SARS-CoV-2 detection by extraction-free qRT-PCR for massive and rapid COVID-19 diagnosis during a pandemic in Armenia

J Virol Methods. 2021 Sep:295:114199. doi: 10.1016/j.jviromet.2021.114199. Epub 2021 Jun 4.


COVID-19 pandemic severely impacted the healthcare and economy on a global scale. It is widely recognized that mass testing is an efficient way to contain the spread of SARS-CoV-2 infection as well as aid in the development of informed policies for disease management. However, the current COVID-19 worldwide infection rates increased the demand for rapid and reliable screening of infection. We compared the performance of qRT-PCR in direct heat-inactivated (H), heat-inactivated and pelleted (HC) samples against RNA in a group of 74 subjects (44 positive and 30 negative). Then we compared the sensitivity of HC in a larger group of 196 COVID-19 positive samples. Our study suggests that HC samples show higher accuracy for SARS-CoV-2 detection PCR assay compared to direct H (89 % vs 83 % of the detection in RNA). The sensitivity of detection using direct samples varied depending on the sample transport and storage media as well as the viral loads (as measured by qRT-PCR Ct levels). Altogether, all the data suggest that purified RNA provides more accurate results, however, direct sample testing with qRT-PCR may help to significantly increase testing capacity. Switching to the direct sample testing is justified if the number of tests is doubled at least.

Keywords: COVID-19; Direct sample qRT-PCR; Heat-Inactivation; Pelleting; SARS-CoV-2; Virus detection.

MeSH terms

  • Armenia / epidemiology
  • COVID-19 / diagnosis*
  • COVID-19 / epidemiology
  • COVID-19 / virology
  • COVID-19 Nucleic Acid Testing / methods*
  • Humans
  • Mass Screening / methods*
  • RNA, Viral / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / isolation & purification*
  • Sensitivity and Specificity
  • Specimen Handling
  • Viral Load
  • Virus Inactivation


  • RNA, Viral