Evaluation of STANDARDTM M10 SARS-CoV-2, a Novel Cartridge-Based Real-Time PCR Assay for the Rapid Identification of Severe Acute Respiratory Syndrome Coronavirus 2
Abstract
:1. Introduction
2. Materials and Methods
2.1. Specimen Collection and Storage
2.2. Cepheid Xpert Xpress SARS-CoV-2 Assay
2.3. STANDARD M10 SARS-CoV-2 Assay
2.4. Limit of Detection (LoD) Calculation on Different SARS-CoV-2 Variants
3. Results
3.1. Comparative Analysis STANDARDTM M10 SARS-CoV-2 vs. Xpert® Xpress SARS-CoV-2
3.2. Analytical Sensitivity on Different Variants
4. Discussion
- Similarity—both tests are encapsulated in disposable cartridges that allow for the extraction of viral RNA and the subsequent amplification and identification by RT-PCR without any operator intervention other than loading the sample into the cartridge. This ensures operator safety and minimizes the possibility of cross-contamination between samples. Both tests are performed using modular instruments: STANDARDTM M10 in the case of STANDARDTM SARS-CoV-2 and GeneXpert in the case of Xpert Xpress SARS-CoV-2. Both instruments are characterized by random access and continuous loading. Responses are rapid (less than 60 min) and allow the clinician to make the best decisions for patient management.
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Chen, N.; Zhou, M.; Dong, X.; Qu, J.; Gong, F.; Han, Y.; Qiu, Y.; Wang, J.; Liu, Y.; Wei, Y.; et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. Lancet 2020, 395, 507–513. [Google Scholar] [CrossRef] [Green Version]
- Zhu, N.; Zhang, D.; Wang, W.; Li, X.; Yang, B.; Song, J.; Zhao, X.; Huang, B.; Shi, W.; Lu, R.; et al. China Novel Coronavirus Investigating and Research Team A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med. 2020, 382, 727–733. [Google Scholar] [CrossRef] [PubMed]
- WHO Coronavirus (COVID-19) Dashboard. Available online: https://covid19.who.int/ (accessed on 28 September 2022).
- Sun, G.; Xue, L.; He, Q.; Zhao, Y.; Xu, W.; Wang, Z. Structural insights into SARS-CoV-2 infection and therapeutics development. Stem Cell Res. 2021, 52, 102219. [Google Scholar] [CrossRef] [PubMed]
- Letko, M.; Marzi, A.; Munster, V. Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses. Nat. Microbiol. 2020, 5, 562–569. [Google Scholar] [CrossRef] [Green Version]
- Lan, J.; Ge, J.; Yu, J.; Shan, S.; Zhou, H.; Fan, S.; Zhang, Q.; Shi, X.; Wang, Q.; Zhang, L.; et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 2021, 581, 215–220. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Duchene, S.; Featherstone, L.; Haritopoulou-Sinanidou, M.; Rambaut, A.; Lemey, P.; Baele, G. Temporal signal and the phylodynamic threshold of SARS-CoV-2. Virus Evol. 2021, 6, veaa061. [Google Scholar] [CrossRef]
- Martin, M.A.; VanInsberghe, D.; Koelle, K. Insights from SARS-CoV-2 sequences. Science 2021, 371, 466–467. [Google Scholar] [CrossRef]
- Yang, Y.; Du, L. SARS-CoV-2 spike protein: A key target for eliciting persistent neutralizing antibodies. Signal Transduct. Target Ther. 2021, 6, 95. [Google Scholar] [CrossRef]
- Hirabara, S.M.; Serdan, T.D.A.; Gorjao, R.; Masi, L.N.; Pithon-Curi, T.C.; Covas, D.T.; Curi, R.; Durigon, E.L. SARS-COV-2 Variants: Differences and potential of immune evasion. Front. Cell Infect. Microbiol. 2022, 11, 781429. [Google Scholar] [CrossRef]
- Boehm, E.; Kronig, I.; Neher, R.A.; Eckerle, I.; Vetter, P.; Kaiser, L.; Geneva Centre for Emerging Viral Diseases. Novel SARS-CoV-2 variants: The pandemics within the pandemic. Clin. Microbiol. Infect. 2021, 27, 1109–1117. [Google Scholar] [CrossRef]
- Fan, L.Q.; Hu, X.Y.; Chen, Y.Y.; Peng, X.L.; Fu, Y.H.; Zheng, Y.P.; Yu, J.M.; He, J.S. Biological significance of the genomic variation and structural dynamics of SARS-CoV-2 B.1.617. Front. Microbiol. 2021, 12, 750725. [Google Scholar] [CrossRef] [PubMed]
- Tian, D.; Sun, Y.; Xu, H.; Ye, Q. The emergence and epidemic characteristics of the highly mutated SARS-CoV-2 Omicron variant. J. Med. Virol. 2022. online ahead of print. [Google Scholar] [CrossRef] [PubMed]
- Zannoli, S.; Dirani, G.; Taddei, F.; Gatti, G.; Poggianti, I.; Denicolò, A.; Arfilli, V.; Manera, M.; Mancini, M.; Battisti, A.; et al. A deletion in the N gene may cause diagnostic escape in SARS-CoV-2 samples. Diagn. Microbiol. Infect Dis. 2022, 102, 115540. [Google Scholar] [CrossRef] [PubMed]
- Bonacci, P.G.; Bivona, D.A.; Bongiorno, D.; Stracquadanio, S.; Massimino, M.; Bonomo, C.; Stracuzzi, A.; Pennisi, P.; Musso, N.; Stefani, S. Low represented mutation clustering in SARS-CoV-2 B.1.1.7 sublineage group with synonymous mutations in the E gene. Diagnostics 2021, 11, 2286. [Google Scholar] [CrossRef]
- Gualano, G.; Musso, M.; Mosti, S.; Mencarini, P.; Mastrobattista, A.; Pareo, C.; Zaccarelli, M.; Migliorisi, P.; Vittozzi, P.; Zumla, A.; et al. Usefulness of bronchoalveolar lavage in the management of patients presenting with lung infiltrates and suspect COVID-19-associated pneumonia: A case report. Int. J. Infect. Dis. 2020, 97, 174–176. [Google Scholar] [CrossRef]
- Saluzzo, F.; Mantegani, P.; Poletti de Chaurand, V.; Cugnata, F.; Rovere-Querini, P.; Cilla, M.; Erba, P.P.; Racca, S.; Tresoldi, C.; Uberti-Foppa, C.; et al. Saliva molecular testing for SARS-CoV-2: Simplifying the diagnosis without losing accuracy. Eur. Respir. J. 2021, 58, 2102099. [Google Scholar] [CrossRef]
- Craney, A.R.; Velu, P.D.; Satlin, M.J.; Fauntleroy, K.A.; Callan, K.; Robertson, A.; La Spina, M.; Lei, B.; Chen, A.; Alston, T.; et al. Comparison of two high-throughput reverse transcription-PCR systems for the detection of Severe Acute Respiratory Syndrome Coronavirus 2. J. Clin. Microbiol. 2020, 58, e00890-20. [Google Scholar] [CrossRef]
- Loeffelholz, M.J.; Alland, D.; Butler-Wu, S.M.; Pandey, U.; Perno, C.F.; Nava, A.; Carroll, K.C.; Mostafa, H.; Davies, E.; McEwan, A.; et al. Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 test. J. Clin. Microbiol. 2020, 58, e00926-20. [Google Scholar] [CrossRef]
- Brandolini, M.; Taddei, F.; Marino, M.M.; Grumiro, L.; Scalcione, A.; Turba, M.E.; Gentilini, F.; Fantini, M.; Zannoli, S.; Dirani, G.; et al. Correlating qRT-PCR, dPCR and viral titration for the identification and quantification of SARS-CoV-2: A new approach for infection management. Viruses 2021, 13, 1022. [Google Scholar] [CrossRef]
- Landis, J.R.; Koch, G.G. The measurement of observer agreement for categorical data. Biometrics 1977, 33, 159–174. [Google Scholar] [CrossRef]
- SD Biosensor, Inc. STANDARD M10 SARS-CoV-2 Assay Package Insert v1.0; SD Biosensor Inc.: Suwon, South Korea, March 2022. [Google Scholar]
- Gómez, C.E.; Perdiguero, B.; Esteban, M. Emerging SARS-CoV-2 Variants and Impact in Global Vaccination Programs against SARS-CoV-2/COVID-19. Vaccines 2021, 9, 243. [Google Scholar] [CrossRef] [PubMed]
- Jung, C.; Kmiec, D.; Koepke, L.; Zech, F.; Jacob, T.; Sparrer, K.M.J.; Kirchhoff, F. Omicron: What makes the latest SARS-CoV-2 variant of concern so concerning? J. Virol. 2022. online ahead of print. [Google Scholar] [CrossRef] [PubMed]
- Damavandi, A.R.; Dowran, R.; Al Sharif, S.; Kashanchi, F.; Jafari, M.R. Molecular variants of SARS-CoV-2: Antigenic properties and current vaccine efficacy. Med. Microbiol. Immunol. 2022, 211, 79–103. [Google Scholar] [CrossRef] [PubMed]
- Notarte, K.I.; Guerrero-Arguero, I.; Velasco, J.V.; Ver, A.T.; Santos de Oliveira, M.H.; Catahay, J.A.; Khan, M.S.D.; Pastrana, A.; Juszczyk, G.; Torrelles, J.B.; et al. Characterization of the significant decline in humoral immune response six months post-SARS-CoV-2 mRNA vaccination: A systematic review. J. Med. Virol. 2022. online ahead of print. [Google Scholar] [CrossRef]
- Zhao, Z.; Li, H.; Wu, X.; Zhong, Y.; Zhang, K.; Zhang, Y.P.; Boerwinkle, E.; Fu, Y.X. Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol. Biol. 2004, 4, 21. [Google Scholar] [CrossRef] [Green Version]
- Dinnes, J.; Deeks, J.J.; Berhane, S.; Taylor, M.; Adriano, A.; Davenport, C.; Dittrich, S.; Emperador, D.; Takwoingi, Y.; Cunningham, J.; et al. Cochrane COVID-19 Diagnostic Test Accuracy Group. Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. Cochrane Database Syst. Rev. 2021, 3, CD013705. [Google Scholar]
- Smithgall, M.C.; Scherberkova, I.; Whittier, S.; Green, D.A. Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2. J. Clin. Virol. 2020, 128, 104428. [Google Scholar] [CrossRef]
- Fox-Lewis, S.; Fox-Lewis, A.; Harrower, J.; Chen, R.; Wang, J.; de Ligt, J.; McAuliffe, G.; Taylor, S.; Smit, E. Lack of N2-gene amplification on the Cepheid Xpert Xpress SARS-CoV-2 assay and potential novel causative mutations: A case series from Auckland, New Zealand. IDCases 2021, 25, e01233. [Google Scholar] [CrossRef]
- Varadhan, H.; Ahuja, V.; Pitman, C.; Dwyer, D.E.; NSW Health Pathology. Weak positive SARS-CoV-2 N2 gene results using the Xpress Xpert assay: The need for an alternate interpretative criteria in a low prevalence setting. Pathology 2022, 54, 116–120. [Google Scholar] [CrossRef]
- Cevik, M.; Tate, M.; Lloyd, O.; Maraolo, A.E.; Schafers, J.; Ho, A. SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: A systematic review and meta-analysis. Lancet Microbe 2020, 2, e13–e22. [Google Scholar] [CrossRef]
- Alexandersen, S.; Chamings, A.; Bhatta, T.J. SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication. Nat. Commun. 2020, 11, 6059. [Google Scholar] [CrossRef] [PubMed]
- Igarashi, E.; Tani, H.; Tamura, K.; Itamochi, M.; Shimada, T.; Saga, Y.; Inasaki, N.; Hasegawa, S.; Yazawa, S.; Sasajima, H.; et al. Viral isolation analysis of SARS-CoV-2 from clinical specimens of COVID-19 patients. J. Infect. Chemother. 2022, 28, 347–351. [Google Scholar] [CrossRef] [PubMed]
- Basile, K.; McPhie, K.; Carter, I.; Alderson, S.; Rahman, H.; Donovan, L.; Kumar, S.; Tran, T.; Ko, D.; Sivaruban, T.; et al. Cell-based culture informs infectivity and safe de-isolation assessments in patients with Coronavirus Disease 2019. Clin. Infect. Dis. 2021, 73, e2952–e2959. [Google Scholar] [CrossRef]
- Bruce, E.A.; Mills, M.G.; Sampoleo, R.; Perchetti, G.A.; Huang, M.; Despres, H.W.; Schmidt, M.M.; Roychoudhury, P.; Shirley, D.J.; Jerome, K.R.; et al. Predicting infectivity: Comparing four PCR-based assays to detect culturable SARS-CoV-2 in clinical samples. EMBO Mol. Med. 2022, 14, e15290. [Google Scholar] [CrossRef]
- Gniazdowski, V.; Morris, C.P.; Wohl, S.; Mehoke, T.; Ramakrishnan, S.; Thielen, P.; Powell, H.; Smith, B.; Armstrong, D.T.; Herrera, M.; et al. Repeated Coronavirus Disease 2019 molecular testing: Correlation of Severe Acute Respiratory Syndrome Coronavirus 2 culture with molecular assays and Cycle Thresholds. Infect. Dis. 2021, 73, e860–e869. [Google Scholar] [CrossRef] [PubMed]
- Burnett, L.; McQueen, M.J.; Jonsson, J.J.; Torricelli, F. IFCC Taskforce on Ethics. IFCC Position Paper: Report of the IFCC Taskforce on Ethics: Introduction and framework. Clin. Chem. Lab. Med. 2007, 45, 1098–1104. [Google Scholar] [CrossRef]
Characteristic | STANDARDTM M10 SARS-CoV-2 | Xpert® Xpress SARS-CoV-2 |
---|---|---|
Instrument | STANDARD M10 | GeneXpert |
Specimen used in the study 1 | NP | NP |
Test duration 2 | 60 min | 50 min |
Loading | Random access | Random access |
Genes detected | orf1Ab, E | E, N |
STANDARDTM M10 SARS-CoV-2 | ||||||
---|---|---|---|---|---|---|
Xpert® Xpress SARS-CoV-2 | Pos | Neg | Tot | Sensitivity | 97.98% | |
Pos | 97 | 2 | 99 | Specificity | 100% | |
Neg | 0 | 96 | 96 | PPV | 100% | |
Tot | 97 | 98 | 195 | NPV | 97.96% |
STANDARDTM M10 SARS-CoV-2 | Xpert® Xpress SARS-CoV-2 | ||||
---|---|---|---|---|---|
Variant/Subvariant Name | Concentration (cp/mL) | E Gene (Ct) * | Orf1ab Gene (Ct) * | E Gene (Ct) * | N2 Gene (Ct) * |
B.1.351 (BETA) | 20,000 | 30.02 | 29.70 | 31.2 | 34.9 |
10,000 | 30.88 | 30.04 | 32.5 | 36.5 | |
5000 | 31.95 | 32.53 | 32.4 | 35.4 | |
2500 | 33.56 | 34.13 | 35.1 | 38.6 | |
1250 | 32.93 | N/A | 40.4 | 39.4 | |
P.1 (GAMMA) | 20,000 | 31.28 | 31.58 | 32.9 | 36.5 |
10,000 | 31.99 | 32.50 | 33.6 | 37.6 | |
5000 | 34.27 | 33.47 | 34.1 | 38.2 | |
2500 | 33.65 | 33.75 | 39.8 | N/A | |
1250 | N/A | N/A | 39.8 | 41.8 | |
B.1.617.2 (DELTA) | 20,000 | 31.22 | 30.91 | 34 | 36.9 |
10,000 | 34.37 | 33.62 | 33.7 | 37.3 | |
5000 | 34.77 | N/A | 36 | 38.4 | |
2500 | 33.86 | 34.53 | 39.5 | 40.8 | |
1250 | 35.43 | N/A | 38.3 | 41.8 | |
B.1.617.2 AY.4.2 (DELTA PLUS) | 20,000 | 33.02 | 33.37 | 34.5 | 37.6 |
10,000 | 34.14 | N/A | 36.1 | 39.1 | |
5000 | 34.45 | N/A | 38 | 40 | |
2500 | N/A | N/A | 42.8 | 42.3 | |
1250 | N/A | N/A | N/A | N/A | |
B.1.1.7 + Δ619_624 N gene (BAGNACAVALLO) | 20,000 | 31.24 | 30.80 | 33.4 | 36.4 |
10,000 | 32.69 | 32.95 | 36 | 38 | |
5000 | 33.19 | 32.39 | 37.4 | 40.1 | |
2500 | N/A | 34.15 | 39.6 | 41.5 | |
1250 | 34.22 | 34.31 | 38.3 | 41.4 | |
B.1.1.529 (OMICRON) | 20,000 | 30.35 | 32.61 | 32 | 34.1 |
10,000 | 31.96 | 31.71 | 33.6 | 35.8 | |
5000 | 31.88 | 33.6 | 33.8 | 36 | |
2500 | 33.33 | N/A | 35.8 | 38.3 | |
1250 | 32.34 | N/A | 35.2 | 37.8 | |
AccuPlex SARS-CoV-2 Molecular Controls Kit | 400 | 32.55 | 31.96 | 34.1 | 37.2 |
200 | 32.59 | N/A | 36.7 | 40.3 | |
100 | 34.95 | N/A | 36.8 | 39.4 | |
50 | N/A | N/A | N/A | 41 | |
25 | N/A | N/A | 40.2 | 41.5 |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Grumiro, L.; Brandolini, M.; Gatti, G.; Scalcione, A.; Taddei, F.; Dirani, G.; Mancini, A.; Denicolò, A.; Manera, M.; Zannoli, S.; et al. Evaluation of STANDARDTM M10 SARS-CoV-2, a Novel Cartridge-Based Real-Time PCR Assay for the Rapid Identification of Severe Acute Respiratory Syndrome Coronavirus 2. Appl. Microbiol. 2022, 2, 873-881. https://doi.org/10.3390/applmicrobiol2040067
Grumiro L, Brandolini M, Gatti G, Scalcione A, Taddei F, Dirani G, Mancini A, Denicolò A, Manera M, Zannoli S, et al. Evaluation of STANDARDTM M10 SARS-CoV-2, a Novel Cartridge-Based Real-Time PCR Assay for the Rapid Identification of Severe Acute Respiratory Syndrome Coronavirus 2. Applied Microbiology. 2022; 2(4):873-881. https://doi.org/10.3390/applmicrobiol2040067
Chicago/Turabian StyleGrumiro, Laura, Martina Brandolini, Giulia Gatti, Agata Scalcione, Francesca Taddei, Giorgio Dirani, Andrea Mancini, Agnese Denicolò, Martina Manera, Silvia Zannoli, and et al. 2022. "Evaluation of STANDARDTM M10 SARS-CoV-2, a Novel Cartridge-Based Real-Time PCR Assay for the Rapid Identification of Severe Acute Respiratory Syndrome Coronavirus 2" Applied Microbiology 2, no. 4: 873-881. https://doi.org/10.3390/applmicrobiol2040067
APA StyleGrumiro, L., Brandolini, M., Gatti, G., Scalcione, A., Taddei, F., Dirani, G., Mancini, A., Denicolò, A., Manera, M., Zannoli, S., Marino, M. M., Morotti, M., Arfilli, V., Battisti, A., Cricca, M., & Sambri, V. (2022). Evaluation of STANDARDTM M10 SARS-CoV-2, a Novel Cartridge-Based Real-Time PCR Assay for the Rapid Identification of Severe Acute Respiratory Syndrome Coronavirus 2. Applied Microbiology, 2(4), 873-881. https://doi.org/10.3390/applmicrobiol2040067