Table 5.
Illumina hits from two cell culture supernatants spiked with eight different virusesa
| Virus | Sensitivity of quantitative (RT)-PCRs |
Supernatant 3LODxa (no. of reads = 7,891,140) |
Supernatant 0.8LODx (no. of reads = 8,342,364) |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Validated LOD (per ml) | CT for 10/100/1,000 plasmid copies (per 5 μl) | Quantitative (RT)-PCR | CT | No. of hits | Identity (%) | Length (hits) | Quantitative (RT)-PCR | CT | No. of hits | Identity (%) | Length (hits) | |
| RhCMV | 3 TCID50 | ND/35/32 | +/+ | 31/30 | 2,142 | 99 | 65 | +/+ | 32/33 | 662 | 99 | 68 |
| HADV-5 | 357 TCID50 | ND/37/33 | +/+ | 38/39 | 13 | 99 | 58 | −/− | 4 | 99 | 59 | |
| HBV | 3,571 IU | ND/40/35 | +/+ | 35/35 | 2 | 99 | 68 | +/+ | 37/37 | 0 | ||
| B19 | 2 | 99 | 70 | 6 | 97 | 70 | ||||||
| BVDV-1-NADL | 10 TCID50 | ND/42/36 | +/+ | 38/38 | 2 | 100 | 71 | +/+ | 45/45 | 1 | 95 | 58 |
| H3N8 | 357 cp | ND/39/36 | +/+ | 33/34 | 10 | 100 | 70 | −/− | 0 | |||
| FLUBV-B/LEE/40 | 357 cp | ND/35/33 | −/− | 4 | 99 | 66 | −/− | 0 | ||||
| HCV | 1,071 IU | ND/>40/ND | +/− | 40/ | 0 | +/− | >40/ | 0 | ||||
MRC5 cell supernatants were spiked with viruses at a concentration corresponding to 3× or 0.8× the limit of detection (LOD) of the validated threshold of detection of corresponding quantitative (RT-)PCRs, as detailed in Table 1. The number of reads generated from the samples and the number of virus-specific hits are given, together with the results from two runs of quantitative (RT-)PCRs (except for B19): validated limits of detection of virus spikes, cycle thresholds (CT) corresponding to a given concentration of positive controls plasmids, and CT corresponding to the samples are shown for comparison. The percent identities were obtained after comparison with the reference sequences (see the text). The length of the hits and the percent identities correspond to averages. Abbreviations: IU, international unit; TCID50, tissue culture infective dose 50%; cp, DNA copies; ND, not determined; LOD, limit of detection of quantitative (RT-)PCR. +/+, +/−, and −/−, results of two independent runs of quantitative (RT-)PCRs.