Table 1.
Amplication and mapping metrics for samples with respiratory viruses detected by RNA-seq and/or by qPCR. Detected virus coverage was scaled by the total number of raw reads divided by 10e6. If the closest reference differed between the multiple contigs for a sample, then the most frequent closest reference sequence was reported. In all cases the closest reference for all contigs of a sample were of the same viral species (i.e., no dual infections were detected)
| Subject | qPCR | RNA-seq mapping metrics | Detected virus | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Virus | Gene | Total reads | Resp. virus reads | % Viral reads | Species | Strain/serotype | Closest reference (NCBI acc) | Virus mapped to NCBI reference | Coverage (scaled) | |||
| Species | Ct | CCL8 | CXCL11 | |||||||||
| Asthma-1 | None | NA | 8426.9 | 109,137.3 | 10,720,551 | 164,870 | 1.54 | HPIV | 4a | KF483663.1 | 98.9% | 1271.6x |
| Control-1 | HRV | 29.36 | 7.7 | 190.8 | 9,818,450 | 74,935 | 0.763 | HEV | C105 | JX393302.1 | 92.8% | 1259.7x |
| Asthma-2 | RSV | 20.05 | 4356.0 | 103,107.1 | 11,597,132 | 58,263 | 0.502 | RSV | A | KJ672478.1 | 99.8% | 473.5x |
| Control-2 | HPIV1 | 24.37 | 749.7 | 13,819.3 | 14,029,017 | 26,045 | 0.186 | HPIV | 1 | KF687314.1 | 99.8% | 172.2x |
| Control-3 | HRV | 24.19 | 170.7 | 4377.0 | 10,591,814 | 4081 | 0.039 | HRV | A55 | DQ473511.1 | 80.8% | 66.9x |
| Asthma-3 | HPIV1 | 25.29 | 3148.7 | 13,129.6 | 9,738,089 | 6648 | 0.068 | HPIV | 1 | KF530212.1 | 99.8% | 64.4x |
| Control-4 | HRV | 25.86 | 7042.3 | 89,477.7 | 16,450,743 | 2878 | 0.017 | HRV | A59 | JN541266.1 | 99.3% | 37.9x |
| Asthma-4 | HRV | 38.15 | 6.4 | 68.5 | 15,103,156 | 829 | 0.005 | HRV | C | JF317015.1 | 99.9% | 11.7x |
| Control-5 | None | NA | 1430.1 | 24,191.0 | 14,863,334 | 2671 | 0.018 | Influenza | B | CY171998.1 | 5.7% | 7.8x |
| Control-6 | HRV | 30.24 | 67.3 | 734.7 | 9,732,129 | 203 | 0.002 | HRV | A59 | JN541266.1 | 99.5% | 4.5x |
| Asthma-5 | HRV | 29.17 | 90.1 | 1010.9 | 8,269,118 | 156 | 0.002 | HRV | A100 | FJ445175.1 | 91.0% | 3.6x |
| Control-7 | None | NA | 4.7 | 166.0 | 10,579,380 | 780 | 0.007 | HCoV | OC43 | KF530099.1 | 95.0% | 3.2x |
| Asthma-6 | HRV | 28.60 | 1780.1 | 89,078.1 | 9,944,802 | 97 | 0.001 | HRV | A55 | DQ473511.1 | 85.6% | 1.7x |
| Control-8 | HMPV | 30.78 | 10.7 | 146.7 | 9,978,447 | 107 | 0.001 | HMPV | A2 | GQ153651.1 | 99.1% | 1.2x |
| Control-9 | HRV | 40.98 | 0.7 | 28.6 | 14,107,522 | 76 | 0.0005 | HRV | C | JF317015.1 | 100% | 1.2x |
| Control-10 | HRV | 44.08 | 1.3 | 58.1 | 14,005,041 | 39 | 0.0003 | HEV | CY135 | KF322116.1 | 15.4% | 0.7x |
| Control-11 | HRV | 33.35 | 1.0 | 20.2 | 15,787,336 | 35 | 0.0002 | RSV | A | EF155421.1 | 100% | 0.5x |
| Control-12 | None | NA | 0.5 | 76.5 | 10,880,596 | 24 | 0.0002 | RSV | A | KJ672484.1 | 100% | 0.2x |
| Asthma-7 | HRV | 37.60 | 2.6 | 90.8 | 16,883,056 | 9 | 5.33e-05 | HCoV | NA* | JX504050.1 | 66.7% | NA* |
| Asthma-8 | RSV | 35.95 | 3.6 | 145.9 | 15,782,330 | 7 | 4.44e-05 | RSV | NA* | KJ672484.1 | 85.7% | NA* |
| Asthma-9 | HRV | 42.14 | 2.1 | 132.1 | 13,910,896 | 5 | 3.59e-05 | HRV | NA* | KC342104.1 | 40% | NA* |
| Control-13 | HRV | 33.51 | 1.7 | 37.8 | 17,449,199 | 4 | 2.29e-05 | HRV | NA* | AB904651.1 | 25% | NA* |
| Control-14 | HRV | 37.76 | 0.8 | 5.3 | 14,074,760 | 0 | 0 | NA | NA | NA | NA | NA |
| Asthma-10 | RSV/HPIV1 | 40.04/37.25 | 3.2 | 95.6 | 15,013,585 | 0 | 0 | NA | NA | NA | NA | NA |
| Control-15 | RSV | 37.8 | 4.9 | 443.7 | 17,496,674 | 0 | 0 | NA | NA | NA | NA | NA |
*Too few reads to perform assembly into contigs