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Recommendations for sample pooling on the Cepheid GeneXpert® system using the Cepheid Xpert® Xpress SARS-CoV-2 assay.
PLoS One. 2020; 15(11):e0241959.Plos

Abstract

The coronavirus disease 2019 (Covid-19) pandemic, caused by SARS-CoV-2, has resulted in a global testing supply shortage. In response, pooled testing has emerged as a promising strategy that can immediately increase testing capacity. In pooled sample testing, multiple samples are combined (or pooled) together and tested as a single unit. If the pool is positive, the individual samples can then be individually tested to identify the positive case(s). Here, we provide support for the adoption of sample pooling with the point-of-care Cepheid Xpert® Xpress SARS-CoV-2 molecular assay. Corroborating previous findings, the limit of detection of this assay was comparable to laboratory-developed reverse-transcription quantitative PCR SARS-CoV-2 tests, with observed detection below 100 copies/mL. The Xpert® Xpress assay detected SARS-CoV-2 after samples with minimum viral loads of 461 copies/mL were pooled in groups of six. Based on these data, we recommend the adoption of pooled testing with the Xpert® Xpress SARS-CoV-2 assay where warranted based on public health needs. The suggested number of samples per pool, or the pooling depth, is unique for each point-of-care testing site and can be determined by the positive test rates. To statistically determine appropriate pooling depth, we have calculated the pooling efficiency for numerous combinations of pool sizes and test rates. This information is included as a supplemental dataset that we encourage public health authorities to use as a guide to make recommendations that will maximize testing capacity and resource conservation.

Authors+Show Affiliations

National HIV and Retrovirology Laboratory, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada.National HIV and Retrovirology Laboratory, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada.National HIV and Retrovirology Laboratory, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada. Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.National HIV and Retrovirology Laboratory, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada.National HIV and Retrovirology Laboratory, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada. Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.National HIV and Retrovirology Laboratory, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada. Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

33166373

Citation

Becker, Michael G., et al. "Recommendations for Sample Pooling On the Cepheid GeneXpert® System Using the Cepheid Xpert® Xpress SARS-CoV-2 Assay." PloS One, vol. 15, no. 11, 2020, pp. e0241959.
Becker MG, Taylor T, Kiazyk S, et al. Recommendations for sample pooling on the Cepheid GeneXpert® system using the Cepheid Xpert® Xpress SARS-CoV-2 assay. PLoS One. 2020;15(11):e0241959.
Becker, M. G., Taylor, T., Kiazyk, S., Cabiles, D. R., Meyers, A. F. A., & Sandstrom, P. A. (2020). Recommendations for sample pooling on the Cepheid GeneXpert® system using the Cepheid Xpert® Xpress SARS-CoV-2 assay. PloS One, 15(11), e0241959. https://doi.org/10.1371/journal.pone.0241959
Becker MG, et al. Recommendations for Sample Pooling On the Cepheid GeneXpert® System Using the Cepheid Xpert® Xpress SARS-CoV-2 Assay. PLoS One. 2020;15(11):e0241959. PubMed PMID: 33166373.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Recommendations for sample pooling on the Cepheid GeneXpert® system using the Cepheid Xpert® Xpress SARS-CoV-2 assay. AU - Becker,Michael G, AU - Taylor,Tracy, AU - Kiazyk,Sandra, AU - Cabiles,Dana R, AU - Meyers,Adrienne F A, AU - Sandstrom,Paul A, Y1 - 2020/11/09/ PY - 2020/06/14/received PY - 2020/10/23/accepted PY - 2020/11/9/entrez PY - 2020/11/10/pubmed PY - 2020/11/20/medline SP - e0241959 EP - e0241959 JF - PloS one JO - PLoS One VL - 15 IS - 11 N2 - The coronavirus disease 2019 (Covid-19) pandemic, caused by SARS-CoV-2, has resulted in a global testing supply shortage. In response, pooled testing has emerged as a promising strategy that can immediately increase testing capacity. In pooled sample testing, multiple samples are combined (or pooled) together and tested as a single unit. If the pool is positive, the individual samples can then be individually tested to identify the positive case(s). Here, we provide support for the adoption of sample pooling with the point-of-care Cepheid Xpert® Xpress SARS-CoV-2 molecular assay. Corroborating previous findings, the limit of detection of this assay was comparable to laboratory-developed reverse-transcription quantitative PCR SARS-CoV-2 tests, with observed detection below 100 copies/mL. The Xpert® Xpress assay detected SARS-CoV-2 after samples with minimum viral loads of 461 copies/mL were pooled in groups of six. Based on these data, we recommend the adoption of pooled testing with the Xpert® Xpress SARS-CoV-2 assay where warranted based on public health needs. The suggested number of samples per pool, or the pooling depth, is unique for each point-of-care testing site and can be determined by the positive test rates. To statistically determine appropriate pooling depth, we have calculated the pooling efficiency for numerous combinations of pool sizes and test rates. This information is included as a supplemental dataset that we encourage public health authorities to use as a guide to make recommendations that will maximize testing capacity and resource conservation. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/33166373/Recommendations_for_sample_pooling_on_the_Cepheid_GeneXpert®_system_using_the_Cepheid_Xpert®_Xpress_SARS_CoV_2_assay_ L2 - https://dx.plos.org/10.1371/journal.pone.0241959 DB - PRIME DP - Unbound Medicine ER -