Implementation and validation of a pooling strategy for a sustainable screening campaign for the presence of SARS-CoV-2.

Mass screening aimed at detecting, in asymptomatic subjects, the presence of SARS-CoV-2 is considered a strategic measure for the control of the present pandemic. It allows virus carriers to be identified and quarantined, thus preventing local spread and protecting vulnerable individuals. Although the screening strategy should be determined by the epidemiological situation, the size of the population that can be screened is indeed limited by the availability of resources. Here we present the implementation of an 8-sample pool strategy that relies on protocols, reagents and equipment currently used in clinical diagnostics. The method permitted to identify, with 100% sensitivity, specificity and accuracy, samples with low viral load, being the limit of detection of 11 viral copies extracted from the equivalent of 133ul of nasopharyngeal sample-pool. When the protocol has been applied, as a proof of principle, in a real population of 3592 consecutive nasopharyngeal swabs collected by healthcare providers in asymptomatic subjects, 20 positive pools were detected and in 100% of cases the positive specimens identified. Considering these performances, the 8-sample pool will allow, in populations with an expected positive rate of less than 1%, reducing costs by at least 80%, being a suitable method for a sustainable mass screening strategy in a population of asymptomatic subjects.

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Biosensors on chip: A critical review from an aspect of micro/nanoscales

Journal of Micromanufacturing ◽

10.1177/2516598419847913 ◽

2019 ◽

Vol 2 (2) ◽

pp. 198-219 ◽

Cited By ~ 2

Author(s):

Geeta Bhatt ◽

Shantanu Bhattacharya

Keyword(s):

Optical Sensors ◽

Microelectromechanical Systems ◽

Electrochemical Sensors ◽

Limit Of Detection ◽

Clinical Diagnostics ◽

Detection Scheme ◽

Performance Factors ◽

On Chip ◽

Mechanical Sensors ◽

Sensitivity Specificity

Biosensors are a very well cherished research topic and have found an inseparable status from clinical diagnostics in specific and society at large. As the name suggests, biosensors or biological sensors are devices which detect the presence of biological entities or their constituents and derivatives. The field started decades ago and has matured quite well since its inception. The most important performance factors that are associated with biosensors are sensitivity, specificity, and limit of detection. The remaining efforts of the biosensor research domain focus on miniaturization aspects of the sensors. The growing advancements in this field have evolved the technology of biosensors to cater to full-scale diagnosis on microchips, bedside diagnostics, reduced cost, and increased speed of diagnostics. Biosensors are characterized through many different aspects; for example, one way is to classify them on the basis of the type of bio-recognition step that they would utilize or another way can be based on the type of detection scheme that they may integrate, etc. Depending on the bio-recognition layer’s properties, biosensors can be cell based, nucleic acid probe based, antibody/antigen based, or aptamer based, while depending on the type of detection scheme, biosensors can be viewed as colorimetric sensors, optical sensors, electrochemical sensors, mechanical sensors, etc. There are some other parallel areas of research like microfluidics and microelectromechanical systems where one of the main applications lies in the biosensor domain. This review article discusses the various aspects of biosensors, from their design, realization, to testing, along with various detection strategies. The assembly includes fabrication strategies particularly for microchip technology-based biosensing solutions, microchannels, integration to microfluidics, etc., while categorization deals with various kinds and applications of different biosensors.

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Contamination of Zearalenone from China in 2019 by a Visual and Digitized Immunochromatographic Assay

Toxins ◽

10.3390/toxins12080521 ◽

2020 ◽

Vol 12 (8) ◽

pp. 521

Author(s):

Xia Hong ◽

Yuhao Mao ◽

Chuqin Yang ◽

Zhenjiang Liu ◽

Ming Li ◽

...

Keyword(s):

Limit Of Detection ◽

High Sensitivity ◽

Site Investigation ◽

Immunochromatographic Assay ◽

Quantitative Detection ◽

Significant Information ◽

Detection Model ◽

Positive Rate ◽

Highly Correlated ◽

Sensitivity Specificity

Zearalenone (ZEN) is a prevalent mycotoxin that needs intensive monitoring. A semi-quantitative and quantitative immunochromatographic assay (ICA) was assembled for investigating ZEN contamination in 187 samples of cereal and their products from China in 2019. The semi-quantitative detection model had a limit of detection (LOD) of 0.50 ng/mL with visual judgment and could be completely inhibited within 5 min at 3.0 ng/mL ZEN. The quantitative detection model had a lower LOD of 0.25 ng/mL, and ZEN could be accurately and digitally detected from 0.25–4.0 ng/mL. The ICA method had a high sensitivity, specificity, and accuracy for on-site ZEN detection. For investigation of the authentic samples, the ZEN-positive rate was 62.6%, and the ZEN-positive levels ranged from 2.7 to 867.0 ng/g, with an average ZEN-positive level being 85.0 ng/g. Of the ZEN-positive samples, 6.0% exceeded the values of the limit levels. The ZEN-positive samples were confirmed to be highly correlated using LC-MS/MS (R2 = 0.9794). This study could provide an efficiency and accuracy approach for ZEN in order to achieve visual and digitized on-site investigation. This significant information about the ZEN contamination levels might contribute to monitoring mycotoxin occurrence and for ensuring food safety.

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Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR

10.1101/2020.03.14.20036129 ◽

2020 ◽

Cited By ~ 12

Author(s):

Lianhua Dong ◽

Junbo Zhou ◽

Chunyan Niu ◽

Quanyi Wang ◽

Yang Pan ◽

...

Keyword(s):

Viral Load ◽

Reverse Transcription ◽

Clinical Symptoms ◽

Limit Of Detection ◽

Digital Pcr ◽

Pharyngeal Swab ◽

Positive Rate ◽

Novel Coronavirus ◽

Sensitivity Specificity ◽

Close Contacts

BACKGROUNDThe outbreak of COVID-19 caused by a novel Coronavirus (termed SARS-CoV-2) has spread to over 140 countries around the world. Currently, reverse transcription quantitative qPCR (RT-qPCR) is used as the gold standard for diagnostics of SARS-CoV-2. However, the positive rate of RT-qPCR assay of pharyngeal swab samples are reported to vary from 30∼60%. More accurate and sensitive methods are urgently needed to support the quality assurance of the RT-qPCR or as an alternative diagnostic approach.METHODSWe established a reverse transcription digital PCR (RT-dPCR) protocol to detect SARS-CoV-2 on 194 clinical pharyngeal swab samples, including 103 suspected patients, 75 close contacts and 16 supposed convalescents.RESULTSThe limit of blanks (LoBs) of the RT-dPCR assays were ∼1.6, ∼1.6 and ∼0.8 copies/reaction for ORF 1ab, N and E genes, respectively. The limit of detection (LoD) was 2 copies/reaction. For the 103 fever suspected patients, the sensitivity of SARS-CoV-2 detection was significantly improved from 28.2% by RT-qPCR to 87.4% by RT-dPCR. For close contacts, the suspect rate was greatly decreased from 21% down to 1%. The overall sensitivity, specificity and diagnostic accuracy of RT-dPCR were 90%, 100% and 93 %, respectively. In addition, quantification of the viral load for convalescents by RT-dPCR showed that a longer observation period was needed in the hospital for elderly patients.CONCLUSIONRT-dPCR could be a confirmatory method for suspected patients diagnosed by RT-qPCR. Furthermore, RT-dPCR was more sensitive and suitable for low viral load specimens from the both patients under isolation and those under observation who may not be exhibiting clinical symptoms.

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Rapid and Sensitive Detection of miRNA Based on AC Electrokinetic Capacitive Sensing for Point-of-Care Applications

Sensors ◽

10.3390/s21123985 ◽

2021 ◽

Vol 21 (12) ◽

pp. 3985

Author(s):

Nan Wan ◽

Yu Jiang ◽

Jiamei Huang ◽

Rania Oueslati ◽

Shigetoshi Eda ◽

...

Keyword(s):

Limit Of Detection ◽

Point Of Care ◽

Low Cost ◽

Clinical Diagnostics ◽

Detection Methods ◽

Capacitive Sensing ◽

Application Potential ◽

Mirna Detection ◽

Mirna 25 ◽

Low Sensitivity

A sensitive and efficient method for microRNAs (miRNAs) detection is strongly desired by clinicians and, in recent years, the search for such a method has drawn much attention. There has been significant interest in using miRNA as biomarkers for multiple diseases and conditions in clinical diagnostics. Presently, most miRNA detection methods suffer from drawbacks, e.g., low sensitivity, long assay time, expensive equipment, trained personnel, or unsuitability for point-of-care. New methodologies are needed to overcome these limitations to allow rapid, sensitive, low-cost, easy-to-use, and portable methods for miRNA detection at the point of care. In this work, to overcome these shortcomings, we integrated capacitive sensing and alternating current electrokinetic effects to detect specific miRNA-16b molecules, as a model, with the limit of detection reaching 1.0 femto molar (fM) levels. The specificity of the sensor was verified by testing miRNA-25, which has the same length as miRNA-16b. The sensor we developed demonstrated significant improvements in sensitivity, response time and cost over other miRNA detection methods, and has application potential at point-of-care.

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Detection of Active BoNT/C and D by EndoPep-MS Using MALDI Biotyper Instrument and Comparison with the Mouse Test Bioassay

Toxins ◽

10.3390/toxins13010010 ◽

2020 ◽

Vol 13 (1) ◽

pp. 10

Author(s):

Ilenia Drigo ◽

Elena Tonon ◽

Simone Pascoletti ◽

Fabrizio Anniballi ◽

Suzanne R. Kalb ◽

...

Keyword(s):

Limit Of Detection ◽

Animal Health ◽

Lethal Dose ◽

Reference Method ◽

Mouse Bioassay ◽

Peptide Fragments ◽

Mass Spectrometers ◽

Detection And Identification ◽

Maldi Biotyper ◽

Sensitivity Specificity

Botulinum neurotoxins (BoNTs) are among the most poisonous known biological substances, and therefore the availability of reliable, easy-to use tools for BoNT detection are important goals for food safety and human and animal health. The reference method for toxin detection and identification is the mouse bioassay (MBA). An EndoPep-MS method for BoNT differentiation has been developed based on mass spectrometry. We have validated and implemented the EndoPep-MS method on a Bruker MALDI Biotyper for the detection of BoNT/C and D serotypes. The method was extensively validated using experimentally and naturally contaminated samples comparing the results with those obtained with the MBA. Overall, the limit of detection (LoD) for both C and D toxins were less than or equal to two mouse lethal dose 50 (mLD50) per 500 µL for all tested matrices with the exception of feces spiked with BoNT/C which showed signals not-related to specific peptide fragments. Diagnostic sensitivity, specificity and positive predictive value were 100% (95% CI: 87.66–100%), 96.08% (95% CI: 86.54–99.52%), and 93.33% (95% CI: 78.25–98.20%), respectively, and accuracy was 97.47% (95% CI: 91.15–99.69%). In conclusion, the tests carried out showed that the EndoPep-MS method, initially developed using more powerful mass spectrometers, can be applied to the Bruker MALDI Biotyper instrument with excellent results including for detection of the proteolytic activity of BoNT/C, BoNT/D, BoNT/CD, and BoNT/DC toxins.

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Analytical assessment of ortho clinical diagnostics high-sensitivity cardiac troponin I assay

Clinical Chemistry and Laboratory Medicine (CCLM) ◽

10.1515/cclm-2020-1115 ◽

2020 ◽

Vol 0 (0) ◽

Author(s):

Peter A. Kavsak ◽

Tara Edge ◽

Chantele Roy ◽

Paul Malinowski ◽

Karen Bamford ◽

...

Keyword(s):

Cardiac Troponin ◽

Troponin I ◽

Limit Of Detection ◽

Clinical Performance ◽

Characteristic Curve ◽

Area Under The Curve ◽

High Sensitivity ◽

Cardiac Troponin I ◽

Clinical Diagnostics ◽

Ortho Clinical Diagnostics

AbstractObjectivesTo analytically evaluate Ortho Clinical Diagnostics VITROS high-sensitivity cardiac troponin I (hs-cTnI) assay in specific matrices with comparison to other hs-cTn assays.MethodsThe limit of detection (LoD), imprecision, interference and stability testing for both serum and lithium heparin (Li-Hep) plasma for the VITROS hs-cTnI assay was determined. We performed Passing-Bablok regression analyses between sample types for the VITROS hs-cTnI assay and compared them to the Abbott ARCHITECT, Beckman Access and the Siemens ADVIA Centaur hs-cTnI assays. We also performed Receiver-operating characteristic curve analyses with the area under the curve (AUC) determined in an emergency department (ED)-study population (n=131) for myocardial infarction (MI).ResultsThe VITROS hs-cTnI LoD was 0.73 ng/L (serum) and 1.4 ng/L (Li-Hep). Stability up to five freeze-thaws was observed for the Ortho hs-cTnI assay, with the analyte stability at room temperature in serum superior to Li-Hep with gross hemolysis also affecting Li-Hep plasma hs-cTnI results. Comparison of Li-Hep to serum concentrations (n=202), yielded proportionally lower concentrations in plasma with the VITROS hs-cTnI assay (slope=0.85; 95% confidence interval [CI]:0.83–0.88). In serum, the VITROS hs-cTnI concentrations were proportionally lower compared to other hs-cTnI assays, with similar slopes observed between assays in samples frozen <−70 °C for 17 years (ED-study) or in 2020. In the ED-study, the VITROS hs-cTnI assay had an AUC of 0.974 (95%CI:0.929–0.994) for MI, similar to the AUCs of other hs-cTn assays.ConclusionsLack of standardization of hs-cTnI assays across manufacturers is evident. The VITROS hs-cTnI assay yields lower concentrations compared to other hs-cTnI assays. Important differences exist between Li-Hep plasma and serum, with evidence of stability and excellent clinical performance comparable to other hs-cTn assays.

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Investigating the clinical usefulness of definitions of progression with 10-2 visual field

British Journal of Ophthalmology ◽

10.1136/bjophthalmol-2020-318188 ◽

2021 ◽

pp. bjophthalmol-2020-318188

Author(s):

Shotaro Asano ◽

Hiroshi Murata ◽

Yuri Fujino ◽

Takehiro Yamashita ◽

Atsuya Miki ◽

...

Keyword(s):

Visual Field ◽

False Positive ◽

False Positive Rate ◽

Clinical Validity ◽

Data Set ◽

Humphrey Field Analyzer ◽

Positive Rate ◽

Using Data ◽

Sensitivity Specificity ◽

Higher Sensitivity

Background/AimTo investigate the clinical validity of the Guided Progression Analysis definition (GPAD) and cluster-based definition (CBD) with the Humphrey Field Analyzer 10-2 test in diagnosing glaucomatous visual field (VF) progression, and to introduce a novel definition with optimised specificity by combining the ‘any-location’ and ‘cluster-based’ approaches (hybrid definition).Methods64 400 stable glaucomatous VFs were simulated from 664 pairs of 10-2 tests (10 sets × 10 VF series × 664 eyes; data set 1). Using these simulated VFs, the specificity to detect progression and the effects of changing the parameters (number of test locations or consecutive VF tests, and percentile cut-off values) were investigated. The hybrid definition was designed as the combination where the specificity was closest to 95.0%. Subsequently, another 5000 actual glaucomatous 10-2 tests from 500 eyes (10 VFs each) were collected (data set 2), and their accuracy (sensitivity, specificity and false positive rate) and the time needed to detect VF progression were evaluated.ResultsThe specificity values calculated using data set 1 with GPAD and CBD were 99.6% and 99.8%. Using data set 2, the hybrid definition had a higher sensitivity than GPAD and CBD, without detriment to the specificity or false positive rate. The hybrid definition also detected progression significantly earlier than GPAD and CBD (at 3.1 years vs 4.2 years and 4.1 years, respectively).ConclusionsGPAD and CBD had specificities of 99.6% and 99.8%, respectively. A novel hybrid definition (with a specificity of 95.5%) had higher sensitivity and enabled earlier detection of progression.

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Evaluation of optimal urine screening and confirmation cut-off values for opiates, at a national reference laboratory

Turkish Journal of Biochemistry ◽

10.1515/tjb-2020-0614 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Çiğdem Karakükcü ◽

Mehmet Zahid Çıracı ◽

Derya Kocer ◽

Mine Yüce Faydalı ◽

Muhittin Abdulkadir Serdar

Keyword(s):

False Positive ◽

False Positive Rate ◽

False Negative ◽

Urine Samples ◽

Reference Laboratory ◽

National Reference Laboratory ◽

Urine Screening ◽

National Reference ◽

Positive Rate ◽

Sensitivity Specificity

Abstract Objectives To obtain optimal immunoassay screening and LC-MS/MS confirmation cut-offs for opiate group tests to reduce false positive (FP) and false negative (FN) rates. Methods A total of 126 urine samples, −50 opiate screening negative, 76 positive according to the threshold of 300 ng/mL by CEDIA method – were confirmed by a full-validated in-house LC-MS/MS method. Sensitivity, specificity, FP, and FN rates were determined at cut-off concentrations of both 300 and 2,000 ng/mL for morphine and codeine, and 10 ng/mL for heroin metabolite 6-mono-acetyl-morphine (6-MAM). Results All CEDIA opiate negative urine samples were negative for morphine, codeine and 6-MAM. Although sensitivity was 100% for each cut-off; specificity was 54.9% at CEDIA cut-off 300 ng/mL vs. LC-MS/MS cut-off 300 ng/mL and, 75% at CEDIA cut-off 2,000 ng/mL vs. LC-MS/MS cut-off 2,000 ng/mL. False positive rate was highest (45.1%) at CEDIA cut-off 300 ng/mL. At CEDIA cut-off 2,000 ng/mL vs. LC-MS/MS cut-off 300 ng/mL, specificity increased to 82.4% and FP rate decreased to 17.6%. All 6-MAM positive samples had CEDIA concentration ≥2,000 ng/mL. Conclusions 2,000 ng/mL for screening and 300 ng/mL for confirmation cut-offs are the most efficient thresholds for the lowest rate of FP opiate results.

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Butyl Benzyl Phthalate in Urban Sewage by Magnetic-Based Immunoassay: Environmental Levels and Risk Assessment

Biosensors ◽

10.3390/bios12010045 ◽

2022 ◽

Vol 12 (1) ◽

pp. 45

Author(s):

Xia Hong ◽

Yin Cui ◽

Ming Li ◽

Yifan Xia ◽

Daolin Du ◽

...

Keyword(s):

Risk Assessment ◽

Drinking Water ◽

Limit Of Detection ◽

Environmental Water ◽

Carcinogenic Risk ◽

Essential Information ◽

Detection Range ◽

Urban Sewage ◽

Butyl Benzyl Phthalate ◽

Positive Rate

A magnetic-based immunoassay (MBI) combined with biotin-streptavidin amplification was proposed for butyl benzyl phthalate (BBP) investigation and risk assessment. The values of LOD (limit of detection, IC10) and IC50 were 0.57 ng/mL and 119.61 ng/mL, with a detection range of 0.57–24977.71 ng/mL for MBI. The specificity, accuracy and precision are well demonstrated. A total of 36 environmental water samples of urban sewage from Zhenjiang, China, were collected and assessed for BBP contamination. The results show that BBP-positive levels ranged from 2.47 to 89.21 ng/mL, with a positive rate of 77.8%. The health effects of BBP in the urban sewage were within a controllable range, and the ambient severity for health (ASI) was below 1.49. The highest value of AS for ecology (ASII) was 7.43, which indicates a potential harm to ecology. The entropy value of risk quotient was below 100, the highest being 59.47, which poses a low risk to the environment and ecology, indicating that there is a need to strengthen BBP controls. The non-carcinogenic risk of BBP exposure from drinking water was higher for females than that for males, and the non-carcinogenic risk from drinking-water and bathing pathways was negligible. This study could provide an alternative method for detecting BBP and essential information for controlling BBP contamination.

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Considerations for performance metrics of metagenomic next generation sequencing analyses

10.1101/2020.12.17.423212 ◽

2020 ◽

Author(s):

Jason G. Kralj ◽

Stephanie L. Servetas ◽

Samuel P. Forry ◽

Scott A. Jackson

Keyword(s):

Performance Metrics ◽

Limit Of Detection ◽

Clinical Performance ◽

Ground Truth ◽

Negative Control ◽

Fitness For Purpose ◽

Performance Metric ◽

The One ◽

Sensitivity Specificity ◽

Harmonic Means

AbstractEvaluating the performance of metagenomics analyses has proven a challenge, due in part to limited ground-truth standards, broad application space, and numerous evaluation methods and metrics. Application of traditional clinical performance metrics (i.e. sensitivity, specificity, etc.) using taxonomic classifiers do not fit the “one-bug-one-test” paradigm. Ultimately, users need methods that evaluate fitness-for-purpose and identify their analyses’ strengths and weaknesses. Within a defined cohort, reporting performance metrics by taxon, rather than by sample, will clarify this evaluation. An estimated limit of detection, positive and negative control samples, and true positive and negative true results are necessary criteria for all investigated taxa. Use of summary metrics should be restricted to comparing results of similar cohorts and data, and should employ harmonic means and continuous products for each performance metric rather than arithmetic mean. Such consideration will ensure meaningful comparisons and evaluation of fitness-for-purpose.

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