Table 2.

Overview of the samples with successful partial ORF2 sequencing, the year of sampling, real-time RT-PCR Ct values, the subtype allocation and the NGS results.

Origin	Sample ID	Year	Material	HEV Ct Value	HEV Subtype	NGS Reads 1	NGS Coverage 1 (%)
Wild boars	WB12	2017	Liver	37.7	3l	7	12.6
	WB33	2018	Liver	24.3	3h_s 2	6304	99.3
	WB36	2018	Liver	28.9	3h_s	686	95.6
	WB39	2018	Liver	34.4	3h_s	156	72.8
	WB40	2018	Liver	33.7	3h_s	254117	100
	WB74	2019	Liver	33.5	3h_s	283	70.7
Pig SLH	PL148	2018	Liver	37.3	3h_s	0	0.0
Pigs CCP	HD1	2018	Liver	32.3	3h_s	174	88.1
	HD8	2018	Liver	37.2	3l	2	4.0
	HD12	2018	Liver	35.7	3h_s	114	74.4
	HD22	2018	Liver	32.0	3h_s	155	82.7
	KW13L	2018	Liver	27.6	3h_s	257	89.1
	KW13F	2018	Feces	21.5	3h_s	6775	98.2
	KW20	2018	Liver	33.3	3h_s	0	0.0
	KW22	2018	Liver	29.4	3h_s	155	82.7
Meat products	BLV00672	2016	Coarse liver paté	28 3	3c	0	0.0
	BLV00691	2016	Smooth liver paté	27	3c	14	23.4
	BLV00735	2016	Liver salsiz	38	3h_s	0	0.0
	BLV00754	2016	Mortadella di fegato	37	3h_s	n.d.	n.a.
	BLV00761	2016	Mortadella di fegato	29	3h_s	n.d.	n.a.
	BLV00916	2017	Smooth liver paté	33	3h_s	n.d.	n.a.
	BLV01126	2018	Deer salsiz	34	3h_s	n.d.
	BLV01189	2019	Saucisse aux choux	32	3h_s	0	0.0
	BLV01185	2019	Saucisse aux choux	32	3h_s	1	1.4
	16LA03650	2016	Mortadella di fegato	34	3h_s	0	0.0
	16LA05705	2016	Mortadella di fegato	31	3h_s	0	0.0

¹ Highest number of quality controlled NGS reads aligning to a HEV reference genome and the respective genome coverage of this reference. ² Swiss cluster within subtype 3h according to phylogenetic analyses. ³ Ct values of meat products as provided by the laboratory of initial testing.