Table 1.

Primer and probes used in this study. All nucleotide positions refer to FJ705359 (strain wbGER27, a German wild boar isolate). Abbreviations: open reading frame (ORF), hyper variable region (HVR), RNA dependent RNA polymerase (RdRp).

Region Name and Internal Length (nt)	Primer Name	Position	Sequence	Step	Product Length (bp)
ORF1 -5´ This study	HEV.ORF1_F1	33–58	CCCAYCAGTTYATWAAGGCTCCTGGC	RT-PCR	493
	HEV.ORF1_R1	497–525	TGCARDGARTANARRGCNAYNCCNGTCTC
	HEV.ORF1_F2	98–126	AAYTCYGCCYTGGCGAATGCTGTGGTGGT	nested PCR	302
	HEV.ORF1_R2	377–399	CCVCGRGTNGGRGCRGWRTACCA
HVR (for genotype 3) This study	HEV.HVR_F1	2069–2091	TTYTCYCCTGGGCAYMTYTGGGA	RT-PCR	401
	HEV.HVR_R1	2441–2469	TTAACCARCCARTCACARTCYGAYTCAAA
	HEV.HVR_F2a	2135–2157	ACYTGGTCHACATCTGGYTTYTC	nested PCR	263 or 293
	HEV.HVR_F2b	2165–2184	TTYTCCCCYCCTGAGGCGGC
	HEV.HVR_R2	2405–2427	TACACCTTRGCSCCRTCRGGRTA
RdRp 280 (4312–4591) (Johne et al. 2010)	HEV-cs	4181–4203	TCGCGCATCACMTTYTTCCARAA	RT-PCR	469
	HEV-cas	4628–4650	GCCATGTTCCAGACDGTRTTCCA
	HEV-csn	4287–4311	GTGCTCTGTTTGGCCCNTGGTTYMG	nested PCR	330
	HEV-casn	4592–4617	CCAGGCTCACCRGARTGYTTCTTCCA
ORF3 225 (5205–5429) This study	HEV.ORF3_F1	5126–5145	MGGKTRGAATGAATAACATG	RT-PCR	326 or 362
	HEV.ORF3_R2	5430–5451	GGCGCTGGGAYTGGTCRCGCCA
	HEV.ORF3_R1	5467–5487	CAGYTGGGGYAGRTCGACGRC
	HEV.ORF3_F2	5182–5204	GGGCTGTTCTGTTKYTGYTCYTC	nested PCR	219 or 269
	HEV.ORF3_R2	5430–5451	GGCGCTGGGAYTGGTCRCGCCA
	HEV.ORF3_R2a	5382–5401	CGAGGGCGAGCTCCAGCCCC
modified Diagnostic-qPCR - This study and (Schlosser et al. 2014)	HEV.Fa	5278–5294	GTGCCGGCGGTGGTTTC	RT-qPCR	81
	HEV.Fb	5278–5296	GTGCCGGCGGTGGTTTCTG
	HEV.R	5340–5359	GCGAAGGGGTTGGTTGGATG
	HEV.P	5300–5320	FAM-TGACMGGGTTGATTCTCAGCC-BHQ1
ORF2 187 (6277–6488) This study	HEV.ORF2_F1	6205–6223	CDGCNACYCGBTTYATGAA	RT-PCR	393
	HEV.ORF2_R1a	6573–6598	GTKAGRGARAGCCAWAGYACATCATT
	HEV.ORF2_R1b	6573–6598	GTRAGNGADAGCCACARRACATCATT
	HEV.ORF2_F2	6276–6301	GCBYTHACNYTRTTYAAYCTTGCTGA	nested PCR	241
	HEV.ORF2_R2	6489–6517	TGYTCRTGYTGRTTRTCRTARTCYTGDAT