| Literature DB >> 35566591 |
Alexander Domnich1, Andrea Orsi1,2, Carlo-Simone Trombetta2, Elisabetta Costa2, Giulia Guarona1, Miriana Lucente1, Valentina Ricucci1, Bianca Bruzzone1, Giancarlo Icardi1,2.
Abstract
Accurate and rapid molecular diagnosis of COVID-19 is a crucial step to tackle the ongoing pandemic. The primary objective of this study was to estimate the real-world performance of the novel RT-PCR STANDARD M10 SARS-CoV-2 assay in a large number of nasopharyngeal (NP) specimens eluted in universal transport medium. The secondary objective was to evaluate the compatibility of this kit in testing NP samples eluted in an inactivated transport medium (essential for point-of-care testing) and lower respiratory tract (LRT) specimens, which are commonly collected in critical care. A total of 591 samples were analyzed. Compared with the standard extraction-based RT-PCR Allplex 2019-nCoV (time-to-result of 270 min), the sensitivities of the STANDARD M10 were 100% (95% CI: 98.1-100%), 95.5% (95% CI: 91.7-97.6%), and 99.5% (95% CI: 97.2-99.9%) for ≥1 gene, the ORF1ab gene, and the E gene, respectively, while the specificity was 100% (95% CI: 98.7-100%). The diagnostic accuracy was 100% in testing both NP samples eluted in an inactivated transport medium and LRT specimens. STANDARD M10 reliably detects SARS-CoV-2 in 60 min, may be used as a POC tool, and is suitable for testing LRT specimens in the critical care setting.Entities:
Keywords: COVID-19; RT-PCR; SARS-CoV-2; critical care; diagnostic accuracy; point-of-care testing
Year: 2022 PMID: 35566591 PMCID: PMC9105343 DOI: 10.3390/jcm11092465
Source DB: PubMed Journal: J Clin Med ISSN: 2077-0383 Impact factor: 4.964
Raw data on target detections by gene target and assay (n = 500).
| Sample Type | Gene Target | Allplex 2019-nCoV Assay, % ( | STANDARD M10 Assay, % ( | ||
|---|---|---|---|---|---|
| Detected | Not Detected | Detected | Not Detected | ||
| Positive | N | 99.5 (199) | 0.5 (1) | – | – |
| RdRp | 90.0 (180) | 10.0 (20) | – | – | |
| E | 97.0 (194) | 3.0 (6) | 99.5 (199) | 0.5 (1) | |
| ORF1ab | – | – | 95.5 (191) | 4.5 (9) | |
| ≥1 | 100 (200) | 0 (0) | 100 (200) | 0 (0) | |
| Negative | N | 0 (0) | 100 (300) | – | – |
| RdRp | 0 (0) | 100 (300) | – | – | |
| E | 0 (0) | 100 (300) | 0 (0) | 100 (300) | |
| ORF1ab | – | – | 0 (0) | 100 (300) | |
| ≥1 | 0 (0) | 100 (300) | 0 (0) | 100 (300) | |
Characteristics of samples with “Presumptive positive” result label in the STANDARD M10 assay (n = 9).
| Sample | Ct Values in the Allplex 2019-nCoV Assay | Ct Values in the STANDARD M10 Assay | |||
|---|---|---|---|---|---|
| N | RdRp | E | ORF1ab | E | |
| 1 | 27 | 29 | 27 | ND | 33 |
| 2 | 32 | 34 | 31 | ND | 30 |
| 3 | 38 | ND | 38 | ND | 32 |
| 4 | 37 | ND | 38 | ND | 32 |
| 5 | 39 | ND | 36 | ND | 29 |
| 6 | 29 | ND | 30 | ND | 28 |
| 7 | 33 | ND | 34 | ND | 36 |
| 8 | 37 | ND | 35 | ND | 33 |
| 9 | 34 | 40 | 32 | ND | 21 |
ND—not detected.
Relative diagnostic accuracy of the STANDARD M10 assay by parameter and gene target (n = 500).
| Parameter | ORF1ab Gene | E Gene | ≥1 Gene |
|---|---|---|---|
| Accuracy, % (95% CI) | 98.2 (96.6–99.1) | 99.8 (98.9–100) | 100 (99.2–100) |
| Sensitivity, % (95% CI) | 95.5 (91.7–97.6) | 99.5 (97.2–99.9) | 100 (98.1–100) |
| Specificity, % (95% CI) | 100 (98.7–100) | 100 (98.7–100) | 100 (98.7–100) |
| Cohen’s | 0.962 (0.875–1) | 0.996 (0.908–1) | 1 (0.912–1) |
Figure 1Negative predictive value (NPV) curves of the STANDARD M10 assay, by hypothetical prevalence and gene target.