Table 2 Zaire ebolavirus Makona performance summary

From: FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science

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%

  1. 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
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