scholarly journals Evaluation of RNA Extraction-Free Method for Detection of SARS-CoV-2 in Salivary Samples for Mass Screening for COVID-19

2021 ◽  
Vol 2021 ◽  
pp. 1-6
Author(s):  
Sally A. Mahmoud ◽  
Subhashini Ganesan ◽  
Esra Ibrahim ◽  
Bhagyashree Thakre ◽  
Juliet G. Teddy ◽  
...  
Keyword(s):  
Predictive Value ◽  
Rna Extraction ◽  
Screening Method ◽  
High Sensitivity ◽  
High Specificity ◽  
Cost Effective ◽  
Kappa Coefficient ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Good Agreement

In this COVID-19 pandemic, there is a dire need for cost-effective and less time-consuming alternatives for SARS-CoV-2 testing. The RNA extraction-free method for detecting SARS-CoV-2 in saliva is a promising option. This study found that it has high sensitivity (85.34%), specificity (95.04%), and was comparable to the gold standard nasopharyngeal swab (NPS) sample tests. The method showed good agreement between salivary and NPS samples, with a kappa coefficient of 0.797. However, there are variations in the sensitivity and specificity based on the RT-PCR kit used. The Thermo Fisher Applied Biosystems showed high sensitivity, positive predictive value (PPV), and negative predictive value (NPV) but also showed a higher percentage of invalid reports. On the other hand, the BGI kit showed high specificity, better agreement (kappa coefficient) between the results of saliva and NPS samples, and higher correlation between the Ct values of saliva and NPS samples. Thus, the RNA extraction-free method for salivary sample serves as an effective alternative screening method for COVID-19.

scholarly journals Evaluation of RNA extraction free method for detection of SARS-COV-2 in salivary samples for mass screening for COVID-19

2021 ◽  
Author(s):  
Sally A. Mahmoud ◽  
Esra Ibrahim ◽  
Subhashini Ganesan ◽  
Bhagyashree Thakre ◽  
Juliet G Teddy ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
Gold Standard ◽  
Rna Extraction ◽  
High Sensitivity ◽  
High Specificity ◽  
Cost Effective ◽  
Kappa Coefficient ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Good Percentage

AbstractIn this current COVID - 19 pandemic, there is a dire need for cost effective and less time-consuming alternatives for SARS-COV-2 testing. The RNA extraction free method for detecting SARS-COV-2 in saliva is a promising option, this study found that it has high sensitivity (85.34%), specificity (95.04%) and was comparable to the gold standard nasopharyngeal swab. The method showed good percentage of agreement (kappa coefficient) 0.797 between salivary and NPS samples. However, there are variations in the sensitivity and specificity based on the RT-PCR kit used. The Thermo Fischer-Applied biosystems showed high sensitivity, PPV and NPV but also showed higher percentage of invalid reports. Whereas the BGI kit showed high specificity, better agreement (kappa coefficient) between the results of saliva and NPS samples and higher correlation between the Ct values of saliva and NPS samples. Thus, the RNA extraction free method for salivary sample serves as an effective alternative for SARS-CoV 2-testing.

scholarly journals Cost-Effective Pooling of DNA from Nasopharyngeal Swab Samples for Large-Scale Detection of Bacteria by Real-Time PCR

2014 ◽  
Vol 53 (3) ◽  
pp. 1002-1004 ◽  
Author(s):  
Sophie Edouard ◽  
Elsa Prudent ◽  
Philippe Gautret ◽  
Ziad A. Memish ◽  
Didier Raoult
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Large Scale ◽  
High Sensitivity ◽  
High Specificity ◽  
Cost Effective ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Scale Detection ◽  
The Cost

We investigated the potential of pooling DNA from nasopharyngeal specimens to reduce the cost of real-time PCR (RT-PCR) for bacterial detection. Lyophilization is required to reconcentrate DNA. This strategy yields a high specificity (86%) and a high sensitivity (96%). We estimate that compared to individual testing, 37% fewer RT-PCR tests are needed.

scholarly journals Prediction of Preterm Birth: Maternal Characteristics, Ultrasound Markers, and Biomarkers: An Updated Overview

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Zeynep Asli Oskovi Kaplan ◽  
A. Seval Ozgu-Erdinc
Keyword(s):  
Preterm Birth ◽  
Screening Method ◽  
High Sensitivity ◽  
High Specificity ◽  
Cost Effective ◽  
Strain Ratio ◽  
Cervical Length ◽  
Health Condition ◽  
Fetal Fibronectin ◽  
Maternal Characteristics

There is not a single or combined screening method for preterm birth with high sensitivity which will truly identify the women at risk for preterm birth while also with high specificity to prevent unnecessary interventions and high treatment costs. Measurement of cervical length is the most cost-effective method that is used in clinical practice. Bedside tests have also been developed for detecting markers like fetal fibronectin, insulin-like growth factor binding protein-1 (IGFBP-1), interleukin-6, and placental alpha-macroglobulin-1. Taking the maternal history, health condition, and sociodemographical factors into consideration is recommended. Ultrasound markers apart from cervical length measurements as uterocervical angle and placental strain ratio are studied. Investigations on metabolomics, proteomics, and microRNA profiling have brought a new aspect on this subject. Maybe in the future, with clear identification of women at true risk for preterm birth, development of more effective preventive strategies will not be unfeasible.

scholarly journals Molecular markers in the diagnosis of thyroid nodules

2013 ◽  
Vol 57 (2) ◽  
pp. 89-97 ◽  
Author(s):  
Laura S. Ward ◽  
Richard T. Kloos
Keyword(s):  
Predictive Value ◽  
High Sensitivity ◽  
High Specificity ◽  
Cost Effective ◽  
Needle Aspiration ◽  
Molecular Diagnostic ◽  
Risk Of Malignancy ◽  
Benign Nodules ◽  
Low Sensitivity ◽  
Rule Out

An indeterminate thyroid nodule cytology result occurs about every sixth fine-needle aspiration. These indeterminate nodules harbor a 24% risk of malignancy (ROM); too high to ignore, but driving surgery where most nodules are benign. Molecular diagnostics have emerged to ideally avoid surgery when appropriate, and to trigger the correct therapeutic surgery when indicated, as opposed to an incomplete diagnostic surgery. No current molecular test offers both high sensitivity and high specificity. A molecular diagnostic test with high sensitivity (e.g. Afirma Gene Expression Classifier sensitivity 90%) offers a high Negative Predictive Value when the ROM is relatively low, such as < 30%. Only such tests can "rule-out" cancer. In this setting, a molecularly benign result suggests the same ROM as that of operated cytologically benign nodules (~6%). Thus, clinical observation can replace diagnostic surgery; increasing quality of life and decreasing medical costs. However, its low specificity cannot "rule-in" cancer as a suspicious result has a Positive Predictive Value (PPV) of ~40%, perhaps too low to routinely reflex to definitive cancer surgery. Conversely, high specificity tests (BRAF, RAS, PPAR/PAX-8, RET/PTC, PTEN) offer high PPV results, and only these tests can "rule-in" cancer. Here a positive molecular result warrants definitive therapeutic surgery. However, their low sensitivity cannot "rule-out" cancer and a negative molecular result cannot dissuade diagnostic surgery; limiting their cost-effectiveness. Whether or not there is a useful and cost-effective role to sequentially combine these approaches, or to modify existing approaches, is under investigation.

scholarly journals A scalable saliva-based, extraction-free rt-lamp protocol for sars-cov-2 diagnosis

2020 ◽  
Author(s):  
Paula Asprino ◽  
Fabiana Bettoni ◽  
Anamaria Camargo ◽  
Diego Coelho ◽  
Guilherme Coppini ◽  
...  
Keyword(s):  
Rna Extraction ◽  
Cost Effective ◽  
Turnaround Time ◽  
Curve Analysis ◽  
Nasopharyngeal Swab ◽  
Screening Methods ◽  
Rt Pcr ◽  
Effective Screening ◽  
Point Curve ◽  
Average Turnaround Time

I.ABSTRACTScalable, cost-effective screening methods are an essential tool to control SARS-CoV-2 spread. We have developed a straight saliva-based, RNA extraction-free, RT-LAMP test that is comparable to current nasopharyngeal swab RT-PCR tests in both sensitivity and specificity. Using a 2-step readout of fluorescence and melting-point curve analysis, the test is scalable to more than 30,000 tests per day with average turnaround time of less than 3 hours. The test was validated using samples from 244 symptomatic patients, and showed sensitivity of 78.9% (vs. 85.5% for nasopharyngeal swabs RT-PCR) and specificity of 100% (vs. 100% for nasopharyngeal swabs RT-PCR). Our method is therefore accurate, robust, time and cost effective and therefore can be used for screening of SARS-CoV-2.

scholarly journals A new Syber Green real time PCR to detect SARS-CoV-2

2020 ◽  
Author(s):  
D.R. Marinowic ◽  
G. Zanirati ◽  
F.V.F. Rodrigues ◽  
M.V.C. Grahl ◽  
A.M. Alcará ◽  
...  
Keyword(s):  
Diagnostic Test ◽  
Large Scale ◽  
Low Cost ◽  
Phylogenetic Analyses ◽  
High Sensitivity ◽  
High Specificity ◽  
Cost Effective ◽  
Etiologic Agent ◽  
Rt Pcr ◽  
Human Respiratory Tract

Abstract Phylogenetic analyses demonstrated that etiologic agent of pandemic outbreak is a betacoronavirus named SARS-CoV-2. For public health interventions, a diagnostic test with high sensitivity and specificity is required. The gold standard protocol for diagnosis by WHO is the RT-PCR. To detect low viral load and large-scale screening a low-cost diagnostic test becomes necessary. Here we develop a cost-effective test capable of to detect the new coronavirues. We validated an auxiliary protocol for molecular diagnosis with RT-PCR SYBR Green methodology to successfully screen negative cases of SARS-CoV-2. Our results demonstrated that a set of primers with high specificity, and no homology with other viruses from Coronovideae family or human respiratory tract pathogenic viruses. Optimization of annealing temperature and polymerization time led to an high specificity in the PCR products. We have developed a more affordable and swift methodology for negative SARS-CoV-2 screening. This methodology can be applied on large scale populational to soften panic and economic burden through guidance for isolation strategies.

scholarly journals Combining machine learning and nanopore construction creates an artificial intelligence nanopore for coronavirus detection

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Masateru Taniguchi ◽  
Shohei Minami ◽  
Chikako Ono ◽  
Rina Hamajima ◽  
Ayumi Morimura ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
High Speed ◽  
Simple Procedure ◽  
Rna Extraction ◽  
Disease Outbreaks ◽  
High Sensitivity ◽  
Cost Effective ◽  
Rt Pcr ◽  
Emerging Viruses

AbstractHigh-throughput, high-accuracy detection of emerging viruses allows for the control of disease outbreaks. Currently, reverse transcription-polymerase chain reaction (RT-PCR) is currently the most-widely used technology to diagnose the presence of SARS-CoV-2. However, RT-PCR requires the extraction of viral RNA from clinical specimens to obtain high sensitivity. Here, we report a method for detecting novel coronaviruses with high sensitivity by using nanopores together with artificial intelligence, a relatively simple procedure that does not require RNA extraction. Our final platform, which we call the artificially intelligent nanopore, consists of machine learning software on a server, a portable high-speed and high-precision current measuring instrument, and scalable, cost-effective semiconducting nanopore modules. We show that artificially intelligent nanopores are successful in accurately identifying four types of coronaviruses similar in size, HCoV-229E, SARS-CoV, MERS-CoV, and SARS-CoV-2. Detection of SARS-CoV-2 in saliva specimen is achieved with a sensitivity of 90% and specificity of 96% with a 5-minute measurement.

scholarly journals A new SYBR Green real-time PCR to detect SARS-CoV-2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
D. R. Marinowic ◽  
G. Zanirati ◽  
F. V. F. Rodrigues ◽  
M. V. C. Grahl ◽  
A. M. Alcará ◽  
...  
Keyword(s):  
Diagnostic Test ◽  
Large Scale ◽  
Low Cost ◽  
High Sensitivity ◽  
High Specificity ◽  
Cost Effective ◽  
Etiologic Agent ◽  
Sybr Green ◽  
Rt Pcr ◽  
Human Respiratory Tract

AbstractPhylogenetic analysis has demonstrated that the etiologic agent of the 2020 pandemic outbreak is a betacoronavirus named SARS-CoV-2. For public health interventions, a diagnostic test with high sensitivity and specificity is required. The gold standard protocol for diagnosis by the Word Health Organization (WHO) is RT-PCR. To detect low viral loads and perform large-scale screening, a low-cost diagnostic test is necessary. Here, we developed a cost-effective test capable of detecting SARS-CoV-2. We validated an auxiliary protocol for molecular diagnosis with the SYBR Green RT-PCR methodology to successfully screen negative cases of SARS-CoV-2. Our results revealed a set of primers with high specificity and no homology with other viruses from the Coronovideae family or human respiratory tract pathogenic viruses, presenting with complementarity only for rhinoviruses/enteroviruses and Legionella spp. Optimization of the annealing temperature and polymerization time led to a high specificity in the PCR products. We have developed a more affordable and swift methodology for negative SARS-CoV-2 screening. This methodology can be applied on a large scale to soften panic and economic burden through guidance for isolation strategies.

scholarly journals Comparison of SARS-COV-2 nasal antigen test to nasopharyngeal RT-PCR in mildly symptomatic patients

2020 ◽  
Author(s):  
Abdulkarim Abdulrahman ◽  
Fathi Mustafa ◽  
Abdulla I AlAwadhi ◽  
Qadar Alansari ◽  
Batool AlAlawi ◽  
...  
Keyword(s):  
Predictive Value ◽  
High Specificity ◽  
Cost Effective ◽  
High Viral Load ◽  
Antigen Test ◽  
Rt Pcr ◽  
Rapid Antigen Detection Test ◽  
Specificity And Sensitivity ◽  
Medical Teams ◽  
Sensitivity Specificity

AbstractIntroductionCOVID 19 has been vastly spreading since December 2019 and the medical teams worldwide are doing their best to limit its spread. In the absence of a vaccine the best way to fight it is by detecting infected cases early and isolate them to prevent its spread. Therefore, a readily available, rapid, and cost-effective test with high specificity and sensitivity for early detection of COVID 19 is required. In this study, we are testing the diagnostic performance of a rapid antigen detection test in mildly symptomatic cases. (RADT).MethodsThe study included 4183 patients who were mildly symptomatic. A nasal sample for the rapid antigen test and a nasopharyngeal sample was taken from each patient. Statistical analysis was conducted to calculate the sensitivity, specificity, positive predictive value, negative predictive value and kappa coefficient of agreement.ResultsThe prevalence of COVID 19 in the study population was 17.5% (733/4183). The calculated sensitivity and specificity were 82.1% and 99.1% respectively. Kappa’s coefficient of agreement between the rapid antigen test and RT-PCR was 0.859 (p < 0.001). A stratified analysis was performed and it showed that the sensitivity of the test improved significantly with lowering the cutoff Ct value to 24.ConclusionThe results of the diagnostic assessment of nasal swabs in the RADT used in our study are promising regarding the potential benefit of using them as a screening tool in mildly symptomatic patients. The diagnostic ability was especially high in cases with high viral load. The rapid antigen test is intended to be used alongside RT-PCR and not replace it. RADT can be of benefit in reducing the use of PCR.

Effective optimization of SARS-CoV-2 laboratory testing variables in an era of supply chain constraints

2020 ◽  
Vol 15 (15) ◽  
pp. 1483-1487
Author(s):  
Nikhil S Sahajpal ◽  
Ashis K Mondal ◽  
Allan Njau ◽  
Sudha Ananth ◽  
Kimya Jones ◽  
...  
Keyword(s):  
Supply Chain ◽  
Rna Extraction ◽  
Nasopharyngeal Swab ◽  
Sample Collection ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Short Supply ◽  
Viral Transport ◽  
3D Printed ◽  
Bridging Studies

RT-PCR-based assays for the detection of SARS-CoV-2 have played an essential role in the current COVID-19 pandemic. However, the sample collection and test reagents are in short supply, primarily due to supply chain issues. Thus, to eliminate testing constraints, we have optimized three key process variables: RNA extraction and RT-PCR reactions, different sample types and media to facilitate SARS-CoV-2 testing. By performing various validation and bridging studies, we have shown that various sample types such as nasopharyngeal swab, bronchioalveolar lavage and saliva, collected using conventional nasopharyngeal swabs, ESwab or 3D-printed swabs and, preserved in viral transport media, universal transport media, 0.9% sodium chloride or Amies media are compatible with RT-PCR assay for COVID-19. Besides, the reduction of PCR reagents by up to fourfold also produces reliable results.

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