The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa.

Journal: PloS one
Published Date: Jan 1, 2020

Abstract

The SARS-CoV-2 pandemic has resulted in shortages of both critical reagents for nucleic acid purification and highly trained staff as supply chains are strained by high demand, public health measures and frequent quarantining and isolation of staff. This created the need for alternate workflows with limited reliance on specialised reagents, equipment and staff. We present here the validation and implementation of such a workflow for preparing samples for downstream SARS-CoV-2 RT-PCR using liquid handling robots. The rapid sample preparation technique evaluated, which included sample centrifugation and heating prior to RT-PCR, showed a 97.37% (95% CI: 92.55-99.28%) positive percent agreement and 97.30% (95% CI: 90.67-99.52%) negative percent agreement compared to nucleic acid purification-based testing. This method was subsequently adopted as the primary sample preparation method in the Groote Schuur Hospital Virology Diagnostic Laboratory in Cape Town, South Africa.

Authors

  • Gert Marais
    Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa.
  • Michelle Naidoo
    Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa.
  • Nei-Yuan Hsiao
    Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa.
  • Ziyaad Valley-Omar
    Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa.
  • Heidi Smuts
    Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa.
  • Diana Hardie
    Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa.

Keywords

External Resources

Popular Topics
Recent Journals