Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection

Clin Microbiol Infect. 2020 Sep;26(9):1248-1253. doi: 10.1016/j.cmi.2020.06.009. Epub 2020 Jun 23.


Introduction: Testing for active SARS-CoV-2 infection is a fundamental tool in the public health measures taken to control the COVID-19 pandemic. Because of the overwhelming use of SARS-CoV-2 reverse transcription (RT)-PCR tests worldwide, the availability of test kits has become a major bottleneck and the need to increase testing throughput is rising. We aim to overcome these challenges by pooling samples together, and performing RNA extraction and RT-PCR in pools.

Methods: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. We tested 184 samples both individually and in pools to estimate the effects of pooling. We further implemented Dorfman pooling with a pool size of eight samples in large-scale clinical tests.

Results: We demonstrated pooling strategies that increase testing throughput while maintaining high sensitivity. A comparison of 184 samples tested individually and in pools of eight samples showed that test results were not significantly affected. Implementing the eight-sample Dorfman pooling to test 26 576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput.

Discussion: Pooling approaches for SARS-CoV-2 testing allow a drastic increase in throughput while maintaining clinical sensitivity. We report the successful large-scale pooled screening of asymptomatic populations.

Keywords: COVID-19; Diagnostics; Group testing; Infectious diseases; RT-PCR.

MeSH terms

  • Betacoronavirus / genetics
  • Betacoronavirus / isolation & purification*
  • COVID-19
  • COVID-19 Testing
  • Clinical Laboratory Techniques / methods*
  • Coronavirus Infections / diagnosis*
  • Coronavirus Infections / epidemiology
  • Diagnostic Tests, Routine
  • Humans
  • Pandemics
  • Pneumonia, Viral / diagnosis*
  • Pneumonia, Viral / epidemiology
  • RNA, Viral / genetics
  • Reproducibility of Results
  • Reverse Transcriptase Polymerase Chain Reaction
  • SARS-CoV-2
  • Sensitivity and Specificity
  • Specimen Handling


  • RNA, Viral