Sensitive Extraction-Free SARS-CoV-2 RNA Virus Detection Using a Novel RNA Preparation Method

Current conventional detection of SARS-CoV-2 involves collection of a patient sample with a nasopharyngeal swab, storage of the swab during transport in a viral transport medium, extraction of RNA, and quantitative reverse transcription PCR (RT-qPCR). We developed a simplified and novel preparation method using a Chelex resin that obviates RNA extraction during viral testing. Direct detection RT-qPCR and digital-droplet PCR was compared to the current conventional method with RNA extraction for simulated samples and patient specimens. The heat-treatment in the presence of Chelex markedly improved detection sensitivity as compared to heat alone, and lack of RNA extraction shortens the overall diagnostic workflow. Furthermore, the initial sample heating step inactivates SARS-CoV-2 infectivity, thus improving workflow safety. This fast RNA preparation and detection method is versatile for a variety of samples, safe for testing personnel, and suitable for standard clinical collection and testing on high throughput platforms.Funding: This work was supported by the Intramural Research Programs of the National Institutes of Health (Clinical Center, NEI, NIDCR).Conflict of Interest: NEI (B.G. and R.B.H.) filed an invention disclosure. NEI has protected the intellectual property around this technology which is available for licensing and co-development. The remaining authors have no competing interests to declare.Ethical Approval: Samples were collected from healthy volunteers and subjects who provided informed consent to National Institutes of Health (NIH) Institutional Review Board (IRB)-approved protocols (20-D-0094, NCT04348240; 20-CC-0128, NCT04424446) at the NIH Clinical Center.