scholarly journals Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes

2021 ◽  
Author(s):  
Timothy A. Brown ◽  
Katherine S. Schaefer ◽  
Arthur Tsang ◽  
Hyun Ah Yi ◽  
Jonathan B. Grimm ◽  
...  
Keyword(s):  
Direct Detection ◽  
Rna Extraction ◽  
Ph Sensitive ◽  
Limiting Factors ◽  
Clinical Samples ◽  
Technical Requirements ◽  
Management Plans ◽  
Amplification Assay ◽  
Widespread Availability ◽  
And Performance

AbstractThe worldwide COVID-19 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce two pH sensitive ‘LAMPshade’ dyes as novel readouts in an isothermal RT- LAMP amplification assay for SARS-CoV-2 RNA. The resulting JaneliaLAMP (jLAMP) assay is robust, simple, inexpensive, has low technical requirements and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.

scholarly journals SARS-CoV-2 Direct Detection Without RNA Isolation With Loop-Mediated Isothermal Amplification (LAMP) and CRISPR-Cas12

2021 ◽  
Vol 8 ◽  
Author(s):  
Alfredo Garcia-Venzor ◽  
Bertha Rueda-Zarazua ◽  
Eduardo Marquez-Garcia ◽  
Vilma Maldonado ◽  
Angelica Moncada-Morales ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Direct Detection ◽  
Direct Method ◽  
Rna Extraction ◽  
Rna Isolation ◽  
High Sensitivity ◽  
High Specificity ◽  
Isothermal Amplification ◽  
Clinical Samples ◽  
Loop Mediated Isothermal Amplification

As to date, more than 49 million confirmed cases of Coronavirus Disease 19 (COVID-19) have been reported worldwide. Current diagnostic protocols use qRT-PCR for viral RNA detection, which is expensive and requires sophisticated equipment, trained personnel and previous RNA extraction. For this reason, we need a faster, direct and more versatile detection method for better epidemiological management of the COVID-19 outbreak. In this work, we propose a direct method without RNA extraction, based on the Loop-mediated isothermal amplification (LAMP) and Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated protein (CRISPR-Cas12) technique that allows the fast detection of SARS-CoV-2 from patient samples with high sensitivity and specificity. We obtained a limit of detection of 16 copies/μL with high specificity and at an affordable cost. The diagnostic test readout can be done with a real-time PCR thermocycler or with the naked eye in a blue-light transilluminator. Our method has been evaluated on a small set of clinical samples with promising results.

Assessment of a Loop‐Mediated Isothermal Amplification Assay targeting lytA genes with conventional PCR for the direct detection of Streptococcus pneumoniae in clinical samples

2013 ◽  
Vol 3 (4) ◽  
pp. 166-171
Author(s):  
Mohammed Ali Marie ◽  
Pradeep C. S. ◽  
James John ◽  
Sanggeetha Gopalkrishnan ◽  
Lakshmana Gowda K. ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Target Genes ◽  
Direct Detection ◽  
Lamp Assay ◽  
Conventional Polymerase Chain Reaction ◽  
Isothermal Amplification ◽  
Clinical Samples ◽  
Bacterial Disease ◽  
Clinical Sensitivity ◽  
Amplification Assay

Streptococcus pneumoniae is one of the most encountered pathogens in developed and developing countries. It is a leading cause of invasive bacterial disease in adults as well as in children. This study focuses on the loop-mediated isothermal amplification (LAMP) assay to validate its suitability for directly detecting lyt A target genes of S. pneumoniae in clinical samples. We studied the clinical sensitivity and specificity of the LAMP assay targeting lyt A using 42 selected CSF specimens from children with suspected meningitis in the Kingdom of Saudi Arabia. Conventional polymerase chain reaction (PCR) and culture tests were also performed. The detection rate of the LAMP assay was significantly higher than the rates of PCR and culture tests and the detection limits (10 copies by LAMP) were considerably lower than those for PCR (103 copies). Our study suggests that LAMP reaction-based detection of target genes of suspected pathogens could be applied in a various clinical settings. In addition, the lower cost of LAMP assay than PCR makes it more economical, allowing its use in laboratories with limited resources.  

Programmable Integrated Photonics

2020 ◽  
Author(s):  
José Capmany ◽  
Daniel Pérez
Keyword(s):  
Integrated Circuit ◽  
Performance Monitoring ◽  
Low Cost ◽  
Limiting Factors ◽  
External Control ◽  
Integrated Photonics ◽  
New Paradigm ◽  
Photonic Integrated Circuit ◽  
And Performance ◽  
Application Fields

Programmable Integrated Photonics (PIP) is a new paradigm that aims at designing common integrated optical hardware configurations, which by suitable programming can implement a variety of functionalities that, in turn, can be exploited as basic operations in many application fields. Programmability enables by means of external control signals both chip reconfiguration for multifunction operation as well as chip stabilization against non-ideal operation due to fluctuations in environmental conditions and fabrication errors. Programming also allows activating parts of the chip, which are not essential for the implementation of a given functionality but can be of help in reducing noise levels through the diversion of undesired reflections. After some years where the Application Specific Photonic Integrated Circuit (ASPIC) paradigm has completely dominated the field of integrated optics, there is an increasing interest in PIP justified by the surge of a number of emerging applications that are and will be calling for true flexibility, reconfigurability as well as low-cost, compact and low-power consuming devices. This book aims to provide a comprehensive introduction to this emergent field covering aspects that range from the basic aspects of technologies and building photonic component blocks to the design alternatives and principles of complex programmable photonics circuits, their limiting factors, techniques for characterization and performance monitoring/control and their salient applications both in the classical as well as in the quantum information fields. The book concentrates and focuses mainly on the distinctive features of programmable photonics as compared to more traditional ASPIC approaches.

scholarly journals Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shan Wei ◽  
Esther Kohl ◽  
Alexandre Djandji ◽  
Stephanie Morgan ◽  
Susan Whittier ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Point Of Care ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Cost Effective ◽  
Clinical Samples ◽  
Nasopharyngeal Swab ◽  
Percentage Agreement ◽  
Testing Method ◽  
Viral Transport

AbstractThe COVID-19 pandemic has resulted in an urgent need for a rapid, point of care diagnostic testing that could be rapidly scaled on a worldwide level. We developed and tested a highly sensitive and robust assay based on reverse transcription loop mediated isothermal amplification (RT-LAMP) that uses readily available reagents and a simple heat block using contrived spike-in and actual clinical samples. RT-LAMP testing on RNA-spiked samples showed a limit of detection (LoD) of 2.5 copies/μl of viral transport media. RT-LAMP testing directly on clinical nasopharyngeal swab samples in viral transport media had an 85% positive percentage agreement (PPA) (17/20), and 100% negative percentage agreement (NPV) and delivered results in 30 min. Our optimized RT-LAMP based testing method is a scalable system that is sufficiently sensitive and robust to test for SARS-CoV-2 directly on clinical nasopharyngeal swab samples in viral transport media in 30 min at the point of care without the need for specialized or proprietary equipment or reagents. This cost-effective and efficient one-step testing method can be readily available for COVID-19 testing world-wide, especially in resource poor settings.

scholarly journals Estimating Deterioration in the Concrete Tie-Ballast Interface Based on Vertical Tie Deflection Profile: A Numerical Study

2016 ◽  
Author(s):  
Hailing Yu
Keyword(s):  
Direct Detection ◽  
Numerical Study ◽  
Interface Condition ◽  
Vertical Deflection ◽  
Cohesive Elements ◽  
Material Loss ◽  
Element Analysis ◽  
Cross Sectional ◽  
Technical Requirements ◽  
Support Conditions

In ballasted concrete tie track, the tie-ballast interface can deteriorate resulting in concrete tie bottom abrasion, ballast pulverization and/or voids in tie-ballast interfaces. Tie-ballast voids toward tie ends can lead to unfavorable center binding support conditions that can result in premature concrete tie failure and possible train derailment. Direct detection of these conditions is difficult. There is a strong interest in assessing the concrete tie-ballast interface conditions indirectly using measured vertical deflections. This paper seeks to establish a link between the vertical deflection profile of a concrete tie top surface and the tie-ballast interface condition using the finite element analysis (FEA) method. The concrete tie is modeled as a concrete matrix embedded with prestressing steel strands or wires. The configurations of two commonly used concrete ties, one with 8 prestressing strands and the other with 20 prestressing wires, are employed in this study. All models are three-dimensional and symmetric about the tie center. A damaged plasticity model that can predict onset and propagation of tensile cracks is applied to the concrete material. The steel-concrete interface is homogenized and represented with a thin layer of cohesive elements sandwiched between steel and concrete elements. Strand- or wire-specific elasto-plastic bond models developed at the Volpe Center are applied to the cohesive elements to account for the interface bonding mechanisms. FE models are developed for both original and worn concrete ties, with the latter assuming hypothetical patterns of reduced cross sections resulting from abrasive interactions with the ballast. Static analyses of pretension release in these concrete ties are conducted, and vertical deflection gradients along tie lengths are calculated and shown to correspond well with the worn cross sectional patterns for a given reinforcement type. The ballast is further modeled with Extended Drucker-Prager plasticity, and hypothetical voids are applied toward the tie ends along the concrete tie-ballast interface to simulate center binding support conditions. The distance range over which the concrete tie is supported in the center is variable and yields different center binding severity. Static simulations are completed with vertical rail seat loads applied on the concrete tie-ballast assembly. The influences of various factors on the vertical deflection profile, including tie type, vertical load magnitude, center binding severity, cross sectional material loss and prestress loss, are examined based on the FEA results. The work presented in this paper demonstrates the potential of using the vertical deflection profile of concrete tie top surfaces to assess deteriorations in the tie-ballast interface. The simulation results further help to clarify minimum technical requirements on inspection technologies that measure concrete tie vertical deflection profiles.

Evaluation of the ARKRAY HA-8190V instrument for HbA1c

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Eline A.E. van der Hagen ◽  
Sanne Leppink ◽  
Karin Bokkers ◽  
Carla Siebelder ◽  
Cas W. Weykamp
Keyword(s):  
Quality Assessment ◽  
Concentration Level ◽  
External Quality Assessment ◽  
Clinical Samples ◽  
Diabetic Patients ◽  
External Quality ◽  
Target Values ◽  
Performance Specifications ◽  
Certification Programme ◽  
And Performance

Abstract Objectives Hemoglobin A1c (HbA1c) is a valuable parameter in the monitoring of diabetic patients and increasingly in diagnosis of diabetes. Manufacturers continuously optimize instruments, currently the main focus is to achieve faster turnaround times. It is important that performance specifications remain of high enough standard, which is evaluated in this study for the new ARKRAY HA-8190V instrument. Methods The Clinical and Laboratory Standards Institute (CLSI) protocols EP-5, EP-9 and EP-10 were applied to investigate imprecision, bias and linearity. In addition potential interferences, performance in External Quality Assessment (EQA) and performance against the HA-8180V instrument in 220 clinical samples was evaluated. Results The HA-8190V demonstrates a CV of ≤0.8% in IFCC SI units (≤0.6% National Glycohemoglobin Standardization Program [NGSP]) at 34 and 102 mmol/mol levels (5.3 and 11.5% NGSP) and a bias of −0.1 mmol/mol (−0.01% NGSP) at a concentration of 50 mmol/mol (6.7% NGSP), but with a significant slope as compared to target values. This results in a bias of −1.0 and 0.9 mmol/mol (−2.0 and 0.9% NGSP) at the 30 and 70 mmol/mol (4.9 and 8.6% NGSP) concentration level. Simulation of participation in the IFCC certification programme results in a Silver score (bias −0.1 mmol/mol, CV 1.1%). Interference in the presence of the most important Hb variants (AS, AC, AE, AD) and elevated HbA2 and HbF concentrations is less than 3 mmol/mol (0.3% NGSP) at a concentration of 50 mmol/mol (6.7% NGSP). Conclusions Analytical performance of the HA-8190V is very good, especially with respect to precision and HbA1c quantification in the presence of the most common Hb variants.

scholarly journals Direct Viral RNA Detection of SARS-CoV-2 and DENV in Inactivated Samples by Real-Time RT-qPCR: Implications for Diagnosis in Resource Limited Settings with Flavivirus Co-Circulation

Pathogens ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1558
Author(s):  
Zhan Qiu Mao ◽  
Mizuki Fukuta ◽  
Jean Claude Balingit ◽  
Thi Thanh Ngan Nguyen ◽  
Co Thach Nguyen ◽  
...  
Keyword(s):  
Real Time ◽  
Early Stage ◽  
Rna Extraction ◽  
Viral Rna ◽  
Clinical Samples ◽  
Heat Inactivation ◽  
Resource Limited Settings ◽  
Rna Detection ◽  
Resource Limited ◽  
Starting Point

The RT-qPCR method remains the gold standard and first-line diagnostic method for the detection of SARS-CoV-2 and flaviviruses, especially in the early stage of viral infection. Rapid and accurate viral detection is a starting point in the containment of the COVID-19 pandemic and flavivirus outbreaks. However, the shortage of diagnostic reagents and supplies, especially in resource-limited countries that experience co-circulation of SARS-CoV-2 and flaviviruses, are limitations that may result in lesser availability of RT-qPCR-based diagnostic tests. In this study, the utility of RNA-free extraction methods was assessed for the direct detection of SARS-CoV-2 and DENV-2 in heat-inactivated or chemical-inactivated samples. The findings demonstrate that direct real-time RT-qPCR is a feasible option in comparison to conventional real-time RT-qPCR based on viral genome extraction-based methods. The utility of heat-inactivation and direct real-time RT-qPCR for SARS-CoV-2, DENV-2 viral RNA detection was demonstrated by using clinical samples of SARS-CoV-2 and DENV-2 and spiked cell culture samples of SARS-CoV-2 and DENV-2. This study provides a simple alternative workflow for flavivirus and SARS-CoV-2 detection that includes heat inactivation and viral RNA extraction-free protocols, with aims to reduce the risk of exposure during processing of SARS-CoV-2 biological specimens and to overcome the supply-chain bottleneck, particularly in resource limited settings with flavivirus co-circulation.

scholarly journals Development and Performance verification of colloidal gold labeled SARS-CoV-2 antigen detection method for routine popular screening of COVID-19 with clinical samples in Poland and China

2021 ◽  
Author(s):  
Chuanxiang Guo ◽  
Li Yao ◽  
Fengling Chen ◽  
Chao Zhang ◽  
Wei Chen
Keyword(s):  
Predictive Value ◽  
Colloidal Gold ◽  
Detection Method ◽  
Age Distribution ◽  
Antigen Detection ◽  
Lateral Flow ◽  
Rapid Screening ◽  
Clinical Samples ◽  
Lateral Flow Strip ◽  
And Performance

In this research, we have constructed and optimized the colloidal gold labeled lateral flow strip (LFS) for rapid detection of antigen of SARS-CoV-2 and rapid screening of COVID-19. Based on the constructed and optimized colloidal gold lateral flow strip, the parameters of the LFS have been well evaluated with the clinical samples in the professional labs. The screening performance have also been evaluated from the aspects including the CT values, age distribution and onset of symptoms. Finally, based on the detection results of 420 clinical samples, the LFS can achieve the screening of COVID-19 with the positive percentage agreement (PPA, sensitivity), negative percent agreement (NPA, specificity), the positive predictive value (PPV) and the negative predictive value (NPV) of 96.8%, 100%, 100% and 96.6%, respectively, indicating the powerful potential for practical screening applications in pandemic control. Of great significance, this developed SARS-CoV-2 antigen detection method has also been successfully utilized for screening of delta-variant of SARS-CoV-2.

A novel non-amplification assay for the detection of Leishmania spp. in clinical samples using gold nanoparticles

2014 ◽  
Vol 96 ◽  
pp. 56-61 ◽  
Author(s):  
Margarita Andreadou ◽  
Emmanouil Liandris ◽  
Maria Gazouli ◽  
Styliani Taka ◽  
Maria Antoniou ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Clinical Samples ◽  
Leishmania Spp ◽  
Amplification Assay
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