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Table 1 Primer and probe sequences used in the respiratory virus multiplex assays

From: Pandemic clinical case definitions are non-specific: multiple respiratory viruses circulating in the early phases of the 2009 influenza pandemic in New South Wales, Australia

Virus (target gene)

Name

Sequence (5′ to 3′ end)

Reference

RSV (nucleoprotein)

RSVF

For: tagtgtrcargcagaaatgg

in-house

 

RSVAR

Rev: agtgrggaaattgagtcaaagat

in-house

 

RSVBR

Rev: rggraattgagttaatgacagc

in-house

 

RSVP

Probe: FAM tgatgcttttggrttrttcaatatatgg BHQ1

in-house

Influenza A (matrix)

AMF2

For: atggaatggctaaagacaagac

[9]

 

AMR2

Rev: cattkagggcattytggac

in-house

 

AMP

Probe: Cal fluo Red610 acgctgcagtcctcgctcact BHQ2

in-house

Influenza B (nucleoprotein)

BNF

For: yaacgatgacatggagagaaac

in-house

 

BNR

Rev: gcctcctgttttgttgtgatc

in-house

 

BNP

Probe: Quasor670 ccttctttsacatctctggcattctt BHQ2

in-house

Parainfluenza 1 (matrix)

PI1F

For: yggaacatcactaggtacaatyac

in-house

 

PI1R

Rev: gagcttcttttctccatcatc

in-house

 

Para1P

Probe: aactcttgcagatcttgcattaccg

in-house

Parainfluenza 2 (matrix)

PI2F

For: tcactgtggtcagttggatgt

in-house

 

PI2R

Rev: ctcaaatgtccgttgacctg

in-house

 

Para2P

Quasor670 aagaatctgatcttaatgagctaatgggc BHQ2

in-house

Parainfluenza 3 (matrix)

PI3F

For: Cal fluo Red610 gaagtgagaagaacagtyaaagc BHQ2

in-house

 

PI3R

Rev: cattgaggagcaagagcaac

in-house

 

Para3P

Probe FAM ttggcatcgaacarcattcc BHQ1

in-house

Rhino & Entero (5′UTR)

Rhi3A

For: gcccctgaatgyggctaa

[10]

 

Rhi4B

Rev: gaaacacggacacccaaagta

[10]

 

Rhi1P

Probe: FAM tggtcccrtcccgcamttgc BHQ1

in-house

 

Rhi2P

Probe: FAM ccrtcccrsaattgctcrttacgac BHQ1

in-house

 

Ent1P

Probe: Cal fluo Red610 cggttccgctgcrgagttrccc BHQ2

in-house

 

Ent2P

Probe: Cal fluo Red610 cggttccgccacrgacttrcgc BHQ2

in-house

hMPV (nucleoprotein)

Meta NLNF

For: catayaarcatgctatattaaaagagtctc

[11]

 

Meta NLNR

Rev: cctatytctgcagcatatttgtaatcag

[11]

 

MetaP

Probe:Quasor670 tcttgytgcaatgatgarggtgtyactgc BHQ2

[11]

Adeno (hexon)

AdeF

For: caaggaygtmaacatgatcctgcag

in-house

 

AdeF

For: raaggatgtdaacatgrtbctdcag

in-house

 

AdeR

Rev: cgttggtrtcgttrcgcagcat

in-house

 

AdeR

Rev: crttggtrtcrttycknarcat

in-house

 

Ade1P

Probe: FAM trgaagckgtgttrtgwgccatggg BHQ1

in-house

 

Ade2P

Probe: FAM tggaggcsgtgttgtgsgccatggg BHQ1

in-house

Human Beta-globin

PCO3

For: acacaactgtgttcactagc

[8]

 

PCO4

Rev: caacttcatccacgttcacc

[8]

 

BGLP

Probe: Quasor670 tcaaacagacaccatggtgcacctga BHQ2

in-house

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Virology Journal

ISSN: 1743-422X