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. 2020 Nov 9;15(11):e0241959.
doi: 10.1371/journal.pone.0241959. eCollection 2020.

Recommendations for sample pooling on the Cepheid GeneXpert® system using the Cepheid Xpert® Xpress SARS-CoV-2 assay

Michael G Becker  1 , Tracy Taylor  1 , Sandra Kiazyk  1   2 , Dana R Cabiles  1 , Adrienne F A Meyers  1   2 , Paul A Sandstrom  1   2
Affiliations

Recommendations for sample pooling on the Cepheid GeneXpert® system using the Cepheid Xpert® Xpress SARS-CoV-2 assay

Michael G Becker et al. PLoS One. .

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Standard curve for the Xpert® Xpress SARS-CoV-2 assay.
Assay targets both the nucleocapsid (N; empty circle with a dashed line) and envelope (E; filled circle with a dotted line). The curve was produced using serially-diluted gamma-irradiated virus culture (GISAID Accession: EPI_ISL_425177) produced at the National Microbiology Laboratory.
Fig 2
Fig 2. The effect of sample pooling on testing capacity at different pool sizes.
Testing capacity is shown for pools of two (black dashed-dotted line), three (green solid line), or six (brown dashed line) samples. For each pool size, testing capacity is plotted against the rate of positive individual tests. The red dotted line represents the point at which pooled testing decreases capacity and is no longer viable. The cross-over point, when three sample pooling is more efficient than six sample pooling, occurs at 7.6%.
See this image and copyright information in PMC

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Grants and funding

The author(s) received no specific funding for this work.