comparative evaluation of cost effective extraction free molecular technique for detection of sars-cov-2 with reference to standard vtm based rt-qpcr method

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.