Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: Comparison with automated systems

PLoS One. 2021 Feb 24;16(2):e0247524. doi: 10.1371/journal.pone.0247524. eCollection 2021.

Abstract

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly reached pandemic levels. Sufficient testing for SARS-CoV-2 has remained essential for tracking and containing the virus. SARS-CoV-2 testing capabilities are still limited in many countries. Here, we explore the use of conventional RNA purification as an alternative to automated systems for detection of SARS-CoV-2 by RT-qPCR. 87 clinical swab specimens were extracted by conventional phenol-chloroform RNA purification and compared to commercial platforms for RNA extraction and the fully integrated Cobas®6800 diagnostic system. Our results show that the conventional RNA extraction is fully comparable to modern automated systems regarding analytical sensitivity and specificity with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. Moreover, the method is easily scalable and implemented in conventional laboratories as a low cost and suitable alternative to automated systems for the detection of SARS-CoV-2.

MeSH terms

  • COVID-19 / diagnosis
  • COVID-19 / virology*
  • COVID-19 Testing / methods
  • Chloroform / chemistry
  • Clinical Laboratory Techniques / methods
  • Humans
  • Molecular Diagnostic Techniques / methods
  • Pandemics
  • Phenol / chemistry
  • RNA / genetics
  • RNA / isolation & purification
  • RNA, Viral / genetics
  • RNA, Viral / isolation & purification*
  • Real-Time Polymerase Chain Reaction / methods
  • SARS-CoV-2 / chemistry
  • SARS-CoV-2 / genetics*
  • Sensitivity and Specificity
  • Specimen Handling / methods

Substances

  • RNA, Viral
  • Phenol
  • RNA
  • Chloroform

Grants and funding

The authors received no specific funding for this work.