Table 2.
Zaire ebolavirus Makona performance summary
| Sample | Real-time PCR (benchmark) Cq value |
MIPS (test device) % Classified |
FDA-ARGOS (MegaBLAST) % Classified |
FDA-ARGOS (Kraken) % Classified |
FDA-ARGOS (LMAT) % Classified |
|---|---|---|---|---|---|
| 3754-2 | 35.11/35.72 | 0.05% | 0.60% | 0.06% | 0.03% |
| 3754-4 | 33.83/33.36 | 0.06% | 0.68% | 0.06% | 0.03% |
| 3811-2 | 36.17/36.14 | 0.07% | 0.56% | 0.08% | 0.04% |
| 3856-1P | 15.95/15.98 | 76.63% | 80.91% | 79.50% | 42.48% |
| 3913-5 | 34.00/33.77 | 0.00% | 0.68% | 0.00% | 0.01% |
| 3958-4 | 32.77/33.28 | 0.04% | 0.65% | 0.05% | 0.05% |
| 3991-2 | 33.92/33.62 | 0.00% | 0.65% | 0.00% | 0.01% |
| 4007-2 | 26.30/26.55 | 21.33% | 22.41% | 21.81% | 12.12% |
| 4015-1 | 21.66/21.66 | 74.87% | 76.35% | 75.82% | 39.35% |
| 4033-1 | 16.59/16.32 | 76.64% | 79.59% | 78.97% | 41.79% |
| 4268-1P | 25.05/25.15 | 29.71% | 30.43% | 29.97% | 15.87% |
| 4468-3 | 35.78/35.91 | 0.04% | 0.59% | 0.05% | 0.03% |
| 4641-3P | 31.81/31.82 | 0.03% | 0.59% | 0.04% | 0.02% |
| 4726-1 | 21.22/21.21 | 53.95% | 56.44% | 54.28% | 30.05% |
| 4845-3 | 35.17/36.71 | 0.00% | 0.66% | 0.01% | 0.01% |
| NTC | N/A | 0.02% | 0.86% | 0.04% | 0.01% |
Illustration of target sequence comparison with FDA-ARGOS reference genomes for diagnostic performance testing. This table shows the traditional benchmark comparison of the EBOV MIPS assay to real-time PCR (RT-PCR) results and target sequence comparison with FDA-ARGOS using three bioinformatics tools (MegaBLAST, Kraken, and LMAT). Benchmark positive values were only noted for samples that yielded duplicative positive results by RT-PCR (bolded). Percent reads classified only refer to percentage of reads that were assigned to Zaire ebolavirus Makona, the remaining reads are non-specific