Challenges and issues of SARS-CoV-2 pool testing.
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ABSTRACT:
SUBMITTER: Eberhardt JN
PROVIDER: S-EPMC7832072 | biostudies-literature | 2020 Nov
REPOSITORIES: biostudies-literature
Publications
Challenges and issues of SARS-CoV-2 pool testing.
Eberhardt Jens N JN Breuckmann Nikolas P NP Eberhardt Christiane S CS
The Lancet. Infectious diseases 20200714 11
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| S-EPMC7833783 | biostudies-literature
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| S-EPMC7836822 | biostudies-literature
Project description:ObjectivesThe global spread of SARS-CoV-2 is a serious public health issue. Large-scale surveillance screenings are crucial but can exceed test capacities. We (A) optimized test conditions and (B) implemented pool testing of respiratory swabs into SARS-CoV-2 diagnostics.Study design(A) We determined the optimal pooling strategy and pool size. In addition, we measured the impact of vortexing prior to sample processing, compared a pipette-pooling method (by combining transport medium of several specimens) and a swab-pooling method (by combining several swabs into a test tube filled with PBS) as well as determined the sensitivities of three PCR assays. (B) Finally, we applied high-throughput pool testing for diagnostics.Results(A) In a low prevalence setting, we defined a preferable pool size of ten in a two-stage hierarchical pool testing strategy. Vortexing of swabs (n = 33) increased cellular yield by a factor of 2.34. By comparing Ct-values of 16 pools generated with two different pooling strategies, pipette-pooling was more efficient compared to swab-pooling. Measuring dilution series of 20 SARS-CoV-2 positive samples in three PCR assays simultaneously revealed detection rates of 85% (assay I), 50% (assay II), and 95% (assay III) at a 1:100 dilution. (B) We systematically pooled 55,690 samples in a period of 44 weeks resulting in a reduction of 47,369 PCR reactions.ConclusionsFor implementing pooling strategies into high-throughput diagnostics, we recommend utilizing a pipette-pooling method, performing sensitivity validation of the PCR assays used, and vortexing swabs prior to analyses. Pool testing for SARS-CoV-2 detection is feasible and effective in a low prevalence setting.
| S-EPMC8552800 | biostudies-literature
Project description:In the current COVID19 crisis many national healthcare systems are confronted with an acute shortage of tests for confirming SARS-CoV-2 infections. For low overall infection levels in the population the pooling of samples can drastically amplify the testing capacity. Here we present a formula to estimate the optimal group-size for pooling, the efficiency gain (tested persons per test), and the expected upper bound of missed infections in pooled testing, all as a function of the population-wide infection levels and the false negative/positive rates of the currently used PCR tests. Assuming an infection level of 0.1% and a false negative rate of 2%, the optimal pool-size is about 34, and an efficiency gain of about 15 tested persons per test is possible. For an infection level of 1% the optimal pool-size is 11, the efficiency gain is 5.1 tested persons per test. For an infection level of 10% the optimal pool-size reduces to about 4, the efficiency gain is about 1.7 tested persons per test. For infection levels of 30% and higher there is no more benefit from pooling. To see to what extent replicates of the pooled tests improve the estimate of the maximal number of missed infections, we present results for 1 to 5 replicates.
| S-EPMC7641378 | biostudies-literature
Project description:BackgroundHospitals need to be protected from SARS-CoV-2 infections to protect vulnerable patients. Thus, a safe, efficient, and cost-effective SARS-CoV-2 testing system for hospitals, in addition to standard hygiene measures and vaccination of staff, is necessary. Here we report on the feasibility and performance of a pool real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) test system at, medium and high incidence.MethodsWe implemented a testing concept based on gargling at home and pooling of samples in the hospital before PCR testing in the laboratory. We used two PCR systems (point of care and standard 96-well plate system) to adapt to challenges in the hospital setting and respond to a rising incidence in the Omicron wave.FindingsDuring our 10-week study period, we performed 697 pool PCRs (8793 tests in total) and identified 65 asymptomatic staff members by pool PCR and 94 symptomatic staff members by positive individual PCR. Virus loads in those detected by pool testing were significantly lower (P<0.001). The test system remained workable even during the peak of the Omicron wave and no outbreaks occurred in any specific area of the hospital during the study period. Unvaccinated individuals were over-represented in the positively tested (37% vs 22% positive tests, P=0.04). The test procedure was well accepted by a majority of the hospital staff (84%).ConclusionRepeated gargle pool rRT-PCR testing can be implemented quickly in hospitals and is an effective, easily adaptable and well-accepted test system for hospitals, even during phases with very high infection rates.
| S-EPMC9166272 | biostudies-literature
Project description:BackgroundThe SARS-CoV-2 pandemic caused millions of infections worldwide. Among the strategies for effective containment, frequent and massive testing was fundamental. Although sample pooling allows multiplying the installed analysis capacity, the definition of the number of samples to include in a pool is commonly guided more by economic parameters than analytical quality.MethodsWe developed a mathematical model to determine the pooling conditions that maximize reagent efficiency and analytical sensitivity. We evaluated 30 samples individually and in 2-sample to 12-sample pools. Using Passing Bablok regressions, we estimated the shift of Ct values in the RT-qPCR reaction for each pool size. With this Ct shift, we estimated sensitivity in the context of the distribution of 1,030 individually evaluated positive samples.FindingsOur results showed that the most significant gain in efficiency occurred in the 4-sample pool, while at pools greater than 8-sample, there was no considerable reagent savings. Sensitivity significantly dropped to 87.18 %-92.52 % for a 4-sample pool and reached as low as 77.09 %-80.87 % in a 12-sample pooling.ConclusionsOur results suggest that a 4-sample pooling maximizes reagent efficiency and analytical sensitivity. These considerations are essential to increase testing capacity and efficiently detect and contain contagious.
| S-EPMC11761315 | biostudies-literature
Project description:Coronavirus disease (Covid-19) has reached unprecedented pandemic levels and is affecting almost every country in the world. Ramping up the testing capacity of a country supposes an essential public health response to this new outbreak. A pool testing strategy where multiple samples are tested in a single reverse transcriptase-polymerase chain reaction (RT-PCR) kit could potentially increase a country's testing capacity. The aim of this study is to propose a simple mathematical model to estimate the optimum number of pooled samples according to the relative prevalence of positive tests in a particular healthcare context, assuming that if a group tests negative, no further testing is done whereas if a group tests positive, all the subjects of the group are retested individually. The model predicts group sizes that range from 11 to 3 subjects. For a prevalence of 10% of positive tests, 40.6% of tests can be saved using testing groups of four subjects. For a 20% prevalence, 17.9% of tests can be saved using groups of three subjects. For higher prevalences, the strategy flattens and loses effectiveness. Pool testing individuals for severe acute respiratory syndrome coronavirus 2 is a valuable strategy that could considerably boost a country's testing capacity. However, further studies are needed to address how large these groups can be, without losing sensitivity on the RT-PCR. The strategy best works in settings with a low prevalence of positive tests. It is best implemented in subgroups with low clinical suspicion. The model can be adapted to specific prevalences, generating a tailored to the context implementation of the pool testing strategy.
| S-EPMC7264525 | biostudies-literature
Project description:BackgroundThe Severe Acute Respiratory Syndrome Coronavirus Disease 2019 (SARS-CoV-2) severely affects those above the age of 60 yr and those with other conditions. This study aimed to review the available evidence on older adult's issues in facing the COVID-19 pandemic.MethodsThe framework is based on scoping review of literature published from Jan 10 to Jul 31, 2020. Medline, Scopus, Web of Science, and Google Scholar databases and other sources of information, to identify grey literature, were selected for data collection. Two researchers independently screened all studies and extracted data. All types of studies published about SARS-CoV-2 and related to older adults' issues were eligible.ResultsOverall, 210 documents were included in the final analysis. Letter to the editor was the most frequent article format (20.95%). Most of the papers were from the United States (38.09%) and published in Jun 2020 (29.52%). After content analysis, six following themes were extracted: Supporting and information sources, e-health services, access to essential supplies, Long Term Care Facilities (LTCFs), physical and mental consequences of self-isolation, neglect of older adults, ageism and age discrimination.ConclusionIn the pandemic, there is an urgent need for interventional research and innovational implementations to address issues related to providing services for older adults. This can help older adults to maintain their physical and mental health, and reduce the spread of infection in nursing homes. Further studies focusing on the rights of the older adults are needed on all issues associated with COVID-19.
| S-EPMC8215059 | biostudies-literature
Project description:Aim: In our study, we propose the use of direct real-time polymerase chain reaction (RT-PCR), this test does not require extraction or a preheating step, which saves a lot of cost, labor, processing time and provides a solution for supply shortage. Materials & methods: We assayed 185 nasopharyngeal samples stored in viral transport media. The indirect method was done with RNA extraction step, and the direct RT-PCR was done without an extraction step, both assays were evaluated on a commercially validated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kit targeting E gene. Results: Our assay showed a sensitivity of 79%, a specificity of 100% and the agreement between methods was 72%. Conclusion: Overall, this simple direct RT-PCR approach can be utilized as a qualitative diagnostic tool for emergency SARS-CoV-2 surveillance in countries with limited resources and may help laboratories to continue testing and at greater frequency despite supply shortages, although with delay in cycle threshold value in comparison with indirect RT-PCR.
| S-EPMC7856914 | biostudies-literature
Project description:School closures have a negative impact on physical and mental well-being, and education, of children and adolescents. A surveillance programme to detect asymptomatic SARS-CoV-2 infection could allow schools to remain open, while protecting the vulnerable. We assessed the feasibility of a programme employing gargle samples and pool testing of individually extracted RNA using rRT-qPCR in a primary and a secondary school in Germany, based on programme logistics and acceptance. Twice a week, five participants per class were selected to provide samples, using an algorithm weighted by a risk-based priority score to increase likelihood of case detection. The positive response rate was 54.8% (550 of 1003 pupils). Logistics evaluation revealed the rate-limiting steps: completing the regular pre-test questionnaire and handing in the samples. Acceptance questionnaire responses indicated strong support for research into developing a surveillance programme and a positive evaluation of gargle tests. Participation was voluntary. As not all pupils participated, individual reminders could lead to participant identification. School-wide implementation of the programme for infection monitoring purposes would enable reminders to be given to all school pupils to address these steps, without compromising participant anonymity. Such a programme would provide a feasible means to monitor asymptomatic respiratory tract infection in schools.
| S-EPMC8484445 | biostudies-literature