Multi-Stage Group Testing Improves Efficiency of Large-Scale COVID-19 Screening

Eberhardt, Jens Niklas; Breuckmann, Nikolas P.; Eberhardt, Christiane

doi:10.1101/2020.04.10.20061176

Cited by 25 publications

(34 citation statements)

References 10 publications

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“…By this time, 7 (0-25) additional patients and/or staff had acquired COVID-19 but did not (yet) show symptoms. The lag until first onset of severe COVID-19 symptoms was greater (12 days from index case, [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21] and coincided with a greater number of undetected infections (23,.…”

Section: Covid-19 Spreads Quickly But Symptoms Lagmentioning

confidence: 99%

“…3,[6][7][8] Yet symptomatic cases represent just the tip of the iceberg: infectious individuals with no, mild, or as-yet undeveloped symptoms are common in COVID-19 outbreaks, and can easily go undetected by syndromic surveillance systems while nonetheless seeding chains of transmission. [9][10][11] Recent studies have indicated that surveillance strategies such as group testing may represent effective and resource-efficient alternatives to standard syndromic surveillance, [12][13][14][15] but few settings have adopted such practices.…”

Section: Introductionmentioning

confidence: 99%

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Optimizing COVID-19 surveillance in long-term care facilities: a modelling study

2020

Preprint

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Background: Long-term care facilities (LTCFs) are particularly vulnerable to nosocomial outbreaks of coronavirus disease 2019 , with high rates of transmission and mortality. Timely epidemiological surveillance is essential to detect and respond to outbreaks, but testing resources are highly limited in the current pandemic context. Methods:We used an individual-based transmission model to simulate COVID-19 spread along interindividual contact networks in the LTCF setting. A range of surveillance strategies were evaluated for their ability to detect simulated outbreaks, assuming limited availability of standard RT-PCR tests. Various epidemiological scenarios were considered, including COVID-19 importation from patient transfers or staff members infected in the community. Findings:We estimated a median delay of 7 (95% uncertainty interval: 2-15) days from importation of an asymptomatic COVID-19-infected patient to first presentation of COVID-19 symptoms among any patients or staff, at which point an additional 7 (0-25) individuals were infected but did not (yet) show symptoms. Across a range of scenarios, the reference surveillance strategy (testing individuals with COVID-like symptoms with signs of severity) took a median 11-21 days to detect an outbreak. Group testing (pooling specimens from multiple individuals for a single RT-PCR test) patients and staff with any COVID-like symptoms was both the most timely and efficient strategy, detecting outbreaks up to twice as quickly as the reference, and more quickly than other considered strategies while using fewer tests. Maximizing use of available tests via testing cascades was more effective . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) and containing the terms ("COVID" OR "coronavirus" OR "nCoV" OR "SARS-CoV-2) AND ("long-term care" OR "LTCF"). We identified 16 articles published in academic journals, mostly outbreak reports and editorials describing a need for improved testing and control measures. Very few of the 179 identified preprints were studies of COVID-19 in long-term care. A separate search for the same COVID terms AND ("transmission model" OR "mathematical model" OR "dynamic model") returned 29 published articles, including an evaluation of surveillance strategies in airports, and a range of transmission models at the country or community levels, but none specifically tailored to healthcare settings, whether hospitals, LTCFs or otherwise. Among 776 preprints, we identified a large number of studies assessing and projecting COVID-19 burden in hospital systems, but only two transmission models specific to healthcare settings, neither of which addressed long-term care settings nor options for epidemiological surveillance. Together, this suggests a lack of research on the unique transmission dynamics and surveillance considerations for COVID-19 in healthcare settings. This gap is further highlighted by ex...

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Section: Covid-19 Spreads Quickly But Symptoms Lagmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Optimizing COVID-19 surveillance in long-term care facilities: a modelling study

2020

Preprint

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“…For an assay with negligible error, a positive test result for a pooled sample would indicate that the molecular alteration is present in one or more subjects in the pool, while a negative test result would indicate the contrary. Since its introduction by Dorfman (8) as a cost-efficient way of screening for syphilis, GT has been applied to many different areas of biomedical research including virology (9-11), genetics (12)(13)(14)(15), drug development (16), and most recently Covid-19 (17)(18)(19). In particular, the feasibility and performance of GT for detecting mutations in tumor have been investigated with promising results (13)(14)(15).…”

Section: Group Testingmentioning

confidence: 99%

Group Testing Can Improve the Cost-Efficiency of Prospective-Retrospective Biomarker Studies

Zhang

Zhang²,

Krushkal³

et al. 2020

Preprint

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Background: Cancer treatment is increasingly dependent on biomarkers for prognostication and treatment selection. Potential biomarkers are frequently evaluated in prospective-retrospective studies in which biomarkers are measured retrospectively on archived specimens after completion of prospective clinical trials. In light of the high costs of some assays, random sampling designs have been proposed that measure biomarkers for a random sub-sample of subjects selected on the basis of observed outcome and possibly other variables. Compared with a standard design that measures biomarkers on all subjects, a random sampling design can be cost-efficient in the sense of reducing the cost of the study substantially while achieving a reasonable level of precision.Methods: For a biomarker that indicates the presence of some molecular alteration (e.g., mutation in a gene), we explore the use of a group testing strategy, which involves physically pooling specimens across subjects and assaying pooled samples for the presence of the molecular alteration of interest, for further improvement in cost-efficiency beyond random sampling. We propose simple and general approaches to estimating the prognostic and predictive values of biomarkers with group testing, and conduct simulation studies to validate the proposed estimation procedures and to assess the cost-efficiency of the group testing design in comparison to the standard and random sampling designs.Results: Simulation results show that the proposed estimation procedures perform well in realistic settings and that a group testing design can have considerably higher cost-efficiency than a random sampling design. Conclusions: Group testing can be used to improve the cost-efficiency of biomarker studies.

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“…Pooled testing is a diagnostic approach where samples from multiple patients are combined and analyzed in a single test reaction 7 . If the reaction is positive, then individual samples that contributed to that reaction need to be retested singly ( Figure 2 ).…”

Section: Introductionmentioning

confidence: 99%

“…More recently, this strategy has been applied in blood banks to screen blood products for HIV-1, hepatitis B and C viruses 9 , 10 . Now, again, this strategy is finding application in identifying SARS-CoV-2 infected individuals in the ongoing COVID-19 pandemic 7 , 11 – 15 .…”

Section: Introductionmentioning

confidence: 99%

Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

Agoti¹,

Mutunga²,

Lambisia³

et al. 2020

Wellcome Open Res

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Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.

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Multi-Stage Group Testing Improves Efficiency of Large-Scale COVID-19 Screening

Cited by 25 publications

References 10 publications

Optimizing COVID-19 surveillance in long-term care facilities: a modelling study

Optimizing COVID-19 surveillance in long-term care facilities: a modelling study

Group Testing Can Improve the Cost-Efficiency of Prospective-Retrospective Biomarker Studies

Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

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