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bioRxiv · 10.1101/2020.06.30.172833

Development of RNA-based assay for rapid detection of SARS-CoV-2 in clinical samples

Kumar, V.·Mishra, S.·Sharma, R.·Agarwal, J.·Ghoshal, U.·Khanna, T.·Sharma, L. K.·Verma, S. K.·Tiwari, S.
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Abstract

The ongoing spread of pandemic coronavirus disease (COVID-19) is caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). In the lack of specific drugs or vaccines for SARS-CoV-2, demands rapid diagnosis and management are crucial for controlling the outbreak in the community. Here we report the development of the first rapid-colorimetric assay capable of detecting SARS-CoV-2 in the human nasopharyngeal RNA sample in less than 30 minutes. We utilized a nanomaterial-based optical sensing platform to detect RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2, where the formation of oligo probe-target hybrid led to salt-induced aggregation and changes in gold-colloid color from pink to blue in visible range. Accordingly, we found a change in colloid color from pink to blue in assay containing nasopharyngeal RNA sample from the subject with clinically diagnosed COVID-19. The colloid retained pink color when the test includes samples from COVID-19 negative subjects or human papillomavirus (HPV) infected women. The results were validated using nasopharangeal RNA samples from suspected COVID-19 subjects (n=136). Using RT-PCR as gold standard, the assay was found to have 85.29% sensitivity and 94.12% specificity. The optimized method has detection limit as little as 0.5 ng of SARS-CoV-2 RNA. Overall, the developed assay rapidly detects SARS-CoV-2 RNA in clinical samples in a cost-effective manner and would be useful in pandemic management by facilitating mass screening.

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Kumar, V., Mishra, S., Sharma, R., Agarwal, J., Ghoshal, U., Khanna, T., Sharma, L. K., Verma, S. K., Tiwari, S.. 2020-06-30. Development of RNA-based assay for rapid detection of SARS-CoV-2 in clinical samples. https://doi.org/10.1101/2020.06.30.172833

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