Quantification of Human and Animal Viruses to Differentiate the Origin of the Fecal Contamination Present in Environmental Samples

Table 1

Oligonucleotide primers and probes used for the detection and quantification of viral indicators.

Primers and probes	Virus	Position^a	Reference	Sequence (5′-3′)
ADF	Human adenovirus (HAdV)	18869–18887		CWTACATGCACATCKCSGG
ADR		18919–18937	[26]	CRCGGGCRAAYTGCACCAG
ADP1		18889–18916		FAM-CCGGGCTCAGGTACTCCGAGGCGTCCT-BHQ1
JE3F	JC polyomavirus (JCPyV)	4317–4339		ATGTTTGCCAGTGATGATGAAAA
JE3R		4251–4277	[27]	GGAAAGTCTTTAGGGTCTTCTACCTTT
JE3P		4313–4482		FAM-AGGATCCCAACACTCTACCCCACCTAAAAAGA-BHQ1
QB-F1-1	Bovine polyomavirus (BPyV)	2122–2144		CTAGATCCTACCCTCAAGGGAAT
QB-R1-1		2177–2198	[28]	TTACTTGGATCTGGACACCAAC
QB-P1-2		2149–2174		FAM-GACAAAGATGGTGTGTATCCTGTTGA-BHQ1
Q-PAdV-F	Porcine adenovirus (PAdV)	20701–20718		AACGGCCGCTACTGCAAG
Q-PAdV-R		20751–20768	[29]	CACATCCAGGTGCCGC
Q-PAdV-P		20722–20737		FAM-AGCAGCAGGCTCTTGAGG-BHQ1
qOv_F	Ovine polyomavirus (OPyV)	VP1^b  region		CAGCTGYAGACATTGTGG
qOv_R			[30]	TCCAATCTGGGCATAAGATT
qOv_P				FAM-ATGATTACCAAGCCAGACAGTGGG-BHQ1
Q-PaV-F	Chicken/turkey parvovirus (ChPV/TuPV)	3326–3345		AGTCCACGAGATTGGCAACA
Q-PaV-R		3388–3407	[31]	GCAGGTTAAAGATTTTCACG
Q-PaV-Pr		3356–3378		6FAM-AATTATTCGAGATGGCGCCCACG-BHQ1

aThe sequence positions are referred to strains J01917.1 (HAdV), NC_001699.1 (JCPyV), D13942 (BPyV), AJ237815 (PAdV), and GU214706 (ChPV/TuPV) from Genbank. bVP1: virion protein 1.