Original Article

Comparative evaluation of cost effective extraction free molecular technique for detection of SARS-CoV-2 with reference to standard VTM based RT-qPCR method

Abstract

Background and Objectives: The entire globe is undergoing an unprecedented challenge of COVID-19. Considering the need of rapid and accurate diagnostic tests for SARS-CoV-2, this study was planned to evaluate the cost effective extraction free RT-PCR technique in comparison to the standard VTM based RT-qPCR method.
Materials and Methods: Paired swabs from nasopharynx and oropharynx were collected for SARS-CoV-2 testing, from 211 adult patients (≥18 years) in VTM and plain sterile tubes (dry swabs). These samples were processed and RT-qPCR was carried out as per standard protocols.
Results: 54.5% of the patients were females and 45.5% were males with sex ratio 1:1.19 (M: F). 38.86% were symptomatic, of which fever (86.59%), cough (79.23%) and breathlessness (46.34%) were the most common symptoms. The positivity by VTM based method and index method was 31.27% and 13.27% respectively. Of the 27 inconclusive results from index method, 37.04% were positive, 48.15% were negative by VTM based method. However, in 40 inconclusive results by VTM based method, 90% were negative and rest remained inconclusive by index method. The sensitivity and specificity of the index method were 39.39% and 85.71% respectively. The overall agreement between VTM based method and index method was 49.59% with estimated Kappa value of 0.19.
Conclusion: VTM based method showed higher sensitivity compared to the index method. The higher positivity by VTM based method, suggests that VTM based method could plausibly be a better detection method of SARS-CoV-2. Still, the index method might add value in a resource limited setups for detection of SARS-CoV-2.

1. Zhu H, Wei L, Niu P. The novel coronavirus outbreak in Wuhan, China. Glob Health Res Policy 2020; 5: 6.
2. Fan Q, Zhang W, Li B, Li DJ, Zhang J, Zhao F. Association between ABO blood group system and COVID-19 susceptibility in Wuhan. Front Cell Infect Microbiol 2020; 10: 404.
3. Kumar R, Nagpal S, Kaushik S, Mendiratta S. COVID-19 diagnostic approaches: different roads to the same destination. Virusdisease 2020; 31: 97-105.
4. Giri B, Pandey S, Shrestha R, Pokharel K, Ligler FS, Neupane BB. Review of analytical performance of COVID-19 detection methods. Anal Bioanal Chem 2021; 413: 35-48.
5. Rahbari R, Moradi N, Abdi M. rRT-PCR for SARS-CoV-2: analytical considerations. Clin Chim Acta 2021; 516: 1-7.
6. World Health Organization. World Health Organization; 2020. Laboratory Testing for Coronavirus Disease 2019 (COVID-19) in Suspected Human Cases: Interim Guidance, 2020.
7. Tang YW, Schmitz JE, Persing DH, Stratton CW. Laboratory diagnosis of COVID-19: current issues and challenges. J Clin Microbiol 2020; 58(6): e00512-20.
8. Bruce EA, Huang ML, Perchetti GA, Tighe S, Laaguiby P, Hoffman JJ, et al. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step. PLoS Biol 2020; 18(10): e3000896.
9. Kiran U, Gokulan CG, Kuncha SK, Vedagiri D, Chander BT, Sekhar AV, et al. Easing diagnosis and pushing the detection limits of SARS-CoV-2. Biol Methods Protoc 2020; 5(1): bpaa017.
10. Badawi A, Ryoo SG. Prevalence of comorbidities in the Middle East respiratory syndrome coronavirus (MERS-CoV): a systematic review and meta-analysis. Int J Infect Dis 2016; 49: 129-133.
11. Channappanavar R, Fett C, Mack M, Ten Eyck PP, Meyerholz DK, Perlman S. Sex-based differences in susceptibility to severe acute respiratory syndrome coronavirus infection. J Immunol 2017; 198: 4046-4053.
12. Chen N, Zhou M, Dong X, Qu J, Gong F, Han 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.
13. Jiang F, Deng L, Zhang L, Cai Y, Cheung CW, Xia Z. Review of the clinical characteristics of coronavirus disease 2019 (COVID-19). J Gen Intern Med 2020; 35: 1545-1549.
14. Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. N Engl J Med 2020; 382: 1199-1207.
15. Zhang JJ, Dong X, Cao YY, Yuan YD, Yang YB, Yan YQ, et al. Clinical characteristics of 140 patients infected by SARS-CoV-2 in Wuhan, China. Allergy 2020; 57: 1730-1741.
16. Jin JM, Bai P, He W, Wu F, Liu XF, Han DM, et al. Gender differences in patients with COVID-19: focus on severity and mortality. Front Public Health 2020; 8: 152.
17. Wang B, Li R, Lu Z, Huang Y. Does comorbidity increase the risk of patients with COVID-19: evidence from meta-analysis. Aging (Albany NY) 2020; 12: 6049-6057.
18. Azer SA. COVID-19: pathophysiology, diagnosis, complications and investigational therapeutics. New Microbes New Infect 2020; 37: 100738.
19. Singhal T. A review of coronavirus disease-2019 (COVID-19). Indian J Pediatr 2020; 87: 281-286.
20. Lima CMAO. Information about the new coronavirus disease (COVID-19). Radiol Bras 2020; 53(2): V–VI.
21. Esbin MN, Whitney ON, Chong S, Maurer A, Darzacq X, Tjian R. Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection. RNA 2020; 26: 771-783.
22. Alcoba-Floreza J, González-Montelongob R, Íñigo-Camposb A, de Artola DG, Gil-Campesinoa H, The Microbiology Technical Support Team, et al. Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples. Int J Infect Dis 2020; 97: 66-68.
Files
IssueVol 13 No 6 (2021) QRcode
SectionOriginal Article(s)
DOI https://doi.org/10.18502/ijm.v13i6.8073
Keywords
COVID-19; SARS-CoV-2; Coronavirus; Molecular diagnostic; Real time polymerase chain reaction

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How to Cite
1.
Dhakad M, Gogoi S, Kumari A, Singh A, Jais M, Prakash A, Pangtey G, Kaur R. Comparative evaluation of cost effective extraction free molecular technique for detection of SARS-CoV-2 with reference to standard VTM based RT-qPCR method. Iran J Microbiol. 2021;13(6):748-756.