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Sensitivity of ID NOW and RT–PCR for detection of SARS-CoV-2 in an ambulatory population

  1. Yuan-Po Tu
  2. Jameel Iqbal  Is a corresponding author
  3. Timothy O'Leary
  1. Urgent Care, The Everett Clinic-Part of Optum, United States
  2. Department of Pathology, James J Peters VA Medical Center, United States
  3. Office of Research and Development Veterans Health Administration, United States
  4. Department of Pathology University of Maryland School of Medicine, United States
Research Article
Cite this article as: eLife 2021;10:e65726 doi: 10.7554/eLife.65726
4 figures, 17 tables and 1 additional file

Figures

PRISMA 2009 flow diagram detailing the studies that were identified, screened, deemed eligible, and finally included in the analysis.

Note that the data from the current clinical evaluation has been included in the analysis.

Forest plots demonstrating the three studies with low risk of patient selection bias utilized in the meta-analysis.

(A) The sensitivity of ID NOW as compared with the reference standard, and the overall sensitivity was estimated to be 82% with a lower 95% confidence bound at 67% and an upper bound of 91%. (B) The sensitivity of RT–PCR and is estimated to be 98% with a 95% CI of 96–99%.

Cycle number distributions for 1182 symptomatic (A) and 164 asymptomatic (B) patients who tested positive for SARS-CoV-2 between July 14 and November 16, 2020, using the Abbott m2000 assay at The Everett Clinic.

For patients with multiple tests, only the first positive test is included. In (C), data for each group of patients has been normalized so that the sum of all bins is 100, allowing better comparison of the distributions. The Abbott m2000 cycle number is generally about 10 cycles less than the Ct reported for PCR assays on other devices.

The collection methodology to ensure proper randomized sampling of nares for simultaneous analysis for SARS-CoV-2 by the ID NOW isothermal amplification and Hologic Panther RT–PCR assays.

A total of two swabs was collected on each patient, with patients having an even birth year number the right nares were collected first followed by a second swipe in the left nares and then for ID NOW point-of-care (POC) testing (depicted as red swab). For those patients, the other swab (blue swab) was sent for SARS-CoV-2 RT–PCR analysis by the Hologic Panther assay. For patients having an even birth year, the swabs sent for testing was reversed with the blue swab sent for ID NOW testing and the red swab sent for RT–PCR analysis.

Tables

Table 1
Results from the clinical evaluation comparing randomized anterior nares samples for the ID NOW compared to the Hologic Panther SARS-CoV-2 RT–PCR assay.
Hologic result
NEGPOSTotal
ID NOW resultNEG9422944
POS02121
Invalid909
Total95123974
 Negative agreement100.00% (82–100%)
 Positive agreement91.30%
(70–98%)
Table 2
Studies included in the systematic review.
StudySiteID NOW sampling deviceResidual
sample
tested?
ID NOW sample dry?Timing of ID NOW testPatient characteristicsPatient selection bias?Index test bias?Flow and timing biasN
(positive rate)
RT–PCRAbbott ID now
Positive/CP
% (95% CI)
Positive/CP
% (95% CI)
Lephart et al., 2020ANFoamNoYesUp to 24 at 4°CConvenience Hosp. and EDUnclearUnclearUnclear88 (31%)27/27
91% (85–100%)
12/27
44% (26–64%)
Basu et al., 2020ANFoamNoYesUp to 24 at 4°CConvenience Hosp. and EDUnclearUnclearUnclear101 (31%)31/32
97% (82–100%)
18/32
56% (38–73%)
Cradic et al., 2020ANFoamNoYesUnclearSymptomaticLowUnclearUnclear182
(7.1%)
13/13
100% (72–100%)
12/13
92% (62–100%)
Harrington et al., 2020ANFoamNoYesUnclearClinic, EDLowUnclearUnclear524
(36%)
186/188
99% (96–100%)
141/188
75% (68–81%)
Jin et al., 2020UUNoYesUnclearUUnclearUnclearUnclear52
(12%)
6/6
100% (52–100%)
4/6
67% (24–94%)
Mitchell and George, 2020NPUYesNoUnclearUHighHighUnclear61
(75%)
46/46
100% (90–100%)
33/46
72% (56–84%)
Moore et al., 2020NPUNoNoUnclearSymptomaticHighUnclearUnclear200
(64%)
127/127
100% (96–100%)
94/127
74% (65–81%)
Rhoads et al., 2020AN,
NP
UYesNoUnclearPCR+HighUnclearUnclear96
(100%)
96/96
100% (95–100%)
90/96
94% (86–97%)
Smithgall et al., 2020NPUYesNoUp to 48 hr at 4°CSelectedHighUnclearUnclear113
(80%)
89/90
99% (94–100%)
65/88
74% (64–82%)
Thwe and Ren, 2020NPUNoYes~2 hrSymptomatic
Hosp. and ED
HighUnclearUnclear129
(7.7%)
15/15
100% (75–100%)
8/15
53% (27–78%)
Zhen et al., 2020bNPManyYes (most)NoUp to 72 hr at 4°CSymptomaticUnclearUnclearUnclear107 (54%)57/58
98% (90–100%)
50/57
88 (76–95)
Comer and Fisk, 2020ANFoamNoYes15 mUHighLowLow117
(0.9%)
1/1
100% (5–100%)
0/1
0% (0–95%)
Ghofrani et al., 2020ANManyNoYesUnclearMostly symptomatic convenienceHighUnclearHigh113
(16%)
17/18
94% (71–99%)
17/18
94% (71–99%)
SoRelle et al., 2020STubeNoNoUnclearUUnclearLowLow59
(39%)
23/23
100% (82–100%)
18/23
78% (56–92%)
Tu (this study)ANFoamNoYes15 msymptomatic and asymptomaticLowLowLow974
(2.4%)
23/23
100% (82–100%)
21/23
91% (70–98%)
  1. *Likely <2 hr in some cases, more than a single type of sampling device was used. When a dry ID NOW foam swab was used as a part of this study, both the table above and the results reflect the use of that device, which is consistent with the current ID NOW package insert. Comparisons based upon use of other transport media are only shown when no data was presented for use of dry swabs.

    Table shows only the comparison between ID NOW and Cobas using dry swabs.

  2. Table shows comparison of saliva tested on ID NOW vs saliva tested using Cepheid Xpert Xpress SARS-CoV-2.

    Abbreviations in table: AN = anterior nares; OP = oropharynx; NP = nasopharynx; S = saliva; U = unknown.

  3. Data are only presented from papers in which it was possible to construct a composite ‘gold standard’ in which a positive result on any platform contributed to create a ‘composite positive (CP)’. Specificity was assumed to be 100% for all platforms/tests. This differs from the method presented in some of the papers incorporated into this table.

Key resources table
Reagent type
(species) or resource
DesignationSource or referenceIdentifiersAdditional
information
Commercial assay, kitID NOW SARS-CoV-2 reagentsAbbottCat. # 190–000 for COVID reagents
Cat. # 190–080 for COVID controls
https://www.fda.gov/media/136525/download
Commercial assay, kitSARS-CoV-2 reagentsHologicCat. # PRD-06420 for the COVID reagents and Cat. # 303014 for the assay fluids reagentshttps://www.hologic.com/sites/default/files/2020-09/AW-21159-001_004_01.pdf
Appendix 1—table 1
Lephart et al., 2020 Confusion matrix.
ID NOW
PositiveNegative
Cepheid
XpertXpress
Positive1215
Negative060
Appendix 1—table 2
Basu et al., 2020 Confusion matrix.
ID NOW
PositiveNegative
Cepheid Xpert XpressPositive1714
Negative169
Appendix 1—table 3
Cradic et al., 2020 Confusion matrix.
ID NOW
PositiveNegative
Diasorin SimplexaPositive121
Negative0169
Appendix 1—table 4
Harrington et al., 2020 Confusion matrix.
ID NOW
PositiveNegative
Abbott m2000Positive13947
Negative2336
Appendix 1—table 5
Jin et al., 2020 Confusion matrix.
ID NOW
PositiveNegative
Roche COBASPositive42
Negative046
Appendix 1—table 6
Mitchell and George, 2020 Confusion matrix.
ID NOW
PositiveNegative
RT–PCR – either CDC or New York EUAPositive3313
Negative015
Appendix 1—table 7
Moore et al., 2020 Confusion matrix.
ID NOW
PositiveNegative
Abbott m2000Positive9431
 Negative073
Appendix 1—table 8
Rhoads et al., 2020 Confusion matrix.
ID NOW
PositiveNegative
Diasorin SimplexaPositive906
Negative00
Appendix 1—table 9
Smithgall et al., 2020 Confusion matrix.
ID NOW
PositiveNegative
Roche COBASPositive6523
Negative025
Appendix 1—table 10
Thwe and Ren, 2020 Confusion matrix.
ID NOW
PositiveNegative
RT–PCRPositive87
Negative0167
Appendix 1—table 11
Zhen et al., 2020b Confusion matrix.
ID NOW
PositiveNegative
Hologic Panther FusionPositive507
Negative050
Appendix 1—table 12
Comer and Fisk, 2020 Confusion matrix.
ID NOW
PositiveNegative
Becton Dickinson BD MAXPositive01
Negative0116
Appendix 1—table 13
Ghofrani et al., 2020 Confusion matrix.
ID NOW
PositiveNegative
RT–PCRPositive161
Negative195
Appendix 1—table 14
SoRelle et al., 2020 Confusion matrix.
ID NOW
PositiveNegative
Cepheid Xpert XpressPositive230
Negative035

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