Evaluation of the commercially available LightMix® Modular E-gene kit using clinical and proficiency testing specimens for SARS-CoV-2 detection

J Clin Virol. 2020 Aug;129:104476. doi: 10.1016/j.jcv.2020.104476. Epub 2020 May 27.

Abstract

Background: Rapid and sensitive diagnostic assays for SARS-CoV-2 detection are required for prompt patient management and infection control. The analytical and clinical performances of LightMix® Modular SARS and Wuhan CoV E-gene kit, a widely used commercial assay for SARS-CoV-2 detection, have not been well studied.

Objective: To evaluate the performance characteristics of the LightMix® E-gene kit in comparison with well-validated in-house developed COVID-19 RT-PCR assays.

Study design: Serial dilutions of SARS-CoV-2 culture isolate extracts were used for analytical sensitivity evaluation. A total of 289 clinical specimens from 186 patients with suspected COVID-19 and 8 proficiency testing (PT) samples were used to evaluate the diagnostic performance of the LightMix® E-gene kit against in-house developed COVID-19-RdRp/Hel and COVID-19-N RT-PCR assays.

Results: The LightMix® E-gene kit had a limit of detection of 1.8 × 10-1 TCID50/mL, which was one log10 lower than those of the two in-house RT-PCR assays. The LightMix® E-gene kit (149/289 [51.6%]) had similar sensitivity as the in-house assays (144/289 [49.8%] for RdRp/Hel and 146/289 [50.5%] for N). All three assays gave correct results for all the PT samples. Cycle threshold (Cp) values of the LightMix® E-gene kit and in-house assays showed excellent correlation. Reproducibility of the Cp values was satisfactory with intra- and inter-assay coefficient of variation values <5%. Importantly, the LightMix® E-gene kit, when used as a stand-alone assay, was equally sensitive as testing algorithms using multiple COVID-19 RT-PCR assays.

Conclusions: The LightMix® E-gene kit is a rapid and sensitive assay for SARS-CoV-2 detection. It has fewer verification requirements compared to laboratory-developed tests.

Keywords: COVID-19; Diagnostic; Evaluation; LightMix E-gene; PCR; SARS-CoV-2.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Betacoronavirus / genetics
  • Betacoronavirus / isolation & purification*
  • COVID-19
  • COVID-19 Testing
  • Clinical Laboratory Techniques / methods*
  • Coronavirus Infections / diagnosis*
  • Female
  • Humans
  • Limit of Detection
  • Male
  • Middle Aged
  • Molecular Diagnostic Techniques / methods*
  • Pandemics
  • Pneumonia, Viral / diagnosis*
  • RNA, Viral / analysis*
  • RNA, Viral / genetics
  • Reference Standards
  • Reproducibility of Results
  • SARS-CoV-2
  • Sensitivity and Specificity
  • Time Factors
  • Young Adult

Substances

  • RNA, Viral