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Table 2 Assays used to detect a range of bacterial, viral and parasitic pathogens.

From: Methods for determining disease burden and calibrating national surveillance data in the United Kingdom: the second study of infectious intestinal disease in the community (IID2 study)

PCR (SOP)

Assay - chemistry

Target Organism

Gene encoding proteins

References

NOR1

SINGLE-5'exonuclease

Norovirus genogroup 1

RNA dependent RNA polyermerase/capsid

[34]

NOR2

DUPLEX-5'exonuclease

Norovirus genogroup 2

Mengo virus mutant vaccine strain MC

RNA dependent RNA polyermerase/capsid

Not known

[35]

Comite Europeen de Normalisation (CEN)

ROTA

SINGLE-5'exonuclease

Rotavirus Group A

Viral Protein 6

[35, 36]

SAPO

DUPLEX-5'exonuclease

Sapovirus

Polymerase-capsid junction (2 probes)

[37]

ASTR

SINGLE-SYBR Green

Astrovirus

Capsid

[38]

ADEN

SINGLE-5'exonuclease

Adenovirus type 40 and 41

Long fibre protein

[39]

CAMP

DUPLEX-5'exonuclease

C. jejuni

C. coli

Membrane associated protein

Lipoprotein of iron binding protein

[40]

SALM

DUPLEX-5'exonuclease

Salmonella enterica

Green Fluorescent Protein gene (gfp) inserted into a E. coli

Glycotransferase

GFP Protein

[41]

EAGG

SINGLE-5'exonuclease

EnteroAggregative E. coli

Anti aggregation transporter

[28, 42]

LIST

SINGLE-5'exonuclease

Listeria monocytogenes

Haemolysin A

[43]

VT1-VT2

DUPLEX-5'exonuclease

Verocytotoxin 1

Verocytotoxin 2

Verocytotoxin 1

Verocytotoxin 2

[44]

GIAR

SINGLE-5'exonuclease

Giardia spp.

Elongation Factor 1 alpha

[43]

CRYP

DUPLEX-5'exonuclease

C. hominis, C. parvum, C. meleagridis, C. felis

Cryptosporidium oocyst wall protein

[43]

CPER

DUPLEX-5'exonuclease

C. perfringens alphatoxin and enterotoxin

Phospholipase C gene of C. perfringens

Enterotoxin gene of enterotoxigenic C. perfringens

[45]

CDIF

MULTIPLEX-

5'exonuclease

Toxin-producing C. difficile

Toxin B gene (tcdB), binary toxin (cdt), and tcdC gene single-base deletion at nucleotide 117 (tcdB)

[4648]