| Literature DB >> 34863057 |
Chet R Voelker1, Anna R Ochoa2, La'Quita Armstrong-Spenrath3, Lisa Lott4, Jennifer S McDaniel5, August N Blackburn4, Lauren E Cornell5, Rachel Mahoney2, Susana N Asin3.
Abstract
We evaluated the sensitivity and specificity of the Biomeme Franklin™ three9 Real-Time PCR Thermocycler and Biomeme SARS-CoV-2 Go-Strips in the detection of SARS-CoV-2. The Biomeme Franklin™ three9 platform is a portable, battery-operated system that could be used in remote settings. We assessed performance of the Biomeme SARS-CoV-2 detection system at a wide range of viral concentrations, examined cross-reactivity of the SARS-CoV-2 Go-Strips against several near-neighbor respiratory pathogens, and evaluated agreement against the BioFire® Respiratory Panel 2.1 in four clinical sample types. Our data indicate the Biomeme Go-Strips can reliably detect SARS-CoV-2 at a concentration of 4.2 × 103 copies/mL. No cross reactivity of the Go-Strips targets was detected against any of the tested near-neighbor respiratory pathogens. Cohen's kappa statistics ranged from 0.68 to 0.92 between results from the Biomeme SARS-CoV-2 Go-Strips and the BioFire® Respiratory Panel 2.1 in all the different sample types. Compared to the BioFire® Respiratory Panel 2.1, the Biomeme SARS-CoV-2 Go-Strips demonstrated statistically significantly lower sensitivity in 3 out of 5 sample types. Overall, our study demonstrates the Biomeme Franklin™ three9 used with the SARS-CoV-2 Go-Strips is an effective system for the detection of SARS-CoV-2 that could potentially be used in a remote or austere environment.Entities:
Keywords: Austere environment; COVID19; Diagnostic testing; Polymerase chain reaction; SARS-CoV-2
Mesh:
Year: 2021 PMID: 34863057 PMCID: PMC8613008 DOI: 10.1016/j.jcv.2021.105046
Source DB: PubMed Journal: J Clin Virol ISSN: 1386-6532 Impact factor: 3.168
Near-Neighbor Pathogen Panel Tested on Biomeme SARS-CoV-2 Go-Strips and BioFire® RP2.1.
| Near-Neighbor Organism | Reference# | Biomeme SARS-CoV-2 Go-Strip | BioFire RP2.1 |
|---|---|---|---|
| Coronavirus 229E | VR-740D | Negative | Detected |
| Coronavirus OC43 | VR-1558D | Negative | Detected |
| Coronavirus NL63 | VR-3263SD | Negative | Detected |
| Coronavirus HKU1 | VR-3262SD | Negative | Detected |
| Parainfluenza 2 | VR-92D | Negative | Detected |
| Parainfluenza 3 | VR-93D | Negative | Detected |
| Parainfluenza 4 | VR-1377D | Negative | Detected |
| 9797DQ | Negative | Detected | |
| 15311DQ | Negative | Detected | |
| 15531D | Negative | Detected | |
| Human Rhinovirus 17 | VR-1663D | Negative | Detected |
| MERS-CoV | VR-3248SD | Negative | N/A |
| SARS-CoV-1 | VR-3280SD | Negative | N/A |
| Enterovirus | VR-1775DQ | Negative | Detected |
| Human metapneumovirus | VR-3250SD | Negative | Detected |
| Influenza A | VR-1736D | Negative | Detected |
| Influenza B | VR-1813 | Negative | Detected |
| Respiratory Syncytial virus | VR-1580DQ | Negative | Detected |
| VR-1360D | Negative | Detected |
Organisms not included on the BioFire® Respiratory Panel 2.1.
Dilution Series of Heat-Inactivated SARS-CoV-2 Tested on Biomeme SARS-CoV-2 Go-Strips.
| Dilution | Copies/mL | Biomeme Go-Strips | Biomeme Go Strips |
|---|---|---|---|
| 1 × 10−1 | 42,000,000 | 6/6 (24.2 ± 5.2) | 6/6 (23.7 ± 0.3) |
| 1 × 10−2 | 4,200,000 | 6/6 (28.0 ± 0.8) | 6/6 (26.8 ± 0.4) |
| 1 × 10−3 | 420,000 | 6/6 (29.8 ± 0.3) | 6/6 (29.3 ± 0.4) |
| 1 × 10−4 | 42,000 | 6/6 (33.2 ± 1.6) | 6/6 (32.8 ± 0.3) |
| 1 × 10−5 | 4200 | 5/6 (37.0, 38.4, 38.5, 38.3, 37.5) | 6/6 (36.7 ± 0.9) |
| 2 × 10−5 | 2100 | 2/6 (39.8, 37.3) | 4/6 (37.7, 37.6, 36.4, 36.7) |
| 4 × 10−5 | 1050 | 3/6 (38.0, 38.5, 37.9) | 0/6 (N/A) |
| 1 × 10−6 | 420 | 1/6 (38.1) | 1/6 (36.3) |
Number of replicates that tested positive divided by total replicates tested.
Mean Ct value ± standard deviation where all replicates tested positive or individual Ct values.
Clinical Evaluation of Biomeme SARS-CoV-2 Go-Strips with BioFire® RP2.1 as Reference Standard.
| Sample Type | Detected BioFire/ Biomeme | Detected BioFire Only | Detected Biomeme Only | Not Detected BioFire/ Biomeme | Kappa | McNemar test p-value | PPA | NPA |
|---|---|---|---|---|---|---|---|---|
| Nasal Swab | 20 | 3 | 0 | 128 | 0.919 [0.828,1.01], | 0.2482 | 0.87 [0.66, 0.97] | 1.00 [0.97, 1.00] |
| NP saline | 23 | 8 | 0 | 114 | 0.819 [0.697,0.941], | 0.0133 | 0.74 [0.55, 0.88] | 1.00 [0.97, 1.00] |
| NP VTM | 20 | 7 | 1 | 86 | 0.790 [0.649,0.930], | 0.0771 | 0.74 [0.54, 0.89] | 0.99 [0.94, 1.00] |
| Oral Swab | 21 | 11 | 0 | 120 | 0.751 [0.609,0.893], | 0.002569 | 0.66 [0.47, 0.81] | 1.00 [0.97, 1.00] |
| Saliva | 19 | 12 | 1 | 82 | 0.676 [0.510,0.842], | 0.005546 | 0.61 [0.42, 0.78] | 0.99 [0.93, 1.00] |
Positive percent agreement.
Negative percent agreement.
Comparison of Biomeme SARS-CoV-2 Go-Strips with Biomeme SARS-CoV-2 Go-Plate.
| Sample Type | Detected Go-Strip/ Go-Plate | Detected Go-Plate Only | Detected Go-Strip Only | Not Detected Go-Strip/ Go-Plate | Kappa | McNemar test p-value | PPA | NPA |
|---|---|---|---|---|---|---|---|---|
| Nasal Swab | 19 | 0 | 1 | 129 | 0.971 [0.913,1.03], | 1 | 1.00 [0.82, 1.00] | 1.00 [0.96, 1.00] |
| NP saline | 22 | 0 | 1 | 122 | 0.974 [0.922,1.025], | 1 | 1.00 [0.85, 1.00] | 0.99 [0.96, 1.00] |
| NP VTM | 20 | 0 | 1 | 67 | 0.968 [0.906,1.031], | 1 | 1.00 [0.83, 1.00] | 0.99 [0.92, 1.00] |
| Oral Swab | 19 | 3 | 2 | 125 | 0.864 [0.747,0.981], | 1 | 0.86 [0.65, 0.97] | 0.98 [0.94, 1.00] |
| Saliva | 17 | 0 | 3 | 91 | 0.903 [0.794,1.011], | 0.2482 | 1.00 [0.80, 1.00] | 0.97 [0.91, 0.99] |
Positive percent agreement.
Negative percent agreement.