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Table 3 Primer and probe sequences for the respiratory multiplex rtPCR

From: During the summer 2009 outbreak of "swine flu" in Scotland what respiratory pathogens were diagnosed as H1N1/2009?

Multiplex

Virus Target

Target Gene

Forward primer sequence

Reverse primer sequence

Probe sequence

1

Influenza B

NS

ATGATCTTACAGTGGAGGATGAAGAA

CGAATTGGCTTTGRATGTCCTT

CY5-ATGGCCATCGGATCCTCAAYTCACTCT-BHQ

 

Influenza C

Matrix

GGCAAGCGACATGCTGAAYA

TCCAGCTGCYTTCATTTGCTTT

VIC-CTCTTCCTTCTGATTTTTTCAAA-MGBNFQ

2

Mycoplasma pneumoniae

Cytadhesin P1 (P1) gene

AAGCAGGAGTGACGGAAACAC

CACCACATCATTCCCCGTATT

CY5-CTCCACCAACAACCTCGCGCCTA-BHQ

 

Human metapneumovirus A

Fusion

GCYGTYAGCTTCAGTCAATTCAA

TCCAGCATTGTCTGAAAATTGC

VIC-CAACATTTAGAAACCTTCT-MGBNFQ

 

Human metapneumovirus B

Fusion

GCYGTYAGCTTCAGTCAATTCAA (Common with A)

GTTATCCCTGCATTGTCTGAAAACT

VIC-CGCACAACATTTAGGAATCTTCT-MGBNFQ

 

Parainfluenza virus 1

HN

GTGATTTAAACCCGGTAATTTCTCA

CCTTGTTCCTGCAGCTATTACAGA

FAM-ACCTATGACATCAACGAC-MGBNFQ

3

Parainfluenza virus 2

HN

ATGAAAACCATTTACCTAAGTGATGGA

CCTCCYGGTATRGCAGTGACTGAAC

VIC-TCAATCGCAAAAGC-MGBNFQ

 

Parainfluenza virus 3

HN

CCAGGGATATAYTAYAAAGGCAAAA

CCGGGRCACCCAGTTGTG

FAM-TGGRTGTTCAAGACCTCCATAYCCGAGAAA-BHQ

 

Parainfluenza virus 4

Fusion

CAGAYAACATCAATCGCCTTACAAA

TGTACCTATGACTGCCCCAAARA

CY5-CCMATCACAAGCTCAGAAATYCAAAGTCGT-BHQ3A

4

Human coronavirus 229E

Nucleocapsid

CAGTCAAATGGGCTGATGCA

AAAGGGCTATAAAGAGAATAAGGTATTCT

FAM-CCCTGACGACCACGTTGTGGTTCA-

BHQ

 

Human coronavirus OC43

Nucleocapsid

CGATGAGGCTATTCCGACTAGGT

CCTTCCTGAGCCTTCAATATAGTAACC

CY5-TCCGCCTGGCACGGTACTCCCT- BHQ

 

Human coronavirus NL63

1a gene

ACGTACTTCTATTATGAAGCATGATATTAA

AGCAGATCTAATGTTATACTTAAAACTACG

VIC-ATTGCCAAGGCTCCTAAACGTACAGGTGTT-TAMRA

5

Respiratory syncitial virus A

NP

AGATCAACTTCTGTCATCCAGCAA

TTCTGCACATCATAATTAGGAG

FAM-CACCATCCAACGGAGCACAGGAGAT-BHQ

 

Respiratory syncitial virus B

NP

AAGATGCAAATCATAAATTCACAGGA

TGATATCCAGCATCTTTAAGTA

FAM-TTTCCCTTCCTAACCTGGACATA-BHQ

 

Rhinovirus

5'-UTR

TGGACAGGGTGTGAAGAGC

CAAAGTAGTCGGTCCCATCC

VIC-TCCTCCGGCCCCTGAATG-TAMRA

 

Adenovirus

Matrix

GCCACGGTGGGGTTTCTAAACTT

GCCCCAGTGGTCTTACATGCACATC

CY5-TGCACCAGACCCGGGCTCAGGTACTCCGA-BHQ