scholarly journals Safe and effective pool testing for SARS-CoV-2 detection

2021 ◽  
Author(s):  
Marie Wunsch ◽  
Dominik Aschemeier ◽  
Eva Heger ◽  
Denise Ehrentraut ◽  
Jan Krueger ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Pool Size ◽  
Public Health Issue ◽  
Viral Loads ◽  
Pooling Strategies ◽  
Pooling Strategy ◽  
Pcr Assays ◽  
Low Prevalence ◽  
The Impact

Background / Objectives: The global spread of SARS-CoV-2 is a serious public health issue. Large-scale surveillance screenings are crucial but can exceed diagnostic test capacities. We set out to optimize test conditions and implemented high throughput pool testing of respiratory swabs into SARS-CoV-2 diagnostics. Study design: In preparation for pool testing, we determined the optimal pooling strategy and pool size. In addition, we measured the impact of vortexing prior to sample processing, compared pipette- and swab-pooling method as well as the sensitivity of three different PCR assays. Results: Using optimized strategies for pooling, we systematically pooled 55,690 samples in a period of 44 weeks resulting in a reduction of 47,369 PCR reactions. In a low prevalence setting, we defined a preferable pool size of ten in a two-stage hierarchical pool testing strategy. Vortexing of the swabs increased cellular yield by a factor of 2.34, and sampling at or shortly after symptom onset was associated with higher viral loads. By comparing different pooling strategies, pipette-pooling was more efficient compared to swab-pooling. Conclusions: For implementing pooling strategies into high throughput diagnostics, we recommend to apply a pipette-pooling method, using pool sizes of ten samples, performing sensitivity validation of the PCR assays used, and vortexing swabs prior to analyses. Our data shows, that pool testing for SARS-CoV-2 detection is feasible and highly effective in a low prevalence setting.

Accelerating Large-Format Metal Additive Manufacturing: How Controls R&D Is Driving Speed, Scale, and Efficiency

2020 ◽  
Author(s):  
Brian T. Gibson ◽  
Paritosh Mhatre ◽  
Michael C. Borish ◽  
Justin L. West ◽  
Emma D. Betters ◽  
...  
Keyword(s):  
Additive Manufacturing ◽  
Large Scale ◽  
Closed Loop ◽  
Size Control ◽  
Pool Size ◽  
Large Format ◽  
Layer Height ◽  
Melt Pool ◽  
The Impact ◽  
Melt Pool Size

Abstract This article highlights work at Oak Ridge National Laboratory’s Manufacturing Demonstration Facility to develop closed-loop, feedback control for laser-wire based Directed Energy Deposition, a form of metal Big Area Additive Manufacturing (m-BAAM), a process being developed in partnership with GKN Aerospace specifically for the production of Ti-6Al-4V pre-forms for aerospace components. A large-scale structural demonstrator component is presented as a case-study in which not just control, but the entire 3D printing workflow for m-BAAM is discussed in detail, including design principles for large-format metal AM, toolpath generation, parameter development, process control, and system operation, as well as post-print net-shape geometric analysis and finish machining. In terms of control, a multi-sensor approach has been utilized to measure both layer height and melt pool size, and multiple modes of closed-loop control have been developed to manipulate process parameters (laser power, print speed, deposition rate) to control these variables. Layer height control and melt pool size control have yielded excellent local (intralayer) and global (component-level) geometry control, and the impact of melt pool size control in particular on thermal gradients and material properties is the subject of continuing research. Further, these modes of control have allowed the process to advance to higher deposition rates (exceeding 7.5 lb/hr), larger parts (1-meter scale), shorter build times, and higher overall efficiency. The control modes are examined individually, highlighting their development, demonstration, and lessons learned, and it is shown how they operate concurrently to enable the printing of a large-scale, near net shape Ti-6Al-4V component.

scholarly journals High-Throughput PCR Assays To Monitor Wolbachia Infection in the Dengue Mosquito (Aedes aegypti) and Drosophila simulans

2012 ◽  
Vol 78 (13) ◽  
pp. 4740-4743 ◽  
Author(s):  
Siu F. Lee ◽  
Vanessa L. White ◽  
Andrew R. Weeks ◽  
Ary A. Hoffmann ◽  
Nancy M. Endersby
Keyword(s):  
Aedes Aegypti ◽  
High Throughput ◽  
Large Scale ◽  
Wolbachia Infection ◽  
Drosophila Simulans ◽  
Content Type ◽  
Pcr Assays ◽  
Cost Efficient

ABSTRACTWe have developed and validated two new fluorescence-based PCR assays to detect theWolbachia wMel strain inAedes aegyptiand thewRi andwAu strains inDrosophila simulans. The new assays are accurate, informative, and cost-efficient for large-scaleWolbachiascreening.

GWAS Indicates the Presence of Rare Immunogenetic Polymorphisms as Possible Predisposition Factors in Aplastic Anemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1093-1093
Author(s):  
Bartlomiej P Przychodzen ◽  
Monika Jasek ◽  
Sandra P Smieszek ◽  
Ron Paquette ◽  
Rainer Richter ◽  
...  
Keyword(s):  
Aplastic Anemia ◽  
Genetic Variants ◽  
Large Scale ◽  
Disease Risk ◽  
Conflicts Of Interest ◽  
New Paradigm ◽  
Genetic Traits ◽  
Network Analyses ◽  
Low Prevalence ◽  
The Impact

Abstract Abstract 1093 Poster Board I-115 While immune mechanisms are involved in the pathogenesis of idiopathic aplastic anemia (AA), due to the impact of exogenous factors and the low prevalence of AA, this disease is not easily amenable to genetic studies. With the advent of whole genome scanning (WGS) technologies such as single nucleotide polymorphism arrays (SNP-A), large scale investigations in various disorders have been conducted. A systems level understanding of particular disease can allows for identification of candidate genetic variants as prognostic and diagnostic markers. We have applied 6.0 SNP-A containing 924644 SNP probes to conduct a comprehensive GWAS in AA with the aim of identifying low prevalence genetic variants that contribute to the pathogenesis of this condition and contribute to individual disease risk. We studied 124 AA patients and significant cohort of 2230 controls that increase detection power using SNP-A. After exclusion of SNP's with call rate of <95% and those with violation of Hardy Weinberg equilibrium (p<.01), 809.802 SNPs (87.5% of initial set) were passed for further investigation. Single allele χ2 statistics for all autosomal markers were performed. 1935 SNP's pointing towards genes with minor allele frequency (MAF) <10% and p<.001 after Bonferroni correction (more stringent than False Discovery Rate) were selected. Of great interest was the top scoring non synonymous SNP (1/38) rs1028180 located in BLZF1 (OR 6.62) involved in cell proliferation and growth. It was represented by singular marker (p<1×10–4) occurring at a heterozygous frequency of 15% vs. 3.5% in controls, and a homozygous frequency of 3.7% vs. 0% in controls. A total of 1 non-synonymous and 3 strongest intronic SNPs were prioritized for final investigation. These included rs9566991, rs1773557 and rs1495963 and directed to informative genes TNFSF11 (OR 6.24), CD247 (OR 3.52) and IL12RB2 (OR 7.04), respectively. Remarkably, several informative LD blocks were identified represented by multiple markers pointing to the presence of informative polymorphisms in the corresponding regions. TNFSF1 gene was represented by marker rs9566991 (p<1×10–3) occurring at the heterozygous frequency of 15.4% vs. 2.7% in controls. The corresponding MAF was 7.6% vs. 1.3%. A second potential locus identified in our study (CD247) was represented by rs1773557 marker (p<1×10–20) occurring at a heterozygous frequency of 19.6% vs. 5.9% in controls, and in homozygous frequency of 0% vs. 0% in controls. Other SNPs including rs1737501, rs1737502 pointed to the same locus. IL12RB2 was represented by a singular marker rs1495963 (p<1×10–6) occurring at the heterozygous frequency of 24% vs. allelic frequency of 3.2% in controls. MAF were 12% versus 1.9%. Another potential loci marked by rs17131583 was TGFBR3. Analysis targeting individual SNP has been the primary focus of GWAS but such an approach offers only limited understanding of the complex diseases as not an individual SNP, and rather a joint action of several SNPs results in particular outcomes. Consequently, in study of AA, we applied the network gene association analysis as a new paradigm incorporating both “operator OR” and “operator AND” thereby allowing for dependence and independence testing. Consequently, the proposed paradigm may lead to identification of meaningful pathways. We performed a simulation study, where genotypes were randomly drawn including homozygous reference, heterozygous and homozygous variant for each SNP Si = 1, 50 where the MAF of SNP is chosen uniformly at random. Of great interest was a pair consisting of rs1737501 CD247 and rs1495963 IL12RB2 both in heterozygous variant, involving operator AND at p<1×10–23. It was reported with occurrence of 12.2% in patients and 0.005% in controls giving a specificity score of 99.995%. In addition to the described pair, SNP in strong LD within CD247 (rs1737502) was scored again together with rs1495963. Functionally, both genes are involved in regulation response. Another pair rs16908086 and rs1773557 that pointed together to CD247 and MRVI2 created a pair with occurrence 21% versus and 3% in controls. In sum, our study constituted the first network analyses of predisposing factors and complex genetic traits enriched in informative loci in immunoregulatory genes. Rare polymorphic variants of these genes may constitute risk factors for development of AA. Disclosures No relevant conflicts of interest to declare.

scholarly journals Swab pooling for large-scale RT-qPCR screening of SARS-CoV-2

2020 ◽  
Author(s):  
Ana Paula Christoff ◽  
Giuliano Netto Flores Cruz ◽  
Aline Fernanda Rodrigues Sereia ◽  
Dellyana Rodrigues Boberg ◽  
Daniela Carolina de Bastiani ◽  
...  
Keyword(s):  
Large Scale ◽  
Sample Collection ◽  
Laboratory Capacity ◽  
Positive Individual ◽  
Sample Pooling ◽  
Pooling Strategies ◽  
Low Prevalence ◽  
Pooled Samples ◽  
Sample Dilution ◽  
Large Scale Screening

Pool testing has been proposed as an alternative for large-scale SARS-CoV-2 screening. However, dilution factors proportional to the number of pooled samples have been a source of major concern regarding its diagnostic performance. Further, sample pooling can lead to increased laboratory workload and operational complexity. Therefore, pooling strategies that minimize sample dilution, loss of sensitivity, and laboratory overload are needed to allow reliable and large-scale screenings of SARS-CoV-2. Here, we describe a pooling procedure in which nasopharyngeal swabs are pooled together at the time of sample collection (swab pooling), decreasing laboratory manipulation and minimizing dilution of the viral RNA present in the samples. Paired analysis of pooled and individual samples from 613 patients revealed 94 positive individual tests. Having individual testing as a reference, no false-positives or false-negatives were observed for swab pooling. A Bayesian model estimated a sensitivity of 99% (Cr.I. 96.9% to 100%) and a specificity of 99.8% (Cr.I. 99.4% to 100%) for the swab pooling procedure. Data from additional 18,922 patients screened with swab pooling were included for further quantitative analysis. Mean Cq differences between individual and corresponding pool samples ranged from 0.1 Cq (Cr.I. -0.98 to 1.17) to 2.09 Cq (Cr.I. 1.24 to 2.94). Overall, 19,535 asymptomatic and presymptomatic patients were screened using 4,400 RT-qPCR assays, resulting in 246 positive patients (positivity rate 1.26%). This corresponds to an increase of 4.4 times in laboratory capacity and a reduction of 77% in required tests. Finally, these data demonstrate that swab pooling can significantly minimize sample dilution and sensitivity issues commonly seen in its traditional counterpart. Therefore, swab pooling represents a major alternative for reliable and large-scale screening of SARS-CoV-2 in low prevalence populations.

scholarly journals Efficient and Practical Sample Pooling for High-Throughput PCR Diagnosis of COVID-19

2020 ◽  
Author(s):  
Haran Shani-Narkiss ◽  
Omri David Gilday ◽  
Nadav Yayon ◽  
Itamar Daniel Landau
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Diagnostic Testing ◽  
Target Frequency ◽  
Public Health Agencies ◽  
Highly Efficient ◽  
Pcr Diagnosis ◽  
Sample Pooling ◽  
Pooling Strategies ◽  
Technical Advances

AbstractIn the global effort to combat the COVID-19 pandemic, governments and public health agencies are striving to rapidly increase the volume and rate of diagnostic testing. The most common form of testing today employs Polymerase Chain Reaction in order to identify the presence of viral RNA in individual patient samples one by one. This process has become one of the most significant bottlenecks to increased testing, especially due to reported shortages in the chemical reagents needed in the PCR reaction.Recent technical advances have enabled High-Throughput PCR, in which multiple samples are pooled into one tube. Such methods can be highly efficient, saving large amounts of time and reagents. However, their efficiency is highly dependent on the frequency of positive samples, which varies significantly across regions and even within regions as testing criterion and conditions change.Here, we present two possible optimized pooling strategies for diagnostic SARS-CoV-2 testing on large scales, both addressing dynamic conditions. In the first, we employ a simple information-theoretic heuristic to derive a highly efficient re-pooling protocol: an estimate of the target frequency determines the initial pool size, and any subsequent pools found positive are re-pooled at half-size and tested again. In the range of very rare target (<0.05), this approach can reduce the number of necessary tests dramatically, for example, achieving a reduction by a factor of 50 for a target frequency of 0.001. The second method is a simpler approach of optimized one-time pooling followed by individual tests on positive pools. We show that this approach is just as efficient for moderate target-product frequencies (0.05<0.2), for example, achieving a two-fold in the number of when the frequency of positive samples is 0.07.These strategies require little investment, and they offer a significant reduction in the amount of materials, equipment and time needed to test large numbers of samples. We show that both these pooling strategies are roughly comparable to the absolute upper-bound efficiency given by Shannon’s source coding theorem. We compare our strategies to the naïve way of testing and to alternative matrix-pooling methods. Most importantly, we offer straightforward, practical pooling instructions for laboratories that perform large scale PCR assays to diagnose SARS-CoV-2 viral particles. These two pooling strategies may offer ways to alleviate the bottleneck currently preventing massive expansion of SARS-CoV-2 testing around the world.

scholarly journals Can the High Sensitivity of Xpert MTB/RIF Ultra Be Harnessed to Save Cartridge Costs? Results from a Pooled Sputum Evaluation in Cambodia

2020 ◽  
Vol 5 (1) ◽  
pp. 27 ◽  
Author(s):  
Monyrath Chry ◽  
Marina Smelyanskaya ◽  
Mom Ky ◽  
Andrew J Codlin ◽  
Danielle Cazabon ◽  
...  
Keyword(s):  
High Sensitivity ◽  
World Health ◽  
Potential Cost ◽  
Pooled Testing ◽  
Molecular Tests ◽  
Pooling Strategies ◽  
Pooling Strategy ◽  
Health Organization ◽  
The Impact ◽  
Positive Results

Despite the World Health Organization recommending the use of rapid molecular tests for diagnosing tuberculosis (TB), uptake has been limited, partially due to high cartridge costs. Other infectious disease programs pool specimens to save on diagnostic test costs. We tested a sputum pooling strategy as part of a TB case finding program using Xpert MTB/RIF Ultra (Ultra). All persons were tested with Ultra individually, and their remaining specimens were also grouped with 3–4 samples for testing in a pooled sample. Individual and pooled testing results were compared to see if people with TB would have been missed when using pooling. We assessed the potential cost and time savings which different pooling strategies could achieve. We tested 584 individual samples and also grouped them in 153 pools for testing separately. Individual testing identified 91 (15.6%) people with positive Ultra results. One hundred percent of individual positive results were also found to be positive by the pooling strategy. Pooling would have saved 27% of cartridge and processing time. Our results are the first to use Ultra in a pooled approach for TB, and demonstrate feasibility in field conditions. Pooling did not miss any TB cases and can save time and money. The impact of pooling is only realized when yield is low.

scholarly journals The impact of childhood lead exposure on adult personality: Evidence from the United States, Europe, and a large-scale natural experiment

2021 ◽  
Vol 118 (29) ◽  
pp. e2020104118
Author(s):  
Ted Schwaba ◽  
Wiebke Bleidorn ◽  
Christopher J. Hopwood ◽  
Jochen E. Gebauer ◽  
P. Jason Rentfrow ◽  
...  
Keyword(s):  
Lead Exposure ◽  
Large Scale ◽  
Natural Experiment ◽  
Well Being ◽  
The United States ◽  
Public Health Issue ◽  
Personality Profiles ◽  
Personality Differences ◽  
Lead Levels ◽  
The Impact

Childhood lead exposure has devastating lifelong consequences, as even low-level exposure stunts intelligence and leads to delinquent behavior. However, these consequences may be more extensive than previously thought because childhood lead exposure may adversely affect normal-range personality traits. Personality influences nearly every aspect of human functioning, from well-being to career earnings to longevity, so effects of lead exposure on personality would have far-reaching societal consequences. In a preregistered investigation, we tested this hypothesis by linking historic atmospheric lead data from 269 US counties and 37 European nations to personality questionnaire data from over 1.5 million people who grew up in these areas. Adjusting for age and socioeconomic status, US adults who grew up in counties with higher atmospheric lead levels had less adaptive personality profiles: they were less agreeable and conscientious and, among younger participants, more neurotic. Next, we utilized a natural experiment, the removal of leaded gasoline because of the 1970 Clean Air Act, to test whether lead exposure caused these personality differences. Participants born after atmospheric lead levels began to decline in their county had more mature, psychologically healthy adult personalities (higher agreeableness and conscientiousness and lower neuroticism), but these findings were not discriminable from pure cohort effects. Finally, we replicated associations in Europeans. European participants who spent their childhood in areas with more atmospheric lead were less agreeable and more neurotic in adulthood. Our findings suggest that further reduction of lead exposure is a critical public health issue.

scholarly journals Large-scale Testing for SARS-CoV-2 using Tapestry Pooling

2020 ◽  
Author(s):  
Anirudh Chakravarthy ◽  
Srikar Krishna ◽  
Sumana Ghosh ◽  
Ajay Tomar ◽  
Sriram Varahan ◽  
...  
Keyword(s):  
Prevalence Rate ◽  
Large Scale ◽  
False Negative ◽  
Pool Size ◽  
Prevalence Rates ◽  
Recovery Algorithm ◽  
Viral Loads ◽  
Large Scale Testing ◽  
The Individual ◽  
Pool Sizes

AbstractWe have previously described Tapestry Pooling, a scheme to enhance the capacity of RT-qPCR testing, and provided experimental evidence with spiked synthetic RNA to show that it can help to scale testing and restart the economy. Here we report on validation studies with Covid19 patient samples for the Tapestry Pooling scheme with prevalence in the range of 1% to 2%. We pooled RNA extracted from patient samples that were previously tested for Covid19, sending each sample to three pools. Following three different pooling schemes, we pipetted 320 samples into 48 pools with pool size of 20 at prevalence rate of 1.6%, 500 samples into 60 pools with pool size of 25 at prevalence rate of 2%, and 961 samples into 93 pools with pool size of 31 at prevalence rate of 1%. Of the 191 RT-qPCR experiments that we performed, only one pool was incorrect (false negative). Our recovery algorithm correctly called results for the individual samples, with a 100% sensitivity and a 99.9% specificity, with only one false positive across all the 1,781 blinded results required to be called. We show up to 10X savings in number of tests required at a range of prevalence rates and pool sizes. These experiments establish that Tapestry Pooling is robust enough to handle the diversity of sample constitutions and viral loads seen in real-world samples.

scholarly journals The impact of childhood lead exposure on adult personality: Evidence from the US, Europe, and a large-scale natural experiment

2021 ◽  
Author(s):  
Ted Schwaba ◽  
Wiebke Bleidorn ◽  
Christopher James Hopwood ◽  
Jochen Gebauer ◽  
Jason Rentfrow ◽  
...  
Keyword(s):  
Lead Exposure ◽  
Large Scale ◽  
Natural Experiment ◽  
Well Being ◽  
Public Health Issue ◽  
Personality Profiles ◽  
Personality Differences ◽  
Lead Levels ◽  
Critical Public Health ◽  
The Impact

Childhood lead exposure has devastating lifelong consequences, as even low-level exposure stunts intelligence and leads to delinquent behavior. But these consequences may be more extensive than previously thought, because childhood lead exposure may adversely affect normal-range personality traits. Personality influences nearly every aspect of human functioning, from well-being to career earnings to longevity, so effects of lead exposure on personality would have far-reaching societal consequences. In a pre-registered investigation, we tested this hypothesis by linking historic atmospheric lead data from 269 US counties and 37 European nations to personality questionnaire data from over 1.5 million people who grew up in these areas. Adjusting for age and SES, US adults who grew up in counties with higher atmospheric lead levels had less adaptive personality profiles: they were less agreeable and conscientious, and, among younger participants, more neurotic. Next, we utilized a natural experiment, removal of leaded gasoline due to the 1970 Clean Air Act, to test whether lead exposure caused these personality differences. Participants born after atmospheric lead levels began to decline in their county had more mature, psychologically healthy adult personalities (higher agreeableness and conscientiousness, and lower neuroticism), but these findings were not discriminable from pure cohort effects. Finally, we replicated associations in Europeans. European participants who spent their childhood in areas with more atmospheric lead were less agreeable and more neurotic in adulthood. Our findings suggest that further reduction of lead exposure is a critical public health issue.

scholarly journals Multicenter evaluation of a fully automated high-throughput SARS-CoV-2 antigen immunoassay

2021 ◽  
Author(s):  
Dominik Noerz ◽  
Flaminia Olearo ◽  
Stojan Perisic ◽  
Matthais Bauer ◽  
Elena Riester ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Molecular Testing ◽  
Viral Loads ◽  
Critical Areas ◽  
Large Scale Testing ◽  
Antigen Assay ◽  
Antigen Tests ◽  
Lateral Flow Tests ◽  
Rna Concentration

Background: Molecular testing for SARS-CoV-2 continues to suffer from delays and shortages. Antigen tests have recently emerged as a viable alternative to detect patients with high viral loads, associated with elevated risk of transmission. While rapid lateral flow tests greatly improved accessibility of SARS-CoV-2 detection in critical areas, their manual nature limits scalability and suitability for large-scale testing schemes. The Elecsys® SARS-CoV-2 Antigen assay allows antigen immunoassays to be carried out on fully automated high-throughput serology platforms. Methods: A total of 3139 nasopharyngeal and oropharyngeal swabs were collected at 3 different testing sites in Germany. Swab samples were pre-characterized by RT-qPCR and consecutively subjected to the antigen immunoassay on either the cobas e411 or cobas e801 analyzers. Results: Of the tested respiratory samples, 392 were PCR positive for SARS-CoV-2 RNA. Median concentration was 2.95×104 (interquartile range [IQR] 5.1×102–3.5×106) copies/mL. Overall sensitivity and specificity of the antigen immunoassay were 60.5% (95% confidence interval [CI] 55.5–65.4) and 99.9% (95% CI 99.6–100), respectively. A 93.7% (95% CI 89.7–96.5) sensitivity was achieved at a viral RNA concentration ≥104 copies/mL (cycle threshold (Ct) value <29.9). Conclusion: The Elecsys SARS-CoV-2 Antigen assay reliably detected patient samples with viral loads of 10,000 copies/mL and higher. It thus represents a viable high-throughput alternative for pre-screening of patients, or in situations where PCR testing is not readily available.

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