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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]