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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 virusesa
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 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
22b 30 HAdVC-6 284 1.0E + 03 6.2
HHV-6 28 HHV-6B 18,411 1.4E + 04 54.8
23b HBoV 15 linear ssDNA HBoV-1 9,470,426 1.6E + 08 100.0
CMV 31 linear dsDNA CMV 653 2.5E + 02 5.3
24b HBoV 17 linear ssDNA HBoV-1 7,966,089 1.1E + 08 100
MPV 29 linear ssRNA HMPV-A 10,629 5.9E + 04 95.7
25b, 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 HRV-C 446 7.0E + 03 9.2
CMV 27 linear dsDNA CMV 34,577 1.7E + 04 24.8
26b 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
27b AdV 32 linear dsDNA HAdVC-2 24 1.3E + 02 3.2
HPIV 37 linear ssRNA HPIV-2 50 6.3E + 02 2.3
28b HRV/EV 31 HRV-A71 1309 3.5E + 04 61.3
EBV 23 linear dsDNA EBV 2556 3.0E + 03 39.3
  1. 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)
  2. aTargeted viruses: viruses detected with real-time PCR
  3. bMultiple viral infections
  4. cCross-checked on duplicate sample (deviation < 0.5 log)