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Pooling samples: a testing option for SARS-CoV-2 during a supply shortage.

Hossein Salimnia1, Robert Mitchell2, Angela Gundel2

  • 1Detroit Medical Center University Laboratories, 4201 St Antoine, Detroit, MI 48201; Department of Pathology, Wayne State University School of Medicine, East Canfield, Detroit, MI 48201.

Diagnostic Microbiology and Infectious Disease
|November 15, 2020
PubMed
Summary

Pooling samples for SARS-CoV-2 testing using the Cepheid GenXpert assay is effective. This method maintains detection accuracy for positive cases and can significantly reduce the number of test kits used, especially at lower prevalence rates.

Keywords:
COVID-19Molecular diagnosisReverse transcriptase PCRSARS-CoV-2Sample pooling

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Area of Science:

  • Clinical diagnostics
  • Virology
  • Molecular biology

Background:

  • The COVID-19 pandemic necessitated rapid and efficient diagnostic testing.
  • The Cepheid GenXpert SARS-CoV-2 assay is a widely used molecular diagnostic tool.
  • Optimizing resource utilization in diagnostic testing is crucial for managing public health crises.

Purpose of the Study:

  • To evaluate the impact of sample pooling on the performance of the Cepheid GenXpert SARS-CoV-2 assay.
  • To determine if pooling 1 positive sample with up to 5 negative samples affects the assay's ability to detect SARS-CoV-2.
  • To assess the potential for cost savings and resource optimization through sample pooling.

Main Methods:

  • Sample pooling strategy: 1 positive sample combined with 1 to 5 negative samples.
  • Testing performed using the Cepheid GenXpert SARS-CoV-2 assay.
  • Detection of SARS-CoV-2 in pooled samples compared to individual testing.

Main Results:

  • Pooling of 1 positive sample with up to 5 negative samples did not negatively affect the detection of SARS-CoV-2.
  • The sensitivity of the assay remained high even with pooled samples.
  • At a 2% prevalence rate, sample pooling could lead to a reduction of up to 70% in test kit usage.

Conclusions:

  • Sample pooling is a viable strategy to enhance efficiency for SARS-CoV-2 detection with the Cepheid GenXpert assay.
  • This approach can significantly conserve testing resources, particularly in low-prevalence settings.
  • Implementing sample pooling can improve the cost-effectiveness of large-scale SARS-CoV-2 screening programs.