Sensitivity of ID NOW and RT–PCR for detection of SARS-CoV-2 in an ambulatory population
- Urgent Care, The Everett Clinic-Part of Optum, United States
- Department of Pathology, James J Peters VA Medical Center, United States
- Office of Research and Development Veterans Health Administration, United States
- Department of Pathology University of Maryland School of Medicine, United States
Figures
Figure 1
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.
Figure 2
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%.
Figure 3
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.
Figure 4
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 | ||||
|---|---|---|---|---|
| NEG | POS | Total | ||
| ID NOW result | NEG | 942 | 2 | 944 |
| POS | 0 | 21 | 21 | |
| Invalid | 9 | 0 | 9 | |
| Total | 951 | 23 | 974 | |
| Negative agreement | 100.00% (82–100%) | |||
| Positive agreement | 91.30% (70–98%) | |||
Table 2
Studies included in the systematic review.
| Study | Site | ID NOW sampling device | Residual sample tested? | ID NOW sample dry? | Timing of ID NOW test | Patient characteristics | Patient selection bias? | Index test bias? | Flow and timing bias | N (positive rate) | RT–PCR | Abbott ID now |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Positive/CP % (95% CI) | Positive/CP % (95% CI) | |||||||||||
| Lephart et al., 2020 | AN | Foam | No | Yes | Up to 24 at 4°C | Convenience Hosp. and ED | Unclear | Unclear | Unclear | 88 (31%) | 27/27 91% (85–100%) | 12/27 44% (26–64%) |
| Basu et al., 2020 | AN | Foam | No | Yes | Up to 24 at 4°C | Convenience Hosp. and ED | Unclear | Unclear | Unclear | 101 (31%) | 31/32 97% (82–100%) | 18/32 56% (38–73%) |
| Cradic et al., 2020 | AN | Foam | No | Yes | Unclear | Symptomatic | Low | Unclear | Unclear | 182 (7.1%) | 13/13 100% (72–100%) | 12/13 92% (62–100%) |
| Harrington et al., 2020 | AN | Foam | No | Yes | Unclear | Clinic, ED | Low | Unclear | Unclear | 524 (36%) | 186/188 99% (96–100%) | 141/188 75% (68–81%) |
| Jin et al., 2020† | U | U | No | Yes | Unclear | U | Unclear | Unclear | Unclear | 52 (12%) | 6/6 100% (52–100%) | 4/6 67% (24–94%) |
| Mitchell and George, 2020 | NP | U | Yes | No | Unclear | U | High | High | Unclear | 61 (75%) | 46/46 100% (90–100%) | 33/46 72% (56–84%) |
| Moore et al., 2020 | NP | U | No | No | Unclear | Symptomatic | High | Unclear | Unclear | 200 (64%) | 127/127 100% (96–100%) | 94/127 74% (65–81%) |
| Rhoads et al., 2020 | AN, NP | U | Yes | No | Unclear | PCR+ | High | Unclear | Unclear | 96 (100%) | 96/96 100% (95–100%) | 90/96 94% (86–97%) |
| Smithgall et al., 2020 | NP | U | Yes | No | Up to 48 hr at 4°C | Selected | High | Unclear | Unclear | 113 (80%) | 89/90 99% (94–100%) | 65/88 74% (64–82%) |
| Thwe and Ren, 2020 | NP | U | No | Yes | ~2 hr | Symptomatic Hosp. and ED | High | Unclear | Unclear | 129 (7.7%) | 15/15 100% (75–100%) | 8/15 53% (27–78%) |
| Zhen et al., 2020b | NP | Many | Yes (most) | No | Up to 72 hr at 4°C | Symptomatic | Unclear | Unclear | Unclear | 107 (54%) | 57/58 98% (90–100%) | 50/57 88 (76–95) |
| Comer and Fisk, 2020 | AN | Foam | No | Yes | 15 m | U | High | Low | Low | 117 (0.9%) | 1/1 100% (5–100%) | 0/1 0% (0–95%) |
| Ghofrani et al., 2020 | AN | Many | No | Yes | Unclear | Mostly symptomatic convenience | High | Unclear | High | 113 (16%) | 17/18 94% (71–99%) | 17/18 94% (71–99%) |
| SoRelle et al., 2020‡ | S | Tube | No | No | Unclear | U | Unclear | Low | Low | 59 (39%) | 23/23 100% (82–100%) | 18/23 78% (56–92%) |
| Tu (this study) | AN | Foam | No | Yes | 15 m | symptomatic and asymptomatic | Low | Low | Low | 974 (2.4%) | 23/23 100% (82–100%) | 21/23 91% (70–98%) |
-
*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.
-
‡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.
-
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 | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Commercial assay, kit | ID NOW SARS-CoV-2 reagents | Abbott | Cat. # 190–000 for COVID reagents Cat. # 190–080 for COVID controls | https://www.fda.gov/media/136525/download |
| Commercial assay, kit | SARS-CoV-2 reagents | Hologic | Cat. # PRD-06420 for the COVID reagents and Cat. # 303014 for the assay fluids reagents | https://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 | |||
|---|---|---|---|
| Positive | Negative | ||
| Cepheid XpertXpress | Positive | 12 | 15 |
| Negative | 0 | 60 | |
Appendix 1—table 2
Basu et al., 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| Cepheid Xpert Xpress | Positive | 17 | 14 |
| Negative | 1 | 69 | |
Appendix 1—table 3
Cradic et al., 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| Diasorin Simplexa | Positive | 12 | 1 |
| Negative | 0 | 169 | |
Appendix 1—table 4
Harrington et al., 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| Abbott m2000 | Positive | 139 | 47 |
| Negative | 2 | 336 | |
Appendix 1—table 5
Jin et al., 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| Roche COBAS | Positive | 4 | 2 |
| Negative | 0 | 46 | |
Appendix 1—table 6
Mitchell and George, 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| RT–PCR – either CDC or New York EUA | Positive | 33 | 13 |
| Negative | 0 | 15 | |
Appendix 1—table 7
Moore et al., 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| Abbott m2000 | Positive | 94 | 31 |
| Negative | 0 | 73 | |
Appendix 1—table 8
Rhoads et al., 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| Diasorin Simplexa | Positive | 90 | 6 |
| Negative | 0 | 0 | |
Appendix 1—table 9
Smithgall et al., 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| Roche COBAS | Positive | 65 | 23 |
| Negative | 0 | 25 | |
Appendix 1—table 10
Thwe and Ren, 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| RT–PCR | Positive | 8 | 7 |
| Negative | 0 | 167 | |
Appendix 1—table 11
Zhen et al., 2020b Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| Hologic Panther Fusion | Positive | 50 | 7 |
| Negative | 0 | 50 | |
Appendix 1—table 12
Comer and Fisk, 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| Becton Dickinson BD MAX | Positive | 0 | 1 |
| Negative | 0 | 116 | |
Appendix 1—table 13
Ghofrani et al., 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| RT–PCR | Positive | 16 | 1 |
| Negative | 1 | 95 | |
Appendix 1—table 14
SoRelle et al., 2020 Confusion matrix.
| ID NOW | |||
|---|---|---|---|
| Positive | Negative | ||
| Cepheid Xpert Xpress | Positive | 23 | 0 |
| Negative | 0 | 35 | |
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Sensitivity of ID NOW and RT–PCR for detection of SARS-CoV-2 in an ambulatory population
eLife 10:e65726.
https://doi.org/10.7554/eLife.65726
