Table 2.
Performance of RNA Sequencing and Pan-Viral Group Polymerase Chain Reaction Compared with Pathogen-Specific Real-Time Polymerase Chain Reaction Performed Per Etiology of Pneumonia in the Community Protocol
| EPIC positive | Positive in this study | RNA-seq | PVG PCR | RNA-seq or PVG PCR | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| RNA-seq | PVG PCR | RNA-seq or PVG PCR | Sens | Spec | Sens | Spec | Sens | Spec | ||
| Patients (n = 63) | ||||||||||
| IAV | 0 | 0 | 0 | 0 | NA | 100% | NA | 100% | NA | NA |
| IBV | 1 | 1 | 0 | 1 | 100% | 100% | 0% | 100% | 100% | 100% |
| HMPV | 8 | 7 | 7 | 8 | 88% | 100% | 88% | 100% | 100% | 100% |
| HRVa | 12 | 12 | 2a | 12 | 100% | 100% | 17% | 100% | 100% | 100% |
| RSV | 24 | 23 | 21 | 23 | 96% | 100% | 88% | 100% | 96% | 100% |
| HPIV | 3 | 2 | 1 | 2 | 67% | 98% | 33% | 98% | 67% | 98% |
| ADV | 3 | 0 | 1 | 1 | 0% | 100% | 33% | 100% | 33% | 100% |
| HCoV | 2 | 2 | 2 | 2 | 100% | 100% | 100% | 100% | 100% | 100% |
| M. pneumoniae | 7 | 7 | ND | 7 | 100% | 98% | ND | ND | 100% | 98% |
| Control subjects (n = 52) | ||||||||||
| IAV | 1 | 0 | 0 | 0 | 0% | 100% | 0% | 100% | 0% | 100% |
| IBV | 0 | 0 | 0 | 0 | NA | 100% | NA | 100% | NA | 100% |
| HMPV | 4 | 0 | 0 | 0 | 0% | 100% | 0% | 100% | 0% | 100% |
| HRVa | 38 | 34 | 5a | 34 | 89% | 96% | 13% | 100% | 89% | 96% |
| RSV | 5 | 0 | 1 | 1 | 0% | 100% | 20% | 100% | 20% | 100% |
| HPIV | 3 | 3 | 2 | 3 | 100% | 98% | 67% | 100% | 100% | 98% |
| ADV | 5 | 0 | 3 | 3 | 0% | 100% | 60% | 100% | 60% | 100% |
| HCoV | 3 | 1 | 2 | 2 | 33% | 100% | 67% | 100% | 67% | 100% |
| M. pneumoniae | 0 | 0 | ND | 0 | NA | 100% | ND | ND | NA | 100% |
Abbreviations: ADV, adenovirus; EPIC, Etiology of Pneumonia in the Community; HCoV, human coronavirus; HMPV, human metapneumovirus; HPIV, human parainfluenza viruses; HRV, human rhinovirus; IAV, influenza A virus; IBV, influenza B virus; M. pneumoniae, Mycoplasma pneumoniae; ND, not done; PVG PCR, pan-viral group polymerase chain reaction; RSV, respiratory syncytial virus; Sens, sensitivity; Spec, specificity.
aThe Picornaviridae polymerase chain reaction targets only a subset of human rhinoviruses.