA ACT TTG CTT AG

   

CoV229E 1A

GGT ACT CCT AAG CCT TCT C G

Nucleocapsid

1

450

CoV229E 1B

TGC ACT AGG GTT AAG AAG AGG

   

CoV229E 1C

TTT GGA AGT GCA GGT GTT GTG G

 

2

100

CoV229E 1D

GAC TAT CAA ACA GCA TAG CAG C

   

ENT 2A

TCC TCC GGC CCC TGA ATG

5' Non-coding

1

120

ENT 2B

GAA ACA CGG ACA CCC AAA GTA

   

ENT 1C

GGC CCC TGA ATG CGG CTA AT

 

2

90

HRV 1B

GGT CCC RTC CCG CAA TT

   

FLA 3A (H1)2

GAA ATT TGC TAT GGC TGA C

Haemagglutinin

1

482

FLA 3B (H1)2

ATA TTT TGG GCA CTC TCC TAT

   

FLA 3C (H1)2

GTC TCT GTA GTG TCT TCA CAT TAT

 

2

197

FLA 3D (H1)2

CCG GAC CCA AAC CCT CTA CTC

   

FLB 1A

GTG ACT GGT GTG ATA CCA CT

Haemagglutinin

1

900

FLB 1B

TGT TTT CAC CCA TAT TGG GC

   

FLB 1C

CAT TTT GCA AAT CTC AAA GG

 

2

767

FLB 1D

TGG AGG CAA TCT GCT TCA CC

   

FLA 2C (H3)2

AGC AAA GCT TTC AGC AAC TG

Haemagglutinin

1

591

FLA 2D (H3)2

GCT TCC ATT TGG AGT GAT GC-3

   

FLA 2E (H3)2

AGT GCT GAA CGT GAC TAT GC

 

2

149

FLA 2F (H3)2

TTT GCT GGC TTC TCT TGG T

   

RSV 2A

GTC TTA CAG CCG TGA TTA GG

Nucleoprotein

1

838

RSV 2B

GGG CTT TCT TTG GTT ACT TC

   

RSVA 2C

GAT GTT ACG GTG GGG AGT CT

 

2

334

RSVA 2D

GTA CAC TGT AGT TAA TCA CA

   

RSVB 2C

AAT GCT AAG ATG GGG AGTTC

 

2

183

RSVB 2D

GAA ATT GAG TTA ATG ACA GC

   

ADV 2A2

GCCGCAGTGGTCTTACATGCACATC

Hexon

1

301

ADV 2B2

CAGCACGCCGCGGATGTCAAAGT

   

ADV 2C32

GACGCCTCGGAGTACCTSWSYCC

 

2

185

ADV 2DD2

TACGAGTACGTGGTGTCCTCKCGRTC

   
  1. 1 HN = Haemagglutinin-neuraminidase gene; 2 Primer sets designed for this study. N.B. 1 = 1st round primer set, 2 = 2nd round primer set; ENT 2A 2B, 1C, HRV 1B primer set = Rhinovirus.
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BMC Microbiology

ISSN: 1471-2180

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