tetano
Editor, Senior Moderator
Iran J Microbiol
. 2021 Dec;13(6):748-756.
doi: 10.18502/ijm.v13i6.8073.
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[SUP] 1 [/SUP], Sanjib Gogoi[SUP] 1 [/SUP], Ansu Kumari[SUP] 1 [/SUP], Aashish Kumar Singh[SUP] 2 [/SUP], Manoj B Jais[SUP] 1 [/SUP], Anupam Prakash[SUP] 2 [/SUP], Ghanshyam Pangtey[SUP] 2 [/SUP], Ravinder Kaur[SUP] 1 [/SUP]
Affiliations
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.
Keywords: COVID-19; Coronavirus; Molecular diagnostic; Real time polymerase chain reaction; SARS-CoV-2.
. 2021 Dec;13(6):748-756.
doi: 10.18502/ijm.v13i6.8073.
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[SUP] 1 [/SUP], Sanjib Gogoi[SUP] 1 [/SUP], Ansu Kumari[SUP] 1 [/SUP], Aashish Kumar Singh[SUP] 2 [/SUP], Manoj B Jais[SUP] 1 [/SUP], Anupam Prakash[SUP] 2 [/SUP], Ghanshyam Pangtey[SUP] 2 [/SUP], Ravinder Kaur[SUP] 1 [/SUP]
Affiliations
- PMID: 35222851
- PMCID: PMC8816692
- DOI: 10.18502/ijm.v13i6.8073
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.
Keywords: COVID-19; Coronavirus; Molecular diagnostic; Real time polymerase chain reaction; SARS-CoV-2.