A Fast and Accessible Method for the Isolation of RNA, DNA, and Protein To Facilitate the Detection of SARS-CoV-2

Abstract

Management of the COVID-19 pandemic requires widespread SARS-CoV-2 testing. A main limitation for widespread SARS-CoV-2 testing is the global shortage of essential supplies, among these, RNA extraction kits. The need for commercial RNA extraction kits places a bottleneck on tests that detect SARS-CoV-2 genetic material, including PCR-based reference tests. Here we propose an alternative method we call PEARL (Precipitation Enhanced Analyte RetrievaL) that addresses this limitation. PEARL uses a lysis solution that disrupts cell membranes and viral envelopes while simultaneously providing conditions suitable for alcohol-based precipitation of RNA, DNA, and proteins. PEARL is a fast, low-cost, and simple method that uses common laboratory reagents and offers comparable performance to commercial RNA extraction kits. PEARL offers an alternative method to isolate host and pathogen nucleic acids and proteins to streamline the detection of DNA and RNA viruses, including SARS-CoV-2.

Detection and evolution of SARS-CoV-2 coronavirus variants of concern with mass spectrometry

“…Such a mass spectrometry-based strategy offers an alternative to conventional PCR-based genetic detection and analysis of the virus [27] where, after RNA extraction from viral specimens, studies of its evolutionary dynamics require the relatively time-consuming generation, interpretation and processing of large genome sequence datasets. The mass spectrometric approach does require the initial isolation, or at least partial purification, of the S-protein but if optimized, using procedures under development [28], this could be performed within a similar timeframe to the many steps needed to isolate, purify and amplify the virus' genes or genome [29]. While mutations within the S-protein or its gene have been the focus of most studies of the variants of concern [4,[6][7][8][9] given the role the protein plays in host cell interactions [3], variant-specific mutations identified within other protein-coding regions [5] (e.g.…”

Frugal Science Powered by Curiosity

“…In later studies, our laboratory also built a 3D-printed version, called the 3D-Fuge, to expand the sample capacity from 10 μL to 2 mL . Other groups across the world have also built on these principles for new design approaches and applications. − Through the frugal science approach, an ancient childhood toy was transformed to a powerful tool for synthetic biology and medical diagnostics.…”

Nucleic Acid Testing of SARS-CoV-2

“…However, a high proportion of host cell genetic materials can be found, which should be removed or reduced for sequencing. The removal or depletion methods of the host genetic materials vary by the type of sample or the virus [ 167 , 168 , 169 , 170 , 171 , 172 , 173 , 174 ]. Due to the nature of the metagenomics approaches, the clinical samples should ideally have a high titer of the pathogens.…”