scholarly journals Clinical validation of RCSMS: a rapid and sensitive CRISPR-Cas12a test for the molecular detection of SARS-CoV-2 from saliva

2021 ◽  
Author(s):  
Joaquín Abugattás Núñez del Prado ◽  
Angélica Quintana Reyes ◽  
Juan Blume La Torre ◽  
Renzo Gutiérrez Loli ◽  
Alejandro Pinzón Olejua ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
Low Cost ◽  
Thermochemical Treatment ◽  
Molecular Techniques ◽  
Current Status ◽  
Molecular Testing ◽  
Clinical Validation ◽  
Gold Standard Method ◽  
Predictive Values ◽  
Technical Requirements

ABSTRACTEarly detection of SARS-CoV-2 using molecular techniques is paramount to the fight against COVID-19. Due to its high sensitivity and specificity, RT-qPCR is the “gold standard” method for this purpose. However, its technical requirements, processing time and elevated costs hamper its use towards massive and timely molecular testing for COVID-19 in rural and socioeconomically deprived areas of Latin America. The advent and rapid evolution of CRISPR-Cas technology has boosted the development of new pathogen detection methodologies. Recently, DETECTR -a combination of isothermal RT-LAMP amplification and Cas12a-mediated enzymatic detection-has been successfully validated in the Netherlands and the USA as a rapid and low-cost alternative to RT-qPCR for the detection of SARS-CoV-2 from nasopharyngeal swabs. Here, we evaluated the performance of RCSMS, a locally adapted variant of DETECTR, to ascertain the presence of SARS-CoV-2 in saliva samples from 276 patients in two hospitals in Lima, Perú (current status over a total of 350 samples). We show that a low-cost thermochemical treatment with TCEP/EDTA is sufficient to inactivate viral particles and cellular nucleases in saliva, eliminating the need to extract viral RNA with commercial kits, as well as the cumbersome nasopharyngeal swab procedure and the requirement of biosafety level 2 laboratories for molecular analyses. Our clinical validation shows that RCSMS detects up to 5 viral copies per reaction in 40 min, with sensitivity and specificity of 93.8% and 99.0% in the field, respectively, relative to RT-qPCR. Since CRISPR-Cas biosensors can be easily reprogrammed by using different guide RNA molecules, RCSMS has the potential to be quickly adapted for the detection of new SARS-CoV-2 variants. Notably, estimation of its negative and positive predictive values suggests that RCSMS can be confidently deployed in both high and low prevalence settings. Furthermore, our field study validates the use of lateral flow strips to easily visualize the presence of SARS-CoV-2, which paves the way to deploy RCSMS as a “point of care” test in environments with limited access to state-of-the-art diagnostic laboratories. In sum, RCSMS is a fast, efficient and inexpensive alternative to RT-qPCR for expanding COVID-19 testing capacity in low- and middle-income countries.

scholarly journals Multi-site clinical validation of Isothermal Amplification based SARS-COV-2 detection assays using different sampling strategies

2021 ◽  
Author(s):  
Kanan T Desai ◽  
Karla Alfaro ◽  
Laura Mendoza ◽  
Matthew Faron ◽  
Brian Mesich ◽  
...  
Keyword(s):  
Viral Load ◽  
Sensitivity And Specificity ◽  
Clinical Performance ◽  
Low Cost ◽  
Isothermal Amplification ◽  
Detection Methods ◽  
Clinical Validation ◽  
Sampling Strategies ◽  
Rt Pcr ◽  
Study Sites

Background: Isothermal amplification-based tests were developed as rapid, low-cost, and simple alternatives to real-time reverse transcriptase-polymerase chain reaction (RT-PCR) tests for SARS-COV-2 detection. Methods: Clinical performance of two isothermal amplification-based tests (Atila Biosystems iAMP COVID-19 detection test and OptiGene COVID-19 Direct Plus RT-LAMP test) was compared to clinical RT-PCR assays using different sampling strategies. A total of 1378 participants were tested across four study sites. Results: Compared to standard of care RT-PCR testing, the overall sensitivity and specificity of the Atila iAMP test for detection of SARS-CoV-2 were 76.2% and 94.9%, respectively, and increased to 88.8% and 89.5%, respectively, after exclusion of an outlier study site. Sensitivity varied based on the anatomic collected site. Sensitivity for nasopharyngeal was 65.4% (range across study sites:52.8%-79.8%), mid-turbinate 88.2%, saliva 55.1% (range across study sites:42.9%-77.8%) and anterior nares 66.7% (range across study sites:63.6%-76.5%). The specificity for these anatomic collection sites ranged from 96.7% to 100%. Sensitivity improved in symptomatic patients (overall 82.7%) and those with a higher viral load (overall 92.4% for ct≤25). Sensitivity and specificity of the OptiGene Direct Plus RT-LAMP test, conducted at a single study-site, were 25.5% and 100%, respectively. Conclusions The Atila iAMP COVID test with mid-turbinate sampling is a rapid, low-cost assay for detecting SARS-COV-2, especially in symptomatic patients and those with a high viral load, and could be used to reduce the risk of SARS-COV-2 transmission in clinical settings. Variation of performance between study sites highlights the need for site-specific clinical validation of these assays before clinical adoption.

scholarly journals The value of serum progesterone level on day of human chorionic gonadotrophin administration / metaphase II oocyte ratio in predicting IVF/ICSI outcome in patients with normal ovarian reserve

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ahmad Mahran ◽  
Mohammed Khairy ◽  
Reham Elkhateeb ◽  
Abdel Rahman Hegazy ◽  
Ayman Abdelmeged ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
Ovarian Response ◽  
Pregnancy Rates ◽  
Clinical Pregnancy ◽  
Progesterone Level ◽  
Receiver Operating Curve ◽  
Serum Progesterone ◽  
Predictive Values ◽  
Significant Difference ◽  
Assisted Reproduction Treatment

Abstract Background The clinical implication of the increased serum progesterone level on the day of HCG administration in assisted reproduction treatment (ART) is still controversial. The current study aimed to compare the predictive value of serum progesterone on day of HCG administration / metaphase II oocyte (P/MII) ratio on IVF/ ICSI outcome to serum progesterone (P) level alone and the ratio of serum progesterone/estradiol level (P/E2) ratio in prediction of pregnancy rates after ART. Material & methods Two hundred patients admitted to the IVF/ICSI program at Minia IVF center in Egypt in the period from October 2016 to May 2018 were included in this study. Serum Progesterone (P) and Estradiol (E2) levels were estimated on the day of HCG administration. The ratio between serum P and the number of MII oocytes (P/MII ratio) was calculated and the predictive values of the three parameters (P, P/E2 ratio and P/MII ratio) in prediction of cycle outcomes were measured. Results P/ MII oocyte ratio was significantly lower in patients who attained clinical pregnancy (n = 97) as compared with those who couldn’t whilst there was no significant difference in P and P/E2 ratio between the two groups. Using a cut off value of 0.125, the sensitivity and specificity of progesterone/ MII ratio in prediction of no pregnancy in IVF/ICSI were 75.7 and 77.1% respectively with the area under The Receiver operating curve (ROC-AUC) = 0.808. The respective values of the ROC-AUC for the P and P/E2 ratio were 0.651 and 0.712 with sensitivity and specificity of 71.2 and 73.5%for P level and of 72.5 and 75.3% for P/E2 ratio. Implantation or clinical pregnancy rates were significantly different between patients with high and low P/MII ratio irrespective of day of embryo transfer (day 3 or 5). Conclusions In patients with normal ovarian response, serum progesterone on day of HCG / MII oocyte ratio can be a useful predictor of pregnancy outcomes and in deciding on freezing of all embryos for later transfer instead of high progesterone level alone.

Association between the FINDRISC score and the risk of metabolic syndrome and hepatic steatosis

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
D Godoi Bernardes Da Silva ◽  
R Dias Santos ◽  
M Sommer Bittencourt ◽  
J.A.M Carvalho ◽  
M Franken ◽  
...  
Keyword(s):  
Metabolic Syndrome ◽  
Hepatic Steatosis ◽  
Longitudinal Analysis ◽  
Metabolic Diseases ◽  
Low Cost ◽  
Cross Sectional ◽  
Predictive Values ◽  
Cross Sectional Analysis ◽  
The Cross ◽  
Sectional Analysis

Abstract Introduction The Finnish Diabetes Risk Score (FINDRISC) was developed in Europe to predict type 2 diabetes mellitus (T2DM) risk without need of laboratory tests. Small cross-sectional studies analyzed the association between RF with metabolic syndrome (MS) or hepatic steatosis (HS). Our objective was to test the association of FINDRISC with MS or HS, in a transversal and longitudinal way. Methods In 41,668 individuals (age 41.9±9.7 years; 30.8% women) who underwent health evaluation between 2008 and 2016 in a single centre in Brazil, we tested the transversal association between FINDRISC and MS or HS, in multivariate models. The same analyzes were performed longitudinally in non-diabetic subgroups, followed for 5±3 years, to test the predictive value of FINDRISC and the incidental risk of MS (n=10,075 individuals) or HS (n=7,097 individuals), using logistic regression. Models were adjusted for confounders such as sex, use of medications for dyslipidemia, smoking, and baseline plasma levels of glucose, creatinine and lipids. A receiver operating characteristic (ROC) curve was used to evaluate the discriminative and predictive values of FINDRISC for MS and HS. Results In the cross-sectional analysis, 2,252 (5%) individuals had MS and 14,176 (34%) HS. In the longitudinal analysis, there were 302 cases of incidental MS (2%) and 1,096 cases of HS (15%). FINDRISC was independently associated with MS and HS in the cross-sectional analysis (respectively, OR 1.27, 95% CI: 1.25–1.28, P<0.001; and OR 1.21, 95% CI: 1.20–1.22, P<0.001, per FINDRISC unit) and in longitudinal analysis (respectively, OR of 1.18, 95% CI: 1.15–1.21, P<0.001; and OR of 1.10, 95% CI: 1.08–1.11, P<0.001, per FINDRISC unit). In comparison with individuals with low FINDRISC, those with moderate, high and very high values showed significant and proportional increases of the 12 to 77 fold in the chance of current SM (P<0.001) and 3 to 10 fold in the chance of HS (P<0.001). During follow-up, these increases were 3 to 10 fold in the chance of incidental MS (P<0.001) and 1 to 3 fold in the chance of HS (P<0.001). The AUC from cross-sectional analysis for MS and HS were respectively 0.82 (95% CI 0.81–0.83) and 0.76 (95% CI 0.75–0.76), and in longitudinal analysis 0.73 (95% CI 0.70–0.76) and 0.63 (95% CI 0.61–0.65), respectively. Conclusion FINDRISC was associated with the presence and onset of MS and HS, but it predicted better metabolic syndrome risk than hepatic steatosis. Therefore, this simple, practical and low-cost score can be useful for population screening and identification of subgroups of individuals at higher risk future metabolic diseases. Funding Acknowledgement Type of funding source: None

scholarly journals Screening for aneurysms of the abdominal aorta using a simple screening device

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
J. W. Brakel ◽  
T. A. Berendsen ◽  
P. M. C. Callenbach ◽  
J. van der Burgh ◽  
R. J. Hissink ◽  
...  
Keyword(s):  
Negative Predictive Value ◽  
Sensitivity And Specificity ◽  
Abdominal Aorta ◽  
Predictive Value ◽  
Cost Effective ◽  
Abdominal Ultrasound ◽  
Predictive Values ◽  
Bladder Scan ◽  
Health Council ◽  
Screening Device

Abstract Introduction Several countries advocate screening for aneurysms of the abdominal aorta (AAA) in selected patients. In the Netherlands, routine screening is currently under review by the National Health Council. In any screening programme, cost-efficiency and accuracy are key. In this study, we evaluate the Aorta Scan (Verathon, Amsterdam, Netherlands), a cost-effective and easy-to-use screening device based on bladder scan technology, which enables untrained personnel to screen for AAA. Methods We subjected 117 patients to an Aorta Scan and compared the results to the gold standard (abdominal ultrasound). We used statistical analysis to determine sensitivity and specificity of the Aorta Scan, as well as the positive and negative predictive values, accuracy, and inter-test agreement (Kappa). Results Sensitivity and specificity were 0.86 and 0.98, respectively. Positive predictive value was 0.98 and negative predictive value was 0.88. Accuracy was determined at 0.92 and the Kappa value was 0.85. When waist–hip circumferences (WHC) of > 115 cm were excluded, sensitivity raised to 0.96, specificity stayed 0.98, positive and negative predictive value were 0.98 and 0.96, respectively, accuracy to 0.97, and Kappa to 0.94. Conclusion Herein, we show that the Aorta Scan is a cost-effective and very accurate screening tool, especially in patients with WHC below 115 cm, which makes it a suitable candidate for implementation into clinical practice, specifically in the setting of screening selected populations for the presence of AAA.

scholarly journals A diabetes risk score for Qatar utilizing a novel mathematical modeling approach to identify individuals at high risk for diabetes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Susanne F. Awad ◽  
Soha R. Dargham ◽  
Amine A. Toumi ◽  
Elsy M. Dumit ◽  
Katie G. El-Nahas ◽  
...  
Keyword(s):  
High Risk ◽  
Sensitivity And Specificity ◽  
Risk Score ◽  
Area Under The Curve ◽  
Diabetes Risk ◽  
Predictive Values ◽  
Predictive Variables ◽  
Comparable Performance ◽  
Representative Random Sample ◽  
Diabetes Risk Score

AbstractWe developed a diabetes risk score using a novel analytical approach and tested its diagnostic performance to detect individuals at high risk of diabetes, by applying it to the Qatari population. A representative random sample of 5,000 Qataris selected at different time points was simulated using a diabetes mathematical model. Logistic regression was used to derive the score using age, sex, obesity, smoking, and physical inactivity as predictive variables. Performance diagnostics, validity, and potential yields of a diabetes testing program were evaluated. In 2020, the area under the curve (AUC) was 0.79 and sensitivity and specificity were 79.0% and 66.8%, respectively. Positive and negative predictive values (PPV and NPV) were 36.1% and 93.0%, with 42.0% of Qataris being at high diabetes risk. In 2030, projected AUC was 0.78 and sensitivity and specificity were 77.5% and 65.8%. PPV and NPV were 36.8% and 92.0%, with 43.0% of Qataris being at high diabetes risk. In 2050, AUC was 0.76 and sensitivity and specificity were 74.4% and 64.5%. PPV and NPV were 40.4% and 88.7%, with 45.0% of Qataris being at high diabetes risk. This model-based score demonstrated comparable performance to a data-derived score. The derived self-complete risk score provides an effective tool for initial diabetes screening, and for targeted lifestyle counselling and prevention programs.

scholarly journals Nanopore Targeted Sequencing for Rapid Gene Mutations Detection in Acute Myeloid Leukemia

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1026 ◽  
Author(s):  
Cumbo ◽  
Minervini ◽  
Orsini ◽  
Anelli ◽  
Zagaria ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Low Cost ◽  
Gene Mutations ◽  
Predictive Biomarkers ◽  
Molecular Testing ◽  
Sequencing Analysis ◽  
Cebpa Mutations ◽  
Targeted Gene Sequencing ◽  
Acute Myeloid

Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold targeted therapy. Next generation sequencing offers the advantage of the simultaneous investigation of numerous genes, but these methods remain expensive and time consuming. In this context, we present a nanopore-based assay for rapid (24 h) sequencing of six genes (NPM1, FLT3, CEBPA, TP53, IDH1 and IDH2) that are recurrently mutated in AML. The study included 22 AML patients at diagnosis; all data were compared with the results of S5 sequencing, and discordant variants were validated by Sanger sequencing. Nanopore approach showed substantial advantages in terms of speed and low cost. Furthermore, the ability to generate long reads allows a more accurate detection of longer FLT3 internal tandem duplications and phasing double CEBPA mutations. In conclusion, we propose a cheap, rapid workflow that can potentially enable all basic molecular biology laboratories to perform detailed targeted gene sequencing analysis in AML patients, in order to define their prognosis and the appropriate treatment.

scholarly journals A new highly sensitive and specific overnight combined screening and diagnostic test for primary aldosteronism

2016 ◽  
Vol 175 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Vaios Tsiavos ◽  
Athina Markou ◽  
Labrini Papanastasiou ◽  
Theodora Kounadi ◽  
Ioannis I Androulakis ◽  
...  
Keyword(s):  
Diagnostic Test ◽  
Sensitivity And Specificity ◽  
Primary Aldosteronism ◽  
Low Cost ◽  
Confirmatory Test ◽  
Outpatient Basis ◽  
Endocrine Hypertension ◽  
Serum Aldosterone ◽  
Highly Sensitive ◽  
Aldosterone To Renin Ratio

Context Primary aldosteronism (PA) is the most common cause of endocrine hypertension that is diagnosed following a two-step process: an initial screening test, based on the serum aldosterone-to-renin ratio (ARR), followed by a relatively laborious and time-consuming confirmatory test to document autonomous aldosterone (ALD) secretion. Objective The aim of this study is to develop a simple overnight test for the early and definite diagnosis of PA. Patients and methods Totally, 148 hypertensive patients underwent a fludrocortisone–dexamethasone suppression test (FDST) and the new overnight diagnostic test (DCVT) using pharmaceutical RAAS (renin–angiotensin–aldosterone system) blockade with dexamethasone, captopril and valsartan. Results Of the 148 patients, 45 were diagnosed as having PA and they all normalized their elevated blood pressure (BP) after administration of spironolactone or eplerenone. The remaining 103 patients were considered as having essential hypertension and served as controls. Using ROC analysis, the estimated sensitivity and specificity were 91 and 100%, respectively, for the post-FDST ARR, whereas 98% and 89% and 100% and 82% for the post-DCVT ARR and post-DCVT ALD, respectively, with selected cutoffs of 0.32ng/dL/μU/mL and 3ng/dL respectively. However, considering these cutoffs simultaneously, the estimated sensitivity and specificity were 98 and 100% respectively. Applying these cutoffs, the diagnosis of PA was confirmed in 44 (98%) of the 45 patients who were considered to have the disease. Conclusions In this study, a highly sensitive and specific, low-cost, rapid, safe, and easy-to-perform diagnostic test (DCVT) for PA is described, which could be utilized on an outpatient basis potentially substituting conventional laborious testing.

scholarly journals Imaging Diagnosis of Right Ventricle Involvement in Chagas Cardiomyopathy

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Minna M. D. Romano ◽  
Henrique T. Moreira ◽  
André Schmidt ◽  
Benedito Carlos Maciel ◽  
José Antônio Marin-Neto
Keyword(s):  
Right Ventricle ◽  
Tissue Characterization ◽  
Low Cost ◽  
Diagnostic Techniques ◽  
Diagnostic Tools ◽  
Deformation Analysis ◽  
Geometrical Shape ◽  
Gold Standard Method ◽  
Chagas Cardiomyopathy ◽  
Health And Disease

Right ventricle (RV) is considered a neglected chamber in cardiology and knowledge about its role in cardiac function was mostly focused on ventricular interdependence. However, progress on the understanding of myocardium diseases primarily involving the RV led to a better comprehension of its role in health and disease. In Chagas disease (CD), there is direct evidence from both basic and clinical research of profound structural RV abnormalities. However, clinical detection of these abnormalities is hindered by technical limitations of imaging diagnostic tools. Echocardiography has been a widespread and low-cost option for the study of patients with CD but, when applied to the RV assessment, faces difficulties such as the absence of a geometrical shape to represent this cavity. More recently, the technique has evolved to a focused guided RV imaging and myocardial deformation analysis. Also, cardiac magnetic resonance (CMR) has been introduced as a gold standard method to evaluate RV cavity volumes. CMR advantages include precise quantitative analyses of both LV and RV volumes and its ability to perform myocardium tissue characterization to identify areas of scar and edema. Evolution of these cardiac diagnostic techniques opened a new path to explore the pathophysiology of RV dysfunction in CD.

scholarly journals A New Evaluation Method for Lumbar Spinal Instability: Passive Lumbar Extension Test

2006 ◽  
Vol 86 (12) ◽  
pp. 1661-1667 ◽  
Author(s):  
Yuichi Kasai ◽  
Koichiro Morishita ◽  
Eiji Kawakita ◽  
Tetsushi Kondo ◽  
Atsumasa Uchida
Keyword(s):  
Likelihood Ratio ◽  
Sensitivity And Specificity ◽  
Evaluation Method ◽  
Positive Likelihood Ratio ◽  
Spinal Instability ◽  
Predictive Values ◽  
Flexion Extension ◽  
Lumbar Extension ◽  
Lumbar Spinal ◽  
Sensitivity Specificity

Abstract Background and PurposeAlthough many studies have described clinical examination measures for the diagnosis of lumbar spinal instability, few of them have investigated the sensitivity and specificity of the measures that were used. The authors devised a passive lumbar extension (PLE) test for assessing lumbar spinal instability. The purpose of this study was to investigate the sensitivity, specificity, and positive likelihood ratio of this test. Subjects and Methods. The PLE test as well as the instability catch sign, painful catch sign, and apprehension sign tests were done for 122 subjects with lumbar degenerative diseases. The subjects were divided into 2 groups—instability positive and instability negative—on the basis of findings on flexion-extension films of the lumbar spine. The sensitivity, specificity, predictive values, and positive likelihood ratio of each test were investigated. Results. The sensitivity and specificity of the PLE test were 84.2% and 90.4%, respectively. These values were higher than those of other signs. The positive likelihood ratio of the PLE test was 8.84 (95% confidence interval=4.51–17.33). Discussion and Conclusion. The PLE test is an effective method for examining patients for lumbar spinal instability and can be performed easily in an outpatient clinic.

scholarly journals Overview of Plant-Derived Vaccine Antigens: Dengue Virus

2011 ◽  
Vol 14 (3) ◽  
pp. 400 ◽  
Author(s):  
Ravindra B Malabadi ◽  
Advaita Ganguly ◽  
Jaime A Teixeira da Silva ◽  
Archana Parashar ◽  
Mavanur R Suresh ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Dengue Virus ◽  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
Low Cost ◽  
Current Status ◽  
Human Immune Deficiency Virus ◽  
Dengue Vaccine ◽  
New Methods ◽  
Vaccine Antigens

ABSTRACT - This review highlights the advantages and current status of plant-derived vaccine development with special reference to the dengue virus. There are numerous problems involved in dengue vaccine development, and there is no vaccine against all four dengue serotypes. Dengue vaccine development using traditional approaches has not been satisfactory in terms of inducing neutralizing antibodies. Recently, these issues were addressed by showing a very good response to inducing neutralizing antibodies by plant-derived dengue vaccine antigens. This indicates the feasibility of using plant-derived vaccine antigens as a low-cost method to combat dengue and other infectious diseases. The application of new methods and strategies such as dendritic cell targeting in cancer therapy, severe acute respiratory syndrome, tuberculosis, human immune deficiency virus, and malaria might play an important role. These new methods are more efficient than traditional protocols. It is expected that in the near future, plant-derived vaccine antigens or antibodies will play an important role in the control of human infectious diseases. This article is open to POST-PUBLICATION REVIEW. Registered readers (see “For Readers”) may comment by clicking on ABSTRACT on the issue’s contents page.

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