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.
Highlights
The coronavirus disease 2019 (COVID-19) pandemic has caused an unprecedented demand for global testing supplies
All dilutions above 60 cp/mL were recorded as SARSCoV-2 positive by the assay (S1 Table), consistent with the previously observed limit of detection [6] for the Xpert1 Xpress SARS-CoV-2 assay of
To determine the effect of sample pooling on the sensitivity of the Xpert1 Xpress SARS-CoV2 assay, five clinical samples were selected with cycle threshold (Ct) values ranging from 23–35 as determined by the Corman RT-qPCR test performed at the Cadham Provincial Laboratory (CPL) in Winnipeg, MB
Summary
The coronavirus disease 2019 (COVID-19) pandemic has caused an unprecedented demand for global testing supplies. Public health officials are searching for innovative ways to increase testing capacity in the face of limited resources. One approach that could be rapidly deployed to increase SARS-CoV-2 testing capacity is pooled sample testing, a method that involves mixing multiple samples and testing them as a single unit, thereby decreasing the resources required to test multiple samples [1,2,3]. Recommendations for sample pooling using the Cepheid Xpert Xpress SARS-CoV-2 assay i.e. the pooling depth, is determined by the sensitivity of the test method as well as the prevalence of disease within the community. Similar strategies should be explored for the SARSCoV-2 point-of-care tests, such as the Cepheid Xpert Xpress SARS-CoV-2 assay
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