Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow

Bal, A.; Pichon, M.; Picard, C.; Casalegno, J. S.; Valette, M.; Schuffenecker, I.; Billard, L.; Vallet, S.; Vilchez, G.; Cheynet, V.; Oriol, G.; Trouillet-Assant, S.; Gillet, Y.; Lina, B.; Brengel-Pesce, K.; Morfin, F.; Josset, L.

doi:10.1186/s12879-018-3446-5

Table 1 Metagenomic NGS results for the validated respiratory samples tested positive with viral real-time PCR.

From: Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow

Sample No.	Real-time PCR Ct values		Viral genome type	mNGS results for targeted viruses^a
Sample No.	Real-time PCR Ct values		Viral genome type	Identification	No. of reads	RPKM	Coverage(%)
1	HRV/EV	25	linear ssRNA	HRV-A19	13,061	5.5E + 06	97.6
2		24		HRV-A19	29,743	8.2E + 06	98.2
3		29		HRV-A63	2672	1.4E + 06	58.1
4		34		HRV-A56	453	1.4E + 04	75.2
5	RSV	27		RSV-B	14,218	1.9E + 06	91.2
6	RSV	36		RSV-A	187	1.5E + 03	22.0
7	MPV	33		HMPV-A	44,556	9.1E + 05	100.0
8	HCoV	20		HCoV NL63	73,878	2.4E + 06	94.2
9		24		HCoV 229E	19,615	1.1E + 06	99.8
10		28		HCoV 229E	20,666	2.4E + 05	100.0
12		36		HCoV NL63	1815	1.3E + 04	9.6
13	MV	23		Measles Virus	289,019	9.1E + 06	98.1
14	IBV	23	fragmented ssRNA	Influenza B	42,212	1.1E + 06	97.2
15	IAV	27		Influenza A(H3N2)	24,234	1.9E + 05	78.6
16		34		Influenza A(H3N2)	1559	1.9E + 04	21.2
17		35		Influenza A(H3N2)	258	1.8E + 03	26.5
18	HBoV	24	linear ssDNA	HBoV-1	79,504	2.7E + 06	100.0
20	AdV	17	linear dsDNA	HAdVC-1	245,2476	1.6E + 07	99.8
21		36		HAdVD-51	18	8.0E + 01	0.6
22^b		30		HAdVC-6	284	1.0E + 03	6.2
22^b	HHV-6	28		HHV-6B	18,411	1.4E + 04	54.8
23^b	HBoV	15	linear ssDNA	HBoV-1	9,470,426	1.6E + 08	100.0
23^b	CMV	31	linear dsDNA	CMV	653	2.5E + 02	5.3
24^b	HBoV	17	linear ssDNA	HBoV-1	7,966,089	1.1E + 08	100
24^b	MPV	29	linear ssRNA	HMPV-A	10,629	5.9E + 04	95.7
25^{b, c}	AdV	26	linear dsDNA	HAdVC-2	2165	6.8E + 03	12.4
	HPIV	26	linear ssRNA	HPIV-3	17,576	1.3E + 05	66.7
	HRV/EV	34	linear ssRNA	HRV-C	446	7.0E + 03	9.2
	CMV	27	linear dsDNA	CMV	34,577	1.7E + 04	24.8
26^b	HRV/EV	26	linear ssRNA	HRV-A78	114,684	1.4E + 07	99.9
	AdV	30	linear dsDNA	HAdVC-2	65	1.6E + 03	9.6
	RSV	30	linear ssRNA	RSV-A	586	3.5E + 04	68.7
27^b	AdV	32	linear dsDNA	HAdVC-2	24	1.3E + 02	3.2
27^b	HPIV	37	linear ssRNA	HPIV-2	50	6.3E + 02	2.3
28^b	HRV/EV	31	linear ssRNA	HRV-A71	1309	3.5E + 04	61.3
28^b	EBV	23	linear dsDNA	EBV	2556	3.0E + 03	39.3

HRV: human rhinovirus, EV: enterovirus, RSV: respiratory syncytial virus, HCoV: human coronavirus, HMPV: human metapneumovirus, HPIV: human parainfluenza virus, MV: measles virus, HBoV: human bocavirus, AdV: adenovirus, HHV: human herpes virus, CMV: cytomegalovirus, EBV: Epstein-Baar virus, Ct: Cycle threshold, RPKM: reads per kilobase of virus reference sequence per million mapped reads (normalization of the number of reads mapping to a targeted viral genome)
^aTargeted viruses: viruses detected with real-time PCR
^bMultiple viral infections
^cCross-checked on duplicate sample (deviation < 0.5 log)

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