scholarly journals High-Throughput Adaptable SARS-CoV-2 Screening for Rapid Identification of Dominant and Emerging Regional Variants

2021 ◽  
Author(s):  
Zita Hubler ◽  
Xiao Song ◽  
Cameron Norris ◽  
Mehul Jani ◽  
David Alouani ◽  
...  
Keyword(s):  
High Throughput ◽  
Screening Program ◽  
Low Cost ◽  
Severe Disease ◽  
Turnaround Time ◽  
Rapid Identification ◽  
List Type ◽  
Low Level ◽  
Tiered Approach ◽  
Selective Sequencing

ABSTRACTObjectivesEmerging SARS-CoV-2 variant strains can be associated with increased transmissibility, more severe disease, and reduced effectiveness of treatments. To improve the availability of regional variant surveillance, we describe a variant genotyping system that is rapid, accurate, adaptable, and able to detect new low-level variants built with existing hospital infrastructure.MethodsWe use a tiered high-throughput SARS-CoV-2 screening program to characterizes variants in a supra-regional health system over 76 days. Combining targeted qPCR and selective sequencing, we screen positive SARS-CoV-2 samples from all hospitals within our health care system for genotyping dominant and emerging variants.ResultsThe median turnaround for genotyping was two days using the high-throughput qPCR-based screen, allowing us to rapidly characterize the emerging Delta variant. In our population, the Delta variant is associated with a lower CT value, lower age at infection, and increased vaccine breakthrough cases. Detection of low-level and potentially emerging variants highlights the utility of a tiered approach.ConclusionsThese findings underscore the need for fast, low-cost, high-throughput monitoring of regional viral sequences as the pandemic unfolds and the emergence of SARS-CoV-2 variants increases. Combing qPCR-based screening with selective sequencing allows for rapid genotyping of variants and dynamic system improvement.Key messagesA tiered approach that uses qPCR-based screening to identify dominant variants and sequencing for unique variants maximizes throughput, turnaround time, and information gleaned from each sample.In our population, the Delta variant became dominant in less than a month and is associated with lower CT, lower age at infection, and increased breakthrough cases.We identified low-level variants, including the variant of interest B.1.621 and a Delta variant with an E484K mutation in our population using existing hospital infrastructure.

scholarly journals Comparison of Abbott COVID-19 testing Platforms for timely results- CMCVAMC experience

2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S138-S139
Author(s):  
S Patel ◽  
J M Petersen ◽  
D Jhala
Keyword(s):  
High Throughput ◽  
Patient Management ◽  
English Literature ◽  
Severe Disease ◽  
Random Access ◽  
Turnaround Time ◽  
P Value ◽  
Time Period ◽  
Average Turnaround Time

Abstract Introduction/Objective COVID-19 is a new disease, caused by the SARS-CoV-2 coronavirus capable of causing severe disease and death. The Alinity-m has a high throughput and random-access features that are not on the Abbott m2000, both of which had been validated and brought into clinical use for high throughput SARS-CoV-2 testing. The additional features of Alinity-m would be expected to improve turnaround time; however, there are no published reports in the English literature comparing the turnaround time between the Abbott m2000 and Alinity-m. Methods/Case Report A retrospective quality assurance search for all SARS-CoV-2 tests performed on the Abbott m2000 and Alinity-m (both Chicago IL) between February 1st 2021 to March 1st, 2021, to capture the turnaround time differences for the Abbott m2000 versus the Alinity-m for the month after the Alinity-m was brought into clinical service after validation. Results (if a Case Study enter NA) There was a total of 318 tests performed on the Abbott m2000 and 1329 tests performed on the Alinity-m during this time period. The average turnaround time on the Alinity was 6 hours, compared with 11 hours on the Abbott m2000. This difference was statistically significant by the t-test (p-value = <0.01). Both the optimized throughput and random-access features of the Alinity-m contributed significantly to this improvement. The Alinity-m is capable of producing results within 115 minutes for the first specimen and then 3 minutes for each sequential specimen. On the other hand, the Abbott m2000 must be batched in limited 8-12 hour runs without random access capability. All the results were reported and communicated to the clinical teams, so the timely patient management can be administrated and surveillance of the same can be done in real time. Conclusion Alinity M has a significant advantage for a random access as well as improved TAT for detection of SARS-CoV-2, leading to prompt patient care and management.

scholarly journals A two-pronged approach for rapid and high-throughput SARS-CoV-2 nucleic acid testing

2020 ◽  
Author(s):  
Neeru Gandotra ◽  
Irina Tikhonova ◽  
Nagarjuna R. Cheemarla ◽  
James Knight ◽  
Ellen Foxman ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Low Cost ◽  
Rna Extraction ◽  
Clinical Specimen ◽  
Rna Isolation ◽  
Turnaround Time ◽  
Ease Of Use ◽  
Diagnostic Tools ◽  
Rt Pcr

AbstractImproved molecular screening and diagnostic tools are needed to substantially increase SARS-CoV-2 testing capacity and throughput while reducing the time to receive test results. Here we developed multiplex reverse transcriptase polymerase chain reaction (m-RT-PCR) for detection of SARS-CoV-2 using rapid DNA electrophoresis and alternatively using multiplex viral sequencing (mVseq). For RNA specimens extracted from nasopharyngeal (NP) swabs in viral transport media (VTM), our assays achieved a sensitivity for SARS-CoV-2 detection corresponding to cycle threshold (Ct) of 37.2 based on testing of these specimens using quantitative reverse transcription PCR (RT-qPCR). For NP swab-VTM specimens without prior RNA extraction, sensitivity was reduced to Ct of 31.6, which was due to lower concentration of SARS-CoV-2 genome copies in VTM compared to RNA-extracted samples. Assay turnaround time was 60 minutes using rapid gel electrophoresis, 90 minutes using Agilent Bioanalyzer, and 24-48 hours using Illumina sequencing, the latter of which required a second PCR to produce a sequence-ready library using m-RT-PCR products as the template. Our assays can be employed for high-throughput sequencing-based detection of SARS-CoV-2 directly from a clinical specimen without RNA isolation, while ease-of-use and low cost of the electrophoresis-based readout enables screening, particularly in resource-constrained settings.

scholarly journals Time- and cost-efficient high-throughput transcriptomics enabled by Bulk RNA Barcoding and sequencing

2018 ◽  
Author(s):  
Daniel Alpern ◽  
Vincent Gardeux ◽  
Julie Russeil ◽  
Bart Deplancke
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
High Throughput ◽  
Low Cost ◽  
Cdna Libraries ◽  
List Type ◽  
Library Preparation ◽  
Rna Seq ◽  
Genome Wide ◽  
Hands On

ABSTRACTGenome-wide gene expression analyses by RNA sequencing (RNA-seq) have quickly become a standard in molecular biology because of the widespread availability of high throughput sequencing technologies. While powerful, RNA-seq still has several limitations, including the time and cost of library preparation, which makes it difficult to profile many samples simultaneously. To deal with these constraints, the single-cell transcriptomics field has implemented the early multiplexing principle, making the library preparation of hundreds of samples (cells) markedly more affordable. However, the current standard methods for bulk transcriptomics (such as TruSeq Stranded mRNA) remain expensive, and relatively little effort has been invested to develop cheaper, but equally robust methods. Here, we present a novel approach, Bulk RNA Barcoding and sequencing (BRB-seq), that combines the multiplexing-driven cost-effectiveness of a single-cell RNA-seq workflow with the performance of a bulk RNA-seq procedure. BRB-seq produces 3’ enriched cDNA libraries that exhibit similar gene expression quantification to TruSeq and that maintain this quality, also in terms of number of detected differentially expressed genes, even with low quality RNA samples. We show that BRB-seq is about 25 times less expensive than TruSeq, enabling the generation of ready to sequence libraries for up to 192 samples in a day with only 2 hours of hands-on time. We conclude that BRB-seq constitutes a powerful alternative to TruSeq as a standard bulk RNA-seq approach. Moreover, we anticipate that this novel method will eventually replace RT-qPCR-based gene expression screens given its capacity to generate genome-wide transcriptomic data at a cost that is comparable to profiling 4 genes using RT-qPCR.‘SoftwareWe developed a suite of open source tools (BRB-seqTools) to aid with processing BRB-seq data and generating count matrices that are used for further analyses. This suite can perform demultiplexing, generate count/UMI matrices and trim BRB-seq constructs and is freely available at http://github.com/DeplanckeLab/BRB-seqToolsHighlightsRapid (~2h hands on time) and low-cost approach to perform transcriptomics on hundreds of RNA samplesStrand specificity preservedPerformance: number of detected genes is equal to Illumina TruSeq Stranded mRNA at same sequencing depthHigh capacity: low cost allows increasing the number of biological replicatesProduces reliable data even with low quality RNA samples (down to RIN value = 2)Complete user-friendly sequencing data pre-processing and analysis pipeline allowing result acquisition in a day

High-throughput screening program for botanical extracts

Planta Medica ◽  
2012 ◽  
Vol 78 (11) ◽  
Author(s):  
L Hingorani ◽  
NP Seeram ◽  
B Ebersole
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Screening Program ◽  
Botanical Extracts

Constructive Optimisation of the Propeller Type Mixing Devices Using the Virtual and Rapid Prototyping

2017 ◽  
Vol 68 (3) ◽  
pp. 453-458 ◽  
Author(s):  
Daniel Besnea ◽  
Alina Spanu ◽  
Iuliana Marlena Prodea ◽  
Gheorghita Tomescu ◽  
Iolanda Constanta Panait
Keyword(s):  
Rapid Prototyping ◽  
Low Cost ◽  
Scale Up ◽  
Three Dimensional ◽  
Rapid Identification ◽  
Multidisciplinary Optimization ◽  
External Diameter ◽  
Process Industries ◽  
Parametric Cad ◽  
Shaft Torque

The paper points out the advantages of rapid prototyping for improving the performances/constructive optimization of mixing devices used in process industries, here exemplified to propeller types ones. The multidisciplinary optimization of the propeller profile affords its design using parametric CAD methods. Starting from the mathematical curve equations proposed for the blade profile, it was determined its three-dimensional virtual model. The challenge has been focused on the variation of propeller pitch and external diameter. Three dimensional ranges were manufactured using the additive manufacturing process with Marker Boot 3D printer. The mixing performances were tested on the mixing equipment measuring the minimum rotational speed and the correspondent shaft torque for complete suspension achieved for each of the three models. The virtual and rapid prototyping method is newly proposed by the authors to obtain the basic data for scale up of the mixing systems, in the case of flexible production (of low quantities), in which both the nature and concentration of the constituents in the final product varies often. It is an efficient and low cost method for the rapid identification of the optimal mixing device configuration, which contributes to the costs reduction and to the growing of the output.

scholarly journals Large-Scale, High-Throughput Validation of Short Hairpin RNA Sequences for RNA Interference

2006 ◽  
Vol 11 (3) ◽  
pp. 236-246 ◽  
Author(s):  
Laurence H. Lamarcq ◽  
Bradley J. Scherer ◽  
Michael L. Phelan ◽  
Nikolai N. Kalnine ◽  
Yen H. Nguyen ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Strong Support ◽  
Gc Content ◽  
Rapid Identification ◽  
Hairpin Rna ◽  
Rna Sequences ◽  
Short Hairpin ◽  
Short Hairpin Rnas ◽  
Interfering Rna

A method for high-throughput cloning and analysis of short hairpin RNAs (shRNAs) is described. Using this approach, 464 shRNAs against 116 different genes were screened for knockdown efficacy, enabling rapid identification of effective shRNAs against 74 genes. Statistical analysis of the effects of various criteria on the activity of the shRNAs confirmed that some of the rules thought to govern small interfering RNA (siRNA) activity also apply to shRNAs. These include moderate GC content, absence of internal hairpins, and asymmetric thermal stability. However, the authors did not find strong support for positionspecific rules. In addition, analysis of the data suggests that not all genes are equally susceptible to RNAinterference (RNAi).

scholarly journals 12. Evaluation of Rapid Phenotypic Testing for KPC Carbapenemase Producing klebsiella Pneumoniae Directly from Positive Blood Cultures by Use of “Hot Chocolate” Plates

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S7-S7
Author(s):  
Alexander Lawandi ◽  
Gleice C Leite ◽  
Brigitte Lefebvre ◽  
Jean Longtin ◽  
Todd C Lee
Keyword(s):  
Klebsiella Pneumoniae ◽  
Carbapenem Resistance ◽  
Empiric Therapy ◽  
Turnaround Time ◽  
Rapid Identification ◽  
Blood Cultures ◽  
Minimal Growth ◽  
Maldi Tof ◽  
Considerable Morbidity ◽  
Hot Chocolate

Abstract Background Invasive infections with Carbapenemase Producing Enterobacterales are associated with considerable morbidity and mortality, in part due to the risk of inappropriate empiric therapy. Consequently, the rapid identification of carbapenem resistance is crucial to the management of these infections. We sought to evaluate possible reductions in turnaround time to identification of this resistance in blood cultures growing these organisms by applying rapid phenotypic test kits to growth from “hot chocolate” plates. Methods 30 blood cultures, spiked with carbapenem resistant Klebsiella pneumoniae isolates or susceptible controls, were inoculated onto chocolate agars that had pre-warmed at 37°C. These plates were incubated at 37ºC for 3.5 hours. The resulting minimal growth was then identified using MALDI-TOF and underwent rapid phenotypic testing using three commercially available products (β-lacta and β-carba, from Bio-Rad, Marnes-la-Coquette, France, and Carba-NP, from bioMérieux, Durham, NC). The time to identification of carbapenem resistance using this method was then compared to that of the conventional laboratory workup. Results The identification was 100% accurate to the species level using MALDI-TOF paired to the 3.5 hour growth on the “hot choocolate” plates. The β-lacta kit identified resistance to 3rd generation cephalosporins for all ESBL and carbapenemase producing Klebsiella pneumoniae isolates, while the β-carba and Carba-NP kits identified carbapenem resistance only in the carbapenemase producers. The sensitivity of all assays was 100% (95% CI 0.87–1.0) and the specificity of carbapenemase detection was 100% (97.5% one-sided CI 0.4–1.0). The corresponding sensitivities and specificities of direct disc diffusion for ertapenem resistance detection were 88.5% (95% CI 0.70–0.98) and 100% (95%CI 0.40–1.0) respectively. The turnaround time for the rapid kits coupled to the “hot chocolate” plates was 4.25 to 5.1 hours as compared to 16 hours for the conventional workup. Conclusion Rapid phenotypic tests performed after inoculation of “hot chocolate” plates are highly sensitive for the presence of carbapenemase production and can be incorporated into the laboratory workflow for Klebisella pneumoniae with important reductions in turnaround time. Disclosures All Authors: No reported disclosures

scholarly journals Organ-specific, multimodal, wireless optoelectronics for high-throughput phenotyping of peripheral neural pathways

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Woo Seok Kim ◽  
Sungcheol Hong ◽  
Milenka Gamero ◽  
Vivekanand Jeevakumar ◽  
Clay M. Smithhart ◽  
...  
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Optoelectronic Device ◽  
Antenna System ◽  
Neural Pathways ◽  
Organ Specific ◽  
Coil Antenna ◽  
Sensory Fibers

AbstractThe vagus nerve supports diverse autonomic functions and behaviors important for health and survival. To understand how specific components of the vagus contribute to behaviors and long-term physiological effects, it is critical to modulate their activity with anatomical specificity in awake, freely behaving conditions using reliable methods. Here, we introduce an organ-specific scalable, multimodal, wireless optoelectronic device for precise and chronic optogenetic manipulations in vivo. When combined with an advanced, coil-antenna system and a multiplexing strategy for powering 8 individual homecages using a single RF transmitter, the proposed wireless telemetry enables low cost, high-throughput, and precise functional mapping of peripheral neural circuits, including long-term behavioral and physiological measurements. Deployment of these technologies reveals an unexpected role for stomach, non-stretch vagal sensory fibers in suppressing appetite and demonstrates the durability of the miniature wireless device inside harsh gastric conditions.

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