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

Megh Singh Dhakad; Sanjib Gogoi; Ansu Kumari; Aashish Kumar Singh; Manoj B. Jais; Anupam Prakash; Ghanshyam Pangtey; Ravinder Kaur

doi:10.18502/ijm.v13i6.8073

Megh Singh Dhakad Department of Microbiology, Lady Hardinge Medical College & Associated Hospitals, New Delhi, India
Sanjib Gogoi Department of Microbiology, Lady Hardinge Medical College & Associated Hospitals, New Delhi, India
Ansu Kumari Department of Microbiology, Lady Hardinge Medical College & Associated Hospitals, New Delhi, India
Aashish Kumar Singh Department of Medicine, Lady Hardinge Medical College & Associated Hospitals, New Delhi, India
Manoj B. Jais Department of Microbiology, Lady Hardinge Medical College & Associated Hospitals, New Delhi, India
Anupam Prakash Department of Medicine, Lady Hardinge Medical College & Associated Hospitals, New Delhi, India
Ghanshyam Pangtey Department of Medicine, Lady Hardinge Medical College & Associated Hospitals, New Delhi, India
Ravinder Kaur Department of Microbiology, Lady Hardinge Medical College & Associated Hospitals, New Delhi, India

DOI: https://doi.org/10.18502/ijm.v13i6.8073

Keywords: COVID-19; SARS-CoV-2; Coronavirus; Molecular diagnostic; Real time polymerase chain reaction

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.