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

By Vinod Kumar, Suman Mishra, Rajni Sharma, Jyotsna Agarwal, Ujjala Ghoshal, Tripti Khanna, Lokendra K Sharma, Santosh K Verma, Swasti Tiwari, Prabhakar Mishra

Posted 30 Jun 2020
bioRxiv DOI: 10.1101/2020.06.30.172833

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 the 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 nasopharyngeal RNA samples from suspected COVID-19 subjects (n=136). Using RT-PCR as a gold standard, the assay was found to have 85.29% sensitivity and 94.12% specificity. The optimized method has a 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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