Detection of low levels of SARS-CoV-2 RNA from nasopharyngeal swabs using three commercial molecular assays

J Clin Virol. 2020 Jul;128:104387. doi: 10.1016/j.jcv.2020.104387. Epub 2020 Apr 28.


In response to the COVID-19 pandemic, commercial molecular assays for SARS-CoV-2 testing have been rapidly developed and broadly deployed in laboratories worldwide. Although these assays have been reported to correlate well, we sought to compare the Xpert® Xpress SARS-CoV-2 to the cobas® SARS-CoV-2 or the Lightmix® Modular SARS and Wuhan CoV E-gene assay for nasopharyngeal (NP) swabs with low levels of SARS-CoV-2 RNA. Thirty-seven NP swabs were studied, including 10 samples with a moderate cycle threshold (Ct) between 30-33.9, and 22 with Ct≥34, and 5 negative for SARS-CoV-2. Overall concordance on initial comparison was 86.5 % (32/37), which was 100 % concordance for samples with Ct values ranging between 30-33.9. Discordance amongst samples showing a Ct ≥34 was 22.7 % (5/22). Endpoint value analysis on the Xpress SARS-CoV-2 within the discordant samples noted two with an endpoint value >5, which were detected by the cobas® or Lightmix®. Testing of SARS-CoV-2 on the three commercial assays was comparable for NP swabs with moderate Ct values, while high Ct values were less concordant. Importantly, analysis of Xpert® endpoint values improved interpretation of discrepant results.

Keywords: COVID-19; Cobas; Endpoint values; Xpert.

Publication types

  • Validation Study

MeSH terms

  • Betacoronavirus / genetics
  • Betacoronavirus / isolation & purification*
  • COVID-19
  • COVID-19 Testing
  • Clinical Laboratory Techniques / methods*
  • Coronavirus Infections / diagnosis*
  • Coronavirus Infections / virology
  • Humans
  • Molecular Diagnostic Techniques / methods*
  • Nasopharynx / virology
  • Pandemics
  • Pneumonia, Viral / diagnosis*
  • Pneumonia, Viral / virology
  • RNA, Viral / analysis
  • Reagent Kits, Diagnostic
  • SARS-CoV-2


  • RNA, Viral
  • Reagent Kits, Diagnostic