Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples

Table 1 Diagnostic samples included in the study

	Sample ID	Date	State	Species	ST	Matrix	Cq	Read Count		Total Reads	Mapped Reads
	Sample ID	Date	State	Species	ST	Matrix	Cq	Ligation	Rapid	Total Reads	Mapped Reads
1	2016BVD01435	2016	NI	Cattle	1b	Plasma	28.8	38,635	442,964	481,599	48,145
2	2016BVD01436	2016	NI	Sheep	1b	Plasma	32.6	60,920	89,008	149,928	57,290
3	2018BVD01695	2018	NI	Cattle	1f	Plasma	19.2	66,753	850,149	916,902	824,299
4	2018BVD06212	2018	NW	Cattle	1d	EDTA blood	22.6	89,898	1,255,060	1,344,958	1,277,809
5	2018BVD06214	2018	NW	Cattle	1d	EDTA blood	21.7	88,264	830,138	918,402	870,123
6	2019BVD04871	2019	NW	Cattle	1d	Plasma	24.0	96,192	981,673	1,077,865	1,040,017
7	2019BVD04882	2019	NW	Cattle	1d	Plasma	21.4	118,619	1,226,328	1,344,947	1,278,462
8	2019BVD04888	2019	NW	Cattle	1d	EDTA blood	19.4	83,659	707,704	791,363	427,131
9	2019BVD04889	2019	NW	Cattle	1d	EDTA blood	28.0	157,898	314,612	472,510	229,627
10	2017BVD04597	2017	BW	Cattle	1b	Ear notch	24.8	52,299	272,345	324,644	302,107
11	D66/11–28	2011	TH	Cattle	2a	EDTA blood	24.4	77,725	465,003	542,728	521,038
12	TV02/13, T136	2013	-	Cattle	2c	Plasma	21.5	67,172	327,089	394,261	385,679

Legend: Selected samples with sample information, read counts divided between the Ligation Sequencing Kit and the Rapid Barcoding Kit, and mapped reads. ST Subtype, NI Lower Saxony, NW North Rhine-Westphalia, BW Baden-Württemberg, TH Thuringia

ISSN: 1746-6148