Sample pooling on the Cepheid Xpert® Xpress SARS-CoV-2 assay

Maryza Graham; Eloise Williams; Nicole Isles; Eka Buadromo; Tebuka Toatu; Julian Druce; Mike Catton; Chantel Lin; Benjamin P Howden; Deborah A Williamson

doi:10.1016/j.diagmicrobio.2020.115238

Sample pooling on the Cepheid Xpert® Xpress SARS-CoV-2 assay

Diagn Microbiol Infect Dis. 2021 Feb;99(2):115238. doi: 10.1016/j.diagmicrobio.2020.115238. Epub 2020 Oct 15.

Authors

Affiliations

¹ Microbiological Diagnostic Unit, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; Department of Microbiology, Monash Health, Melbourne, Australia. Electronic address: [email protected].
² Department of Microbiology, Royal Melbourne Hospital, Melbourne, Australia.
³ Microbiological Diagnostic Unit, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
⁴ The Pacific Community, Public Health Division, Suva, Fiji.
⁵ Victorian Infectious Diseases Reference Laboratory, Melbourne Health at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
⁶ Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty, Institute for Infection and Immunity, Melbourne, Australia.
⁷ Microbiological Diagnostic Unit, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty, Institute for Infection and Immunity, Melbourne, Australia.
⁸ Microbiological Diagnostic Unit, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; Department of Microbiology, Royal Melbourne Hospital, Melbourne, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty, Institute for Infection and Immunity, Melbourne, Australia.

Abstract

The COVID-19 pandemic has placed unprecedented global demand on laboratory supplies required for testing. Sample pooling has been investigated by laboratories as a strategy to preserve testing capacity. We evaluate the performance of Cepheid Xpert® Xpress SARS-CoV-2 RT-PCR assay for testing samples in pools of 4 and 6. Clinical samples containing SARS-CoV-2, and confirmed negative clinical samples were used to create sample pools. Clinical samples had 'neat' Xpert® E gene cycle threshold values ranging between 20 and 28 and all were detected qualitatively when contained in pools of 4 or 6 samples. For these samples, pooling had a median change in cycle threshold value of 2.0 in pools of 4, and of 2.9 in pools of 6. With the use of Cepheid Xpert® Xpress SARS-CoV-2 RT-PCR assay, pooling of 4 or 6 samples may be an effective strategy to increase testing capacity.

Keywords: Cepheid; GeneXpert; Pooling; SARS-CoV-2.

MeSH terms

COVID-19 / diagnosis*
COVID-19 Testing / methods*
Clinical Laboratory Techniques / methods*
Humans
Molecular Diagnostic Techniques / methods*
Nasopharynx / virology
Reverse Transcriptase Polymerase Chain Reaction / methods*
SARS-CoV-2 / genetics
Sensitivity and Specificity