Comparison of RNA extraction methods for the detection of SARS-CoV-2 by RT-PCR

ABSTRACT

ObjectivesThe SARS-CoV-2 pandemic outbreak has stressed health care systems as well as medical supply chains, but diagnostic testing is an essential public health measure to control viral spread. Here we test the suitability of different RNA extraction methods for integration into a diagnostic workflow for coronavirus testing. MethodsWe applied six RNA extraction methods on the same 24 SARS-CoV-2 positive patient samples and quantified their results by subsequent reverse-transcriptase PCR (RT-PCR) of three viral genes. These methods included a) column-based extraction, b) phenol-chloroform extraction, as well as c) extraction using magnetic beads (i.e., one commercial kit as well as three different magnetic beads in combination with home-brewed buffers and solutions). ResultsWe achieved diagnostic-quality RT-PCR results with all methods, and there was no significant difference between the tested methods, except for one magnetic bead protocol with home-brewed buffers, in which the number of positive tested genes was significantly lower. ConclusionsFive of the six RNA extraction methods are interchangeable in a diagnostic workflow. Since some methods are more scalable than others, and have comparable results on RT-PCR quantitation, they may be more amenable to high-throughput sample processing pipelines. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/20172494v1_ufig1.gif" ALT="Figure 1"> View larger version (46K) org.highwire.dtl.DTLVardef@f9ff33org.highwire.dtl.DTLVardef@e17c21org.highwire.dtl.DTLVardef@19c8c37org.highwire.dtl.DTLVardef@b9aa2d_HPS_FORMAT_FIGEXP M_FIG C_FIG