scholarly journals Evaluation of Sample Pooling for SARS-CoV-2 Detection in Nasopharyngeal Swab and Saliva Samples with the Idylla SARS-CoV-2 Test

2021 ◽  
Author(s):  
Paul Hofman ◽  
Maryline Allegra ◽  
Myriam Salah ◽  
Jonathan Benzaquen ◽  
Virginie Tanga ◽  
...  
Keyword(s):  
Pool Size ◽  
Nasopharyngeal Swab ◽  
Foreseeable Future ◽  
Testing Strategies ◽  
Sample Pooling

To control outbreaks of coronavirus disease 2019 (COVID-19) and to avoid reagent shortages, testing strategies must be adapted and maintained for the foreseeable future. We analyzed the feasibility of pooling NPS and saliva samples for SARS-CoV-2 testing with the Idylla SARS-CoV-2 test, and we found that sensitivity was dependent on the pool size.

scholarly journals Identifying optimal COVID-19 testing strategies for schools and businesses: Balancing testing frequency, individual test technology, and cost

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248783 ◽  
Author(s):  
Gregory D. Lyng ◽  
Natalie E. Sheils ◽  
Caleb J. Kennedy ◽  
Daniel O. Griffin ◽  
Ethan M. Berke
Keyword(s):  
High Frequency ◽  
Cost Savings ◽  
Disease Prevalence ◽  
Sensitivity Test ◽  
Cumulative Number ◽  
Test Sensitivity ◽  
Testing Strategies ◽  
Testing Frequency ◽  
Sample Pooling ◽  
The Impact

Background COVID-19 test sensitivity and specificity have been widely examined and discussed, yet optimal use of these tests will depend on the goals of testing, the population or setting, and the anticipated underlying disease prevalence. We model various combinations of key variables to identify and compare a range of effective and practical surveillance strategies for schools and businesses. Methods We coupled a simulated data set incorporating actual community prevalence and test performance characteristics to a susceptible, infectious, removed (SIR) compartmental model, modeling the impact of base and tunable variables including test sensitivity, testing frequency, results lag, sample pooling, disease prevalence, externally-acquired infections, symptom checking, and test cost on outcomes including case reduction and false positives. Findings Increasing testing frequency was associated with a non-linear positive effect on cases averted over 100 days. While precise reductions in cumulative number of infections depended on community disease prevalence, testing every 3 days versus every 14 days (even with a lower sensitivity test) reduces the disease burden substantially. Pooling provided cost savings and made a high-frequency approach practical; one high-performing strategy, testing every 3 days, yielded per person per day costs as low as $1.32. Interpretation A range of practically viable testing strategies emerged for schools and businesses. Key characteristics of these strategies include high frequency testing with a moderate or high sensitivity test and minimal results delay. Sample pooling allowed for operational efficiency and cost savings with minimal loss of model performance.

scholarly journals Evaluation of pool-based testing approaches to enable population-wide screening for COVID-19

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243692
Author(s):  
Timo de Wolff ◽  
Dirk Pflüger ◽  
Michael Rehme ◽  
Janin Heuer ◽  
Martin-Immanuel Bittner
Keyword(s):  
Infection Rate ◽  
Primary Study ◽  
Viral Spread ◽  
Test Characteristics ◽  
Testing Strategies ◽  
Resource Limited ◽  
Input Parameters ◽  
Sample Pooling ◽  
Broad Variety ◽  
The Uk

Objective Rapid testing is paramount during a pandemic to prevent continued viral spread and excess morbidity and mortality. This study investigates whether testing strategies based on sample pooling can increase the speed and throughput of screening for SARS-CoV-2, especially in resource-limited settings. Methods In a mathematical modelling approach conducted in May 2020, six different testing strategies were simulated based on key input parameters such as infection rate, test characteristics, population size, and testing capacity. The situations in five countries were simulated, reflecting a broad variety of population sizes and testing capacities. The primary study outcome measurements were time and number of tests required, number of cases identified, and number of false positives. Findings The performance of all tested methods depends on the input parameters, i.e. the specific circumstances of a screening campaign. To screen one tenth of each country’s population at an infection rate of 1%, realistic optimised testing strategies enable such a campaign to be completed in ca. 29 days in the US, 71 in the UK, 25 in Singapore, 17 in Italy, and 10 in Germany. This is ca. eight times faster compared to individual testing. When infection rates are lower, or when employing an optimal, yet more complex pooling method, the gains are more pronounced. Pool-based approaches also reduce the number of false positive diagnoses by a factor of up to 100. Conclusions The results of this study provide a rationale for adoption of pool-based testing strategies to increase speed and throughput of testing for SARS-CoV-2, hence saving time and resources compared with individual testing.

scholarly journals Increasing SARS-CoV-2 RT-qPCR testing capacity by sample pooling

2020 ◽  
Author(s):  
Julia Alcoba-Florez ◽  
Helena Gil-Campesino ◽  
Diego García-Martínez de Artola ◽  
Oscar Díez-Gil ◽  
Agustín Valenzuela-Fernández ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
Tertiary Hospital ◽  
Pool Size ◽  
The Real ◽  
Minimal Loss ◽  
Sample Pooling ◽  
One Step ◽  
The Individual ◽  
Limited Testing ◽  
Pool Sizes

AbstractObjectivesLimited testing capacity has characterized the ongoing COVID-19 pandemic in Spain, hampering a timely control of outbreaks and the possibilities to reduce the escalation of community transmissions. Here we investigated the potential of using pooling of samples followed by one-step retrotranscription and quantitative PCR (RT-qPCR) to increase SARS-CoV-2 testing capacity.MethodsWe first evaluated different sample pooling (1:5, 1:10 and 1:15) prior to RNA extractions followed by standard RT-qPCR for SARS-CoV-2/COVID-19 diagnosis. The pool size achieving reproducible results in independent tests was then used for assessing nasopharyngeal samples in a tertiary hospital during August 2020.ResultsWe found that pool size of five samples achieved the highest sensitivity compared to pool sizes of 10 and 15, showing a mean (± SD) Ct shift of 3.5 ± 2.2 between the pooled test and positive samples in the pool. We then used a pool size of five to test a total of 895 pools (4,475 prospective samples) using two different RT-qPCR kits available at that time. The Real Accurate Quadruplex corona-plus PCR Kit (PathoFinder) reported the lowest mean Ct (± SD) shift (2.2 ± 2.4) among the pool and the individual samples. The strategy allows detecting individual samples in the positive pools with Cts in the range of 16.7-39.4.ConclusionsWe found that pools of five samples combined with RT-qPCR solutions helped to increase SARS-CoV-2 testing capacity with minimal loss of sensitivity compared to that resulting from testing the samples independently.

scholarly journals Pooling of Nasopharyngeal Swab Specimens for SARS-CoV-2 detection by RT-PCR

2020 ◽  
Author(s):  
Ignacio Torres ◽  
Eliseo Albert ◽  
David Navarro
Keyword(s):  
Large Population ◽  
Rdrp Gene ◽  
Contact Tracing ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Case Identification ◽  
E Gene ◽  
Sample Pooling ◽  
Community Transmission ◽  
Pcr Targeting

ABSTRACTSystematic testing of large population groups by RT-PCR is mandatory to Covid-19 case identification and contact tracing in order to minimize the likelyhood of resurgence in contagion. Sample pooling for RT-PCR has been effectively used to detect community transmission of SARS CoV-2. Nevertheless, this procedure may decrease the sensitivity of RT-PCR assays due to specimen dilution. We evaluated the efficacy of this strategy for diagnosis of Covid-19 using a sensitive commercially-available RT-PCR targeting SARS CoV-2 E and RdRp genes in a single reaction. A total of 20 mini-pools containing either 5 (n=10) or 10 (n=10) nasopharyngeal exudates collected in universal transport medium were made, each of which including a unique positive NP specimen. Positive specimens yielding CT <32 for the E gene (6 out of 10) or <35.2 for the RdRP gene (7 out of 10) were detected in mini-pools of both sizes. In contrast, most NP samples displaying CTs > 35.8 for the E gene or 35.7 for the RdRP gene remained undetected in mini-pools of 5 specimens (3/4 and 2/3, respectively) or in mini-pools of 10 samples (4/4 and 3/3, respectively.

scholarly journals Optimal size of sample pooling for RNA pool testing: an avant-garde for scaling up SARS CoV 2 testing

2020 ◽  
Author(s):  
Khodare Arvind ◽  
Padhi Abhishek ◽  
Gupta Ekta ◽  
Agarwal Reshu ◽  
Dubey Shantanu ◽  
...  
Keyword(s):  
Clinical Sample ◽  
Scale Up ◽  
Maximum Size ◽  
Scaling Up ◽  
Positive Sample ◽  
Pool Size ◽  
Optimal Size ◽  
Innovative Strategies ◽  
Diagnostic Kits ◽  
Sample Pooling

AbstractIntroductionTimely diagnosis is essential for the containment of the disease and breaks in the chain of transmission of SARS-CoV-2. The present situation demands countries to scale up their testing and design innovative strategies to conserve diagnostic kits and reagents. The pooling of samples saves time, manpower, and most importantly diagnostic kits and reagents. In the present study, we tried to define the pool size that could be applied with acceptable confidence for testing.Material and methodsWe used repeatedly tested positive clinical sample elutes having different levels of SARS CoV 2 RNA and negative sample elutes to prepare seven series of 11 pools each, having pool sizes ranging from 2 to 48 samples to estimate the optimal pool size. Each pool had one positive sample elute in different compositions. All the pools were tested by SARS CoV 2 RT-qPCR.ResultsOut of the 77 pools, only 53 (68.8%) were found positive. The sensitivity of pools of 2 to 48 samples was decreased from 100% (95% CL; 98.4-100) to 41.41% (95% CL; 34.9-48.1). The maximum size of the pool with acceptable sensitivity (>95%) was found to be of 6 samples. For the pool size of 6 samples, the sensitivity was 97.8% and the efficiency of pooling was 0.38.ConclusionThe pooling of samples is a practical way for scaling up testing and ultimately containing the further spread of the COVID-19 pandemic.

scholarly journals Implementation of Antibody Rapid Diagnostic Testing versus Real-Time Reverse Transcription-PCR Sample Pooling in the Screening of COVID-19: a Case of Different Testing Strategies in Africa

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Tinashe K. Nyazika ◽  
Rabelani Kaela ◽  
Mathias Mugoni ◽  
Kudakwashe Musomekwa ◽  
Eric Kyei-Baafour ◽  
...  
Keyword(s):  
Real Time ◽  
Reverse Transcription ◽  
Disease Burden ◽  
Diagnostic Testing ◽  
Single Test ◽  
African Countries ◽  
Rapid Diagnostic Testing ◽  
Reverse Transcription Pcr ◽  
Testing Strategies ◽  
Sample Pooling

ABSTRACT Coronavirus disease 2019 (COVID-19) has wreaked havoc across the globe; although the number of cases in Africa remains lower than in other regions, it is on a gradual upward trajectory. To date, COVID-19 cases have been reported in 54 out of 55 African countries. However, due to limited severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time reverse transcription-PCR (rRT-PCR) testing capacity and scarcity of testing reagents, it is probable that the total number of cases could far exceed published statistics. In this viewpoint, using Ghana, Malawi, South Africa, and Zimbabwe as examples of countries that have implemented different testing strategies, we argue that the implementation of sample pooling for rRT-PCR over antibody rapid diagnostic testing could have a greater impact in assessing disease burden. Sample pooling offers huge advantages compared to single test rRT-PCR, as it reduces diagnostic costs, personnel time, burnout, and analytical run times. Africa is already strained in terms of testing resources for COVID-19; hence, cheaper alternative ways need to be implemented to conserve resources, maximize mass testing, and reduce transmission in the wider population.

scholarly journals Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Imene Handous ◽  
Naila Hannachi ◽  
Manel Marzouk ◽  
Olfa Hazgui ◽  
Nissaf Bouafif Ep Ben Alaya ◽  
...  
Keyword(s):  
High Viral Load ◽  
Nasopharyngeal Swab ◽  
Individual Sample ◽  
Rt Pcr ◽  
False Negatives ◽  
Pooled Testing ◽  
Sample Pooling ◽  
Sample Testing ◽  
The Mean ◽  
Low Prevalence

Abstract Background The detection of SARS-CoV-2 using qRT-PCR with the pooling of samples can reduce workload and costs especially when the prevalence rate of COVID-19 in a population is low. To analyse the effect of pooling samples on the sensitivity of RT-qPCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection, we compared the cycle threshold (Ct) values of pools of 5 and 10 that tested positive with Ct values of individual samples that tested positive in that pool. Twenty positive nasopharyngeal (NP) specimens with low to high viral load were selected and pooled individually with four and nine negative NP. Results In NP specimens, the sensitivity of pools of 5 and 10 were 90 and 85%, compared to individual sample testing, respectively. The RT-qPCR sensitivity of pools of 5 and 10 against individual testing were not significantly different (p > 0.05). Detection of positive samples with low Ct values (< 36) was consistently achieved in pools of 5 and 10. However, there were higher false negatives when samples with high ct values (> 36) were pooled and tested. The mean Ct values obtained with the 5-sample pooled testing exceeded individual sample testing by 1.85 ± 1.09 cycles, while Ct values obtained with the 10-sample pooling exceeded individual sample testing by 3.4 ± 1.65 cycles. Conclusions In a low prevalence setting, testing capacity can be increased by pooling 5 or 10 samples, but the risk of additional false negatives needs to be considered

scholarly journals Head-to-head comparison of SARS-CoV-2 antigen-detecting rapid test with professional-collected anterior nasal versus nasopharyngeal swab

2020 ◽  
Author(s):  
Andreas K. Lindner ◽  
Olga Nikolai ◽  
Chiara Rohardt ◽  
Susen Burock ◽  
Claudia Hülso ◽  
...  
Keyword(s):  
Healthcare Professionals ◽  
Rapid Test ◽  
High Viral Load ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Test Procedures ◽  
Testing Strategies ◽  
Percent Agreement ◽  
Accuracy Study ◽  
Antigen Testing

AbstractBackgroundNasopharyngeal (NP) swab samples for antigen-detecting rapid diagnostic tests (Ag-RDTs) require qualified healthcare professionals and are frequently perceived as uncomfortable by patients.MethodsWe performed a manufacturer-independent, prospective diagnostic accuracy study, comparing professional-collected anterior nasal (AN) to nasopharyngeal swab, using the test kits of a WHO-listed SARS-CoV-2 Ag-RDT (STANDARD Q COVID-19 Ag Test, SD Biosensor), which is also being distributed by Roche. Individuals with high suspicion for COVID-19 infection were tested. The reference standard was RT-PCR using a combined oro-/nasopharyngeal swab sample. Percent positive and negative agreement, as well as sensitivity and specificity were calculated.ResultsAmong the 179 participants, 41 (22.9%) tested positive for SARS-CoV-2 by RT-PCR. The positive percent agreement of the two different sampling techniques for the Ag-RDT was 93.5% (CI 79.3-98.2). The negative percent agreement was 95.9% (CI 91.4-98.1). The Ag-RDT with AN-sampling showed a sensitivity of 80.5% (33/41 PCR positives detected; CI 66.0-89.8) and specificity of 98.6% (CI 94.9-99.6) compared to RT-PCR. The sensitivity with NP-sampling was 73.2% (30/41 PCR positives detected; CI 58.1-84.3) and specificity was 99.3% (CI 96.0-100). In patients with high viral load (>7.0 log10 RNA SARS-CoV2/swab), the sensitivity of the Ag-RDT with AN-sampling was 100% and 94.7% with NP-sampling.ConclusionThis study demonstrates that sensitivity of a WHO-listed SARS-CoV-2 Ag-RDT using a professional AN-sampling kit is at least equal to that of the NP-sampling kit, although confidence intervals overlap. Of note, differences in the IFUs of the test procedures could have contributed to different sensitivities. AN-sampling can be performed with less training, reduces patient discomfort, and it enables scaling of antigen testing strategies. Additional studies of patient self-sampling should be considered to further facilitate the scaling-up of Ag-RDT testing.

scholarly journals Identifying Optimal COVID-19 Testing Strategies for Schools and Businesses: Balancing Testing Frequency, Individual Test Technology, and Cost

2020 ◽  
Author(s):  
Gregory D. Lyng ◽  
Natalie E. Sheils ◽  
Caleb J. Kennedy ◽  
Daniel Griffin ◽  
Ethan M. Berke
Keyword(s):  
High Frequency ◽  
Cost Savings ◽  
Disease Prevalence ◽  
Sensitivity Test ◽  
Cumulative Number ◽  
Test Sensitivity ◽  
Testing Strategies ◽  
Testing Frequency ◽  
Sample Pooling ◽  
The Impact

ABSTRACTBackgroundCOVID-19 test sensitivity and specificity have been widely examined and discussed yet optimal use of these tests will depend on the goals of testing, the population or setting, and the anticipated underlying disease prevalence. We model various combinations of key variables to identify and compare a range of effective and practical surveillance strategies for schools and businesses.MethodsWe coupled a simulated data set incorporating actual community prevalence and test performance characteristics to a susceptible, infectious, removed (SIR) compartmental model, modeling the impact of base and tunable variables including test sensitivity, testing frequency, results lag, sample pooling, disease prevalence, externally-acquired infections, and test cost on outcomes case reduction.ResultsIncreasing testing frequency was associated with a non-linear positive effect on cases averted over 100 days. While precise reductions in cumulative number of infections depended on community disease prevalence, testing every 3 days versus every 14 days (even with a lower sensitivity test) reduces the disease burden substantially. Pooling provided cost savings and made a high-frequency approach practical; one high-performing strategy, testing every 3 days, yielded per person per day costs as low as $1.32.ConclusionsA range of practically viable testing strategies emerged for schools and businesses. Key characteristics of these strategies include high frequency testing with a moderate or high sensitivity test and minimal results delay. Sample pooling allowed for operational efficiency and cost savings with minimal loss of model performance.

scholarly journals Effectiveness of Sample Pooling Strategies for SARS-CoV-2 Mass Screening by RT-PCR: A Scoping Review

2020 ◽  
Vol 12 (03) ◽  
pp. 212-218 ◽  
Author(s):  
Sangeeta Deka ◽  
Deepjyoti Kalita
Keyword(s):  
Limit Of Detection ◽  
Large Population ◽  
Pool Size ◽  
High Threshold ◽  
Conservation Of Resources ◽  
Rt Pcr ◽  
Sample Pooling ◽  
Sample Testing ◽  
Low Prevalence ◽  
Pooled Sample

AbstractThe ongoing COVID-19 pandemic has hugely impacted the economy of many countries, and there is an acute shortage of diagnostic resources. With the exponential increase in the number of cases and necessity to screen large number of people, there is a steep increase in the demand for diagnostic kits. Pooled-sample testing is a promising strategy to screen a large population rapidly with limited resources. The aim of this work was to compile a cohesive literature review of the effectiveness and accuracy of pooled-sample testing in the detection of SARS-CoV-2 and critically analyze its limitations. Medline, Google Scholar, Embase, and preprint servers (e.g., bioRxiv) were searched for literature on pooled testing for diagnosis of COVID-19, and out of initial 60 articles/reports, nine original articles were retained. Optimal pool size (number of samples in a pool) seemed to be dependent on factors like prevalence or rate of positivity in community. In low-prevalence localities pool size of around 30 seemed to be effective as observed by some authors. All the researchers had found significant reduction in number of tests (depending on pool size, stages, and pooling design), leading to conservation of resources. Pooling can be done with extracted RNA eluate or directly with patient’s sample before extraction. This leads to further reduction in consumables, time and manpower. Risk of false negativity in samples with high-threshold cycle (i.e., low-viral load) value was a concern. Some researchers suggest adding few additional cycles to lower the chances of missing positive cases with low-Ct value. Lower limit of detection (LoD) of RT-PCR kits, that is, sensitivity of kits was another factor to consider. Thus, in a country like India, given the economic benefit and scarcity of resources, pooling strategy can be very effective, especially in low-prevalence areas and in low-risk contacts.

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