TABLE 2.
RT-PCR results, mNGS reads, and viral genome alignment coverage from EBOV testing for 70 patient samples from the outbreak
| Sample | mNGS |
mNGS with probe enrichment |
PCR results |
mNGS result for ZEBOVb | Final classificationc | Clinical outcome | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total no. of reads | No. of reads to ZEBOV | % coverage to ZEBOV | Total # of reads | No. of reads to ZEBOV | Fold enrichment | % coverage to ZEBOV | % increase in coverage | qRT-PCR (DRC) | qRT-PCR (US) | Confirmatory RT-PCR (US) | CTa | Calculated viral load | ||||
| BOE_007 | 13,530,534 | 10 | 4.2 | 149,261 | 1,459 | 146 | 51.3 | 47.1 | + | + | + | 36.2 | 6.25E+04 | + | Confirmed EVD | Deceased |
| BOE_011 | 21,029,450 | 184,925 | 99.8 | NTd | + | + | 26.4 | 3.31E+07 | + | Confirmed EVD | Deceased | |||||
| BOE_013 | 13,217,428 | 2,058 | 52.2 | 8,906,945 | 302,816 | 147 | 84.4 | 32.2 | + | + | + | 33.3 | 4.00E+05 | + | Confirmed EVD | Alive |
| BOE_015 | 14,040,176 | 530 | 11.5 | 314,033 | 114,990 | 217 | 62.4 | 50.9 | NT | + | – | 34 | 2.55E+05 | + | Confirmed EVD | Alive |
| BOE_016 | 11,644,602 | 5 | 1.4 | 87,398 | 860 | 172 | 40.6 | 39.3 | + | – | + | Confirmed EVD | Deceased | |||
| BOE_017 | 19,519,018 | 4,181 | 54.2 | 262,011 | 207,168 | 50 | 76.2 | 22.0 | NT | + | – | 32 | 9.18E+05 | + | Confirmed EVD | Deceased |
| BOE_021 | 14,305,256 | 2 | 1.1 | 49,814 | 1,298 | 649 | 49.7 | 48.7 | NT | + | – | 36.3 | 5.86E+04 | + | Confirmed EVD | Deceased |
| BOE_023 | 22,032,448 | 14,057 | 100.0 | NT | + | + | 25.3 | 6.69E+07 | + | Confirmed EVD | Deceased | |||||
| BOE_034 | 8,537,192 | 2 | 0.6 | 20,573 | 1,574 | 787 | 49.8 | 49.2 | + | + | – | 38 | 1.97E+04 | + | Confirmed EVD | Alive |
| BOE_035 | 13,874,416 | 1 | 0.4 | 203,976 | 97 | 97 | 17.2 | 16.8 | + | – | + | Confirmed EVD | Deceased | |||
| BOE_036 | 18,921,752 | 286,723 | 100.0 | NT | + | + | 23.4 | 2.26E+08 | + | Confirmed EVD | Deceased | |||||
| BOE_037 | 9,992,378 | 1 | 0.4 | 97,227 | 52 | 52 | 10.7 | 10.3 | NT | + | + | 35.7 | 8.60E+04 | + | Confirmed EVD | Deceased |
| BOE_039 | 9,190,338 | 1 | 0.4 | 107,133 | 85 | 85 | 18.3 | 17.9 | + | + | NT | 36.2 | 6.25E+04 | + | Confirmed EVD | Deceased |
| BOE_045 | 16,321,890 | 0 | + | – | – | Confirmed EVD | Deceased | |||||||||
| BOE_046 | 13,683,244 | 0 | + | – | – | Confirmed EVD | Deceased | |||||||||
| BOE_063 | 17,469,266 | 0 | + | + | NT | 35.1 | 1.26E+05 | – | Confirmed EVD | Alive | ||||||
| BOE_064 | 15,368,202 | 1 | 0.4 | 100,420 | 80 | 16.1 | 15.7 | – | + | NT | 40.9 | 3.08E+03 | + | Confirmed EVD | Alive | |
| BOE_065 | 19,320,118 | 20 | 7.7 | 140,155 | 2,685 | 27.6 | 19.9 | – | + | + | 29.1 | 5.88E+06 | + | Confirmed EVD | Alive | |
| BOE_069 | 26,924,516 | 855 | 5.6 | 80,760 | 29,174 | 12.2 | 6.6 | + | + | + | 33.6 | 3.30E+05 | + | Confirmed EVD | Deceased | |
| BOE_070 | 19,749,830 | 73,147 | 95.5 | 1,494,384 | 1,466,174 | 97.9 | 2.4 | + | + | + | 24.4 | 1.19E+08 | + | Confirmed EVD | Deceased | |
| BOE_078 | 26,936,926 | 1 | 0.4 | 5,817 | 863 | 63.4 | 63.0 | – | + | + | 36.5 | 5.15E+04 | + | Confirmed EVD | Alive | |
| BOE_084 | 18,760,962 | 419 | 39.1 | 35,536 | 9,805 | 84.3 | 45.2 | NT | + | + | 27.6 | 1.53E+07 | + | Confirmed EVD | Unknown | |
| BOE_006 | 13,861,466 | 0 | + | – | – | Probable EVD | Alive | |||||||||
| BOE_012 | 17,121,118 | 0 | + | – | – | Probable EVD | Alive | |||||||||
| BOE_020 | 13,128,106 | 0 | + | – | – | Probable EVD | Deceased | |||||||||
| BOE_030 | 17,942,078 | 0 | NT | + | NT | 38.1 | 1.85E+04 | – | Probable EVD | Deceased | ||||||
| BOE_033 | 16,194,794 | 0 | + | – | – | Probable EVD | Alive | |||||||||
| BOE_048 | 18,787,656 | 5 | 1.2 | 68,449 | 211 | 42 | 19.5 | 18.3 | NT | – | + | Probable EVD | Deceased | |||
| BOE_053 | 12,228,468 | 0 | NT | + | NT | 35.4 | 1.04E+05 | – | Probable EVD | Alive | ||||||
| BOE_055 | 19,528,904 | 0 | NT | + | NT | 34.8 | 1.53E+05 | – | Probable EVD | Deceased | ||||||
| BOE_060 | 19,274,440 | 0 | + | – | – | Probable EVD | Deceased | |||||||||
| BOE_061 | 17,877,356 | 0 | + | – | – | Probable EVD | Deceased | |||||||||
| BOE_062 | 18,406,940 | 0 | + | – | – | Probable EVD | Alive | |||||||||
| BOE_067 | 20,992,354 | 0 | + | – | – | Probable EVD | Deceased | |||||||||
| BOE_068 | 18,685,602 | 0 | + | – | – | Probable EVD | Deceased | |||||||||
| BOE_073 | 20,308,534 | 1 | 0.4 | 34,880 | 2,044 | 72.8 | 72.4 | NT | – | + | Probable EVD | Unknown | ||||
| BOE_079 | 24,925,148 | 1 | 0.4 | 11,030 | 2,674 | 75.3 | 74.9 | – | – | + | Probable EVD | Deceased | ||||
| BOE_001 | 22,533,096 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_005 | 24,918,444 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_008 | 21,723,630 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_009 | 18,807,290 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_010 | 15,523,496 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_014 | 24,153,028 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_026 | 30,814,980 | 0 | NT | – | – | Indeterminate EVD | Alive | |||||||||
| BOE_027 | 24,490,500 | 0 | NT | – | – | Indeterminate EVD | Alive | |||||||||
| BOE_029 | 15,545,630 | 0 | NT | – | – | Indeterminate EVD | Alive | |||||||||
| BOE_038 | 13,575,740 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_040 | 10,043,588 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_041 | 14,152,364 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_042 | 14,562,248 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_043 | 14,959,330 | 0 | NT | – | – | Indeterminate EVD | Alive | |||||||||
| BOE_044 | 21,893,586 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_049 | 15,698,664 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_050 | 19,856,236 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_051 | 19,560,668 | 0 | NT | – | – | Indeterminate EVD | Alive | |||||||||
| BOE_052 | 13,683,924 | 0 | NT | – | – | Indeterminate EVD | Alive | |||||||||
| BOE_054 | 5,551,494 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_056 | 16,011,850 | 0 | NT | – | – | Indeterminate EVD | Alive | |||||||||
| BOE_057 | 18,324,516 | 0 | NT | – | – | Indeterminate EVD | Alive | |||||||||
| BOE_058 | 17,418,264 | 0 | NT | – | – | Indeterminate EVD | Deceased | |||||||||
| BOE_059 | 18,728,830 | 0 | NT | – | – | Indeterminate EVD | Unknown | |||||||||
| BOE_086 | 18,849,366 | 0 | NT | – | – | Indeterminate EVD | Unknown | |||||||||
| BOE_087 | 18,183,444 | 0 | NT | – | – | Indeterminate EVD | Unknown | |||||||||
| BOE_022 | 17,245,420 | 0 | – | – | – | Non-EVD | Alive | |||||||||
| BOE_028 | 20,692,650 | 0 | – | – | – | Non-EVD | Alive | |||||||||
| BOE_066 | 15,492,274 | 0 | – | – | – | Non-EVD | Alive | |||||||||
| BOE_074 | 18,121,652 | 0 | – | – | – | Non-EVD | Alive | |||||||||
| BOE_075 | 6,756,328 | 0 | – | – | – | Non-EVD | Alive | |||||||||
| BOE_076 | 11,615,728 | 0 | – | – | – | Non-EVD | Alive | |||||||||
| BOE_077 | 15,569,022 | 0 | – | – | – | Non-EVD | Alive | |||||||||
a
CT, cycle threshold.
b
ZEBOV, Zaire Ebola virus.
c
Cases were classified as “confirmed EVD” if positive by at least 2 of the 3 following molecular tests: mNGS, qRT-PCRDRC, and qRT-PCRUS; “probable EVD” if positive by 1 of the 3 tests; “non-EVD” if negative by all 3 tests (and qRT-PCRDRC testing had been performed); or “indeterminate EVD” otherwise.
d
NT, not tested.