Dataset Information

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

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.

SUBMITTER: Becker MG

PROVIDER: S-EPMC7652318 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Becker Michael G MG Taylor Tracy T Kiazyk Sandra S Cabiles Dana R DR Meyers Adrienne F A AFA Sandstrom Paul A PA

PloS one 20201109 11

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 s ...[more]

PMID: 33166373

Similar Datasets

Project description:BackgroundIn Kenya, access to early infant diagnosis and viral load monitoring services for HIV patients on ART is significantly hampered by sample transportation challenges and long turnaround times. Near patient care testing technologies have the potential to obviate such constraints. The Cepheid GeneXpert was launched in 2010 as a TB assay and in 2014 as a potential point of care HIV viral load assay. Whereas it is widely is used for TB in Kenya, its utility for HIV testing has not been evaluated.ObjectiveTo investigate the performance and usability characteristics of the GeneXpert HIV-1 qualitative and quantitative assay.MethodsThis was a cross sectional study among 911 HIV Exposed infants and 310 HIV positive adults. Existing machines used for routine TB diagnosis were used in this study. The diagnostic accuracy of the qualitative assay was assessed using Roche CAP/CTM while the quantitative assay was assessed using with Abbott m2000 as the reference assays respectively. Statistical analysis was done using Stata/MP Version 14 for Mac. Concordance values and misclassification were calculated at the clinical cutoff of 1000 cp/ml.ResultsThe sensitivity, specificity and accuracy of the GeneXpert HIV-1 qualitative assay were 99.23% (95% CI 97.24-99.90%), 98.91% (95% CI 97.76-99.55%) and 99.00% respectively. For the quantitative assay, they were 92.50% (95% CI 79.61-98.43%), 100.00% and 97.00% respectively. All 30 (100%) users reported that the GeneXpert machine was easy to use, workflow was simple and TB diagnosis was not negatively affected. In our hands, the median turn-around time for an individual qualitative and quantitative test was 90 minutes. A total of 58 (4.34%) errors and 28 (2.10%) invalid outcomes were experienced; 44 (3.29%) tests did not run to completion due to power outages.ConclusionGeneXpert HIV-1 qualitative and quantitative assay is an accurate test for the diagnosis of HIV in infants and for viral load monitoring. At the point of care, the GeneXpert machine's simple work flow, ease of use and short test turnaround time present the potential to improve access to HIV testing and viral load monitoring. To integrate HIV diagnosis into the existing GeneXpert platforms for TB Diagnosis, there is need to scale up the infrastructure and to change the way work is done.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets