Evaluation of Dry Swab Direct RTPCR Method for Detection of SARS-Cov2 in a Tertiary Care Hospital
Authors/Creators
- 1. Associate Professor, Department of Pathology, Panimalar Medical College Hospital & Research Institute
- 2. Assistant Professor, Department of Pathology, Panimalar Medical College Hospital & Research Institute
- 3. Assistant Professor, Department of Microbiology, Panimalar Medical College Hospital & Research Institute
- 4. Professor, Department of Microbiology, Panimalar Medical College Hospital & Research Institute
- 5. Professor, Department of Biochemistry and Molecular Virology Panimalar Medical College Hospital & Research Institute
- 6. Tutor, Department of Microbiology, Panimalar Medical College Hospital & Research Institute
Description
Introduction: The ongoing SARS-CoV-2 pandemic has led to shortages of laboratory-based testing kits and reagents worldwide and manufacturers have developed simple testing strategies for easy use and convenience. The Dry Swab-based Direct RT-PCR is a simple and quick method for SARS-COV2 detection which has been developed by Meril Diagnostics Pvt. Ltd. This method is a simple variation of the existing RT-PCR testing, making the extraction step easy and can expedite the testing capacity and reduces the turnaround time. Objectives: The aim of this study was to assess the diagnostic accuracy (sensitivity, specificity, positive predictive value and negative predictive value) of Meril extraction-free dry swab kit and compare its diagnostic performance with the usual RTPCR testing aided with extraction process using swabs collected in viral transport medium. Materials and Methods: This is a cross sectional (facility-based study) conducted at a tertiary care hospital in South India. The nasopharyngeal or oropharyngeal dry swab was taken under aseptic precautions, kept in a sterile collection tube and sent to the laboratory for further testing. The dry swab was processed as per the manufacturer’s instructions and proceeded with RTPCR testing as per the PCR kit protocol. The same individual’s VTM swab samples were also processed using the extraction kit and then proceeded with RTPCR protocol and the comparisons between the two test methods were done. Results: Among the 133 patients who were included in the study, RT-PCR testing with conventional extraction was positive for 19 individuals, with a prevalence of 14.29% and negative for 114 patients (85.71%). The Meril extraction free dry swab kit test was positive for 21 patients (15.79%) and negative for individuals112 (84.21%). The comparison analysis shows a Sensitivity of 94.7%, Specificity 97.4%Positive Predictive Value 85.7% And Negative Predictive Value 99.1%. Area under the Curve (AUC) indicates that the dry swab kit was able to distinguish between true positive and true negative very efficiently. Conclusion: Nasopharyngeal and oropharyngeal swabs stored in dry collection tubes area robust and inexpensive method for SARS-CoV-2 testing. The efficiency is almost equal to RTPCR testing. It can be deployed for large scale testing considering the advantages.
Abstract (English)
Introduction: The ongoing SARS-CoV-2 pandemic has led to shortages of laboratory-based testing kits and reagents worldwide and manufacturers have developed simple testing strategies for easy use and convenience. The Dry Swab-based Direct RT-PCR is a simple and quick method for SARS-COV2 detection which has been developed by Meril Diagnostics Pvt. Ltd. This method is a simple variation of the existing RT-PCR testing, making the extraction step easy and can expedite the testing capacity and reduces the turnaround time. Objectives: The aim of this study was to assess the diagnostic accuracy (sensitivity, specificity, positive predictive value and negative predictive value) of Meril extraction-free dry swab kit and compare its diagnostic performance with the usual RTPCR testing aided with extraction process using swabs collected in viral transport medium. Materials and Methods: This is a cross sectional (facility-based study) conducted at a tertiary care hospital in South India. The nasopharyngeal or oropharyngeal dry swab was taken under aseptic precautions, kept in a sterile collection tube and sent to the laboratory for further testing. The dry swab was processed as per the manufacturer’s instructions and proceeded with RTPCR testing as per the PCR kit protocol. The same individual’s VTM swab samples were also processed using the extraction kit and then proceeded with RTPCR protocol and the comparisons between the two test methods were done. Results: Among the 133 patients who were included in the study, RT-PCR testing with conventional extraction was positive for 19 individuals, with a prevalence of 14.29% and negative for 114 patients (85.71%). The Meril extraction free dry swab kit test was positive for 21 patients (15.79%) and negative for individuals112 (84.21%). The comparison analysis shows a Sensitivity of 94.7%, Specificity 97.4%Positive Predictive Value 85.7% And Negative Predictive Value 99.1%. Area under the Curve (AUC) indicates that the dry swab kit was able to distinguish between true positive and true negative very efficiently. Conclusion: Nasopharyngeal and oropharyngeal swabs stored in dry collection tubes area robust and inexpensive method for SARS-CoV-2 testing. The efficiency is almost equal to RTPCR testing. It can be deployed for large scale testing considering the advantages.
Files
IJPCR,Vol15,Issue9,Article46.pdf
Files
(416.1 kB)
| Name | Size | Download all |
|---|---|---|
|
md5:a2c87181fe2832e7b32c12ab317ed0b9
|
416.1 kB | Preview Download |
Additional details
Dates
- Accepted
-
2023-07-30
Software
- Repository URL
- https://impactfactor.org/PDF/IJPCR/15/IJPCR,Vol15,Issue9,Article46.pdf
- Development Status
- Active
References
- 1. Bijal A Parikh, Meghan A Wallace, Broc T McCune, Carey-Ann D Burnham, Neil W Anderson, The Effects of "Dry Swab" Incubation on SARS-CoV-2 Molecular Testing, The Journal of Applied Laboratory Medicine, Volume 6, Issue 5, September 2021, Pages 1281–1286. 2. World Health Organization COVID19 dashboard – Total number of cases and deaths due to COVID19 in India. https://covid19.who.int/region/searo/country/in.3. Perchetti GA, Huang ML, Peddu V, Jerome KR, Greninger AL. Stability of SARS-CoV-2 in Phosphate-Buffered Saline for Molecular Detection. J Clin Microbiol. 2020;58(8): e01094-20. Published 2020 Jul 23. 4. Validation of a novel molecular assay to the diagnostic of COVID-19 based on real time PCR with high resolution melting. Ferreira BIdS, da Silva-Gomes NL, Coelho WLdCNP, da Costa VD, Carneiro VCdS, et al. (2021) Validation of a novel molecular assay to the diagnostic of COVID-19 based on real time PCR with high resolution melting. PLOS ONE 16(11): e0260087. 5. Dry Swab Method of sample collection for SARS-CoV2 testing can be used for culturing virus. Sushma Ram, M.halib Enayathullah, Yash Parekh, Karthik Bharadwaj Tallapaka, Rakesh K Mishra, Kiran Kumar BokarabioRxiv 2021.03.23.436593. 6. Meril manufactures commercial kits for CCMB's Dry Swab Direct RT-PCR tests. https://www.ccmb.res.in/presscovrg/pressnote_0 2_06_2021.pdf. 7. Rogers AA, Baumann RE, Borillo GA, et al. Evaluation of transport media and specimen transport conditions for the detection of SARSCoV-2 by use of real-time reverse transcriptionPCR. J Clin Microbiol 2020;58. 8. Interim Guidelines for Collecting and Handling of Clinical Specimens for COVID-19 Testing.https://www.cdc.gov/coronavirus/2019- ncov/lab/guidelines-clinical-specimens.html. 9. Meril COVID 19 One Step RTPCR kit: https://www.merillife.com/medicaldevices/diagnostics/covid-19/molecularbiology/covid-19-one-step-rt-pcr-kit. 10. Pathodetect COVID 19 Qualitative RT _ PCR kit insert https://mylabdiscoverysolutions.com/clinical/inf ections/covid-19/ 11. Gokulan, C.G., Kiran, U., Kuncha, S.K. et al. Temporal stability and detection sensitivity of the dry swab-based diagnosis of SARS-CoV-2. J Biosci 46, 95 (2021). 12. Dhakad MS, Gogoi S, Kumari A, Singh AK, Jais MB, Prakash A, Pangtey G, Kaur R. Comparative evaluation of cost-effective extraction free molecular technique for detection of SARSCoV-2 with reference to standard VTM based RT-qPCR method. Iran J Microbiol. 2021 Dec;13(6):748-756. 13. Alcoba-Florez J, Gil-Campesino H, Artola DG, González-Montelongo R, Valenzuela-Fernández A, Ciuffreda L, Flores C. Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection. Int J Infect Dis. 2020 Oct; 99:190-192.