Table 3.
Detection of qPCR Virus Positive Respiratory Samples with mNGS
| Material | Routine diagnostics |
mNGS |
||||
|---|---|---|---|---|---|---|
| PCR positive | Cq value | Virus genus | Genus reads∗ | Virus species | Species reads∗ | |
| NP wash | RV | 30.7 | Enterovirus | 0 | Rhinovirus | 0 |
| PIV1 | 17.1 | Respirovirus | 58,619 | Human respirovirus 1 | 56,407 | |
| ADV | 33.6 | Mastadenovirus | 0 | Human mastadenovirus C | 0 | |
| NP wash | MPV | 24 | Metapneumovirus | 127 | Human metapneumovirus | 123 |
| BAL | NL63 | 24.4 | Alphacoronavirus | 1999 | Human coronavirus NL63 | 2176 |
| HKU1 | 28.2 | Betacoronavirus | 1 | Human coronavirus HKU1 | 1 | |
| Sputum | RV | 32 | Enterovirus | 2326 | Rhinovirus C | 2204 |
| NP wash | INFA | 22.2 | Alphainfluenzavirus | 1490 | Influenza A virus (A/California/07/2009 (H1N1)) | 1490 |
| NP wash | MPV | 33.4 | Metapneumovirus | 1 | Human metapneumovirus | 3 |
| ADV | 19.3 | Mastadenovirus | 125 | Human mastadenovirus C | 123 | |
| Sputum | PIV4 | 21 | Orthorubulavirus | 7729 | Human rubulavirus virus 4 (subtype a) | 6798 |
| NP wash | HBOV | 22.3 | Bocaparvovirus | 7 | Human bocavirus | 7 |
| NP wash | MPV | 22.2 | Metapneumovirus | 139 | Human metapneumovirus | 312 |
| NP wash | INFB | 16.5 | Betainfluenzavirus | 4971 | Influenza B virus (B/Lee/1940) | 4971 |
| NP wash | RV | 25.4 | Enterovirus | 8 | Rhinovirus A | 6 |
| RSV | 30.7 | Orthopneumovirus | 32 | Human orthopneumovirus | 32 | |
| NP wash | INFB | 21.4 | Betainfluenzavirus | 2686 | Influenza B virus (B/Lee/1940) | 2686 |
| NP wash | RSV | 17.8 | Orthopneumovirus | 29,900 | Human orthopneumovirus | 22,483 |
| NP wash | RV | 34.4 | Enterovirus | 0 | Rhinovirus | 0 |
| INFB | 22.6 | Betainfluenzavirus | 68,972 | Influenza B virus (B/Lee/1940) | 68,972 | |
| BAL | INFB | 34.8 | Betainfluenzavirus | 0 | Influenza B virus | 0 |
| HBOV | 34.1 | Bocaparvovirus | 0 | Human bocavirus | 0 | |
| NP wash | HKU1 | 24.3 | Betacoronavirus | 534 | Human coronavirus HKU1 | 535 |
| NP wash | RV | 16.8 | Enterovirus | 3877 | Rhinovirus A | 1721 |
| NP wash | RV | 27.4 | Enterovirus | 1 | Rhinovirus B | 2 |
| HBOV | 19 | Bocaparvovirus | 1014 | Human bocavirus | 1064 | |
| NP wash | INFA | 22.1 | Alphainfluenzavirus | 657 | Influenza A virus (A/California/07/2009 (H1N1)) | 657 |
| NP wash | RSV | 17.2 | Orthopneumovirus | 31,179 | Human orthopneumovirus | 72 |
| NP wash | RV | 17.7 | Enterovirus | 50,642 | Rhinovirus A | 29,293 |
ADV, adenovirus; BAL, bronchoalveolar lavage; Cq, quantification cycle; HBOV, human bocavirus; HKU1, coronavirus HKU1; INFA, influenza A virus; INFB, influenza B virus; mNGS, metagenomic next-generation sequencing; MPV, metapneumovirus; NL63, coronavirus NL63; NP, nasopharyngeal; PIV, parainfluenza virus; qPCR, real-time quantitative PCR; RSV, respiratory syncytial virus; RV, rhinovirus.
∗
Number of reads assigned to the genus or species of the target virus.