Table 3. qPCR positive samples with respective mNGS results.
| Samples | qPCR positive (%) | Cq values range | mNGS species positive (%) | mNGS species reads (range) | Coverage (%, range) |
|---|---|---|---|---|---|
| All targets | 23/88 (26) | 19–38 | 23/88 (26) | 0–1,317,490 | 3–100 |
| Influenza A | 3/23 (13) | 29–36 | 3/23 (13) | 9–559 | 3–98 |
| Cov NL63 | 2/23 (9) | 32 | 2/23 (9) | 1,347–127,284 | 93–100 |
| Cov OC43 | 1/23 (4) | 27 | 2*/23 (4) | 72,644–1,317,490 | 99–99 |
| PIV3 | 2/23 (9) | 26–36 | 2/23 (9) | 59–288,877 | 14–99 |
| PIV4 | 1/23 (4) | 24 | 1/23 (4) | 185,235 | 100–100 |
| Rhinovirus | 14/23 (61) | 19–38 | 13**/23 (57)RV-A: 6/13RV-B: 2/13RV-C: 5/13 |
0–310,491 32–27,096 13,445–18,206 217–310,491 |
94–100 100–100 30–100 |
*Retesting by qPCR confirmed the OC43 finding of mNGS
** Rhinovirus not detected with mNGS had PCR Cq value 38