Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens

Table 1 Result summary of non-ribosomal rPCR and Miseq run

Virus^a	Sample ID	Sample type	Cp values	% of enteroviral read	% Genome coverage	Internal gap length (bp)	Mean coverage	Accession numbers	Pairwise identity (%)
CV-A6	1	RS	22.69	90.2	99.5	0	26542	KX430795	100
	1	RS	22.69	85.1	100	0	22630	KX430796	100
	2	TS	28.34	11.2	97.5	0	1173	KX430797	100
	2	TS	28.34	10.9	95.3	0	1119	KX430798	100
	3	RS	30.5	7.9	97.7	0	1822	KX430799	100
	3	RS	30.5	8.3	97.3	57	2244	KX430800	100
	4	TS	32.06	7.1	75	1625	1328	KX430801	99.96
	4	TS	32.06	13.3	96.8	41	3061	KX430802	99.96
CV-A10	5	RS	20.92	40.7	99.2	0	11189	KX430803	100
	5	RS	20.92	53.8	98	0	12725	KX430804	100
	6	RS	23.59	53.1	97.5	0	17439	KX430805	100
	6	RS	23.59	51.9	97.6	0	14086	KX430806	100
	7	RS	26.71	18.2	98	0	4299	KX430807	99.99
	7	RS	26.71	14.5	97	0	3820	KX430808	99.99
	8	TS	33.2	42.4	94	0	12216	KX430809	99.99
	8	TS	33.2	30.5	97.2	26	8412	KX430810	99.99
CV-A16	9	TS	24.97	83.8	99.7	0	3161	KX430811	100
	9	TS	24.97	80.1	99	0	20597	KX430812	100
	10	TS	26.72	2	91	71	475	KX430813	100
	10	TS	26.72	2.1	96	0	509	KX430814	100
	11	TS	33.26	4.5	96	0	971	KX430815	100
	11	TS	33.26	4.2	86	712	1101	KX430816	100
EV-A71	12	TS	31.1	0.2	72.5	1447	5.3	KX430817	100
EV-A71	12	TS	31.1	0.3	94	0	52.6	KX430818	100

^aMiseq run was multiplexed. Only run output of relevant samples were shown here; CV-A6: coxsackievirus A6, CV-A10: coxsackievirus A10, CV-A16: coxsackievirus A16 and EV-A71 B5: enterovirus A71 subgenogroup B5; TS: Throat swab; RS: rectal swab

ISSN: 1743-422X