An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance

Abstract With a view to extending testing capabilities for the ongoing SARS-CoV-2 pandemic we have developed a test that lowers cost and does not require real time quantitative reverse transcription polymerase chain reaction (RT-qPCR). We developed a reverse transcription nested PCR endpoint assay (...

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Bibliographic Details
Published in:bioRxiv 2020-06
Main Authors: Davda, Jayeshkumar Narsibhai, Frank, Keith, Sivakumar Prakash, Purohit, Gunjan, Devi Prasad Vijayashankar, Dhiviya Vedagiri, Karthik Bharadwaj Tallapaka, Harshan, Krishnan Harinivas, Archana Bharadwaj Siva, Mishra, Rakesh Kumar, Dhawan, Jyotsna, Siddiqi, Imran
Format: Article
Language:English
Subjects:
Efficiency
Pandemics
Polymerase chain reaction
Reverse transcription
Severe acute respiratory syndrome coronavirus 2
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Summary:Abstract With a view to extending testing capabilities for the ongoing SARS-CoV-2 pandemic we have developed a test that lowers cost and does not require real time quantitative reverse transcription polymerase chain reaction (RT-qPCR). We developed a reverse transcription nested PCR endpoint assay (RT-nPCR) and showed that RT-nPCR has comparable performance to the standard RT-qPCR test. In the course of comparing the results of both tests, we found that the standard RT-qPCR test can have low detection efficiency (less than 50%) in a real testing scenario which may be only partly explained by low viral representation in many samples. This finding points to the importance of directly monitoring detection efficiency in test environments. We also suggest measures that would improve detection efficiency. Competing Interest Statement The authors have declared no competing interest.
DOI:10.1101/2020.06.08.139477