scholarly journals Molecular Beacon Assay Development for Severe Acute Respiratory Syndrome Coronavirus 2 Detection

Sensors ◽  
2021 ◽  
Vol 21 (21) ◽  
pp. 7015
Author(s):  
Josué Carvalho ◽  
Jéssica Lopes-Nunes ◽  
Joana Figueiredo ◽  
Tiago Santos ◽  
André Miranda ◽  
...  
Keyword(s):  
Molecular Beacon ◽  
Total Duration ◽  
Clinical Samples ◽  
Test Duration ◽  
Upper Respiratory Tract ◽  
Design And Optimization ◽  
Global Pandemic ◽  
Detection Assay ◽  
G Quadruplex ◽  
Fluorescence Reading

The fast spread of SARS-CoV-2 has led to a global pandemic, calling for fast and accurate assays to allow infection diagnosis and prevention of transmission. We aimed to develop a molecular beacon (MB)-based detection assay for SARS-CoV-2, designed to detect the ORF1ab and S genes, proposing a two-stage COVID-19 testing strategy. The novelty of this work lies in the design and optimization of two MBs for detection of SARS-CoV-2, namely, concentration, fluorescence plateaus of hybridization, reaction temperature and real-time results. We also identify putative G-quadruplex (G4) regions in the genome of SARS-CoV-2. A total of 458 nasopharyngeal and throat swab samples (426 positive and 32 negative) were tested with the MB assay and the fluorescence levels compared with the cycle threshold (Ct) values obtained from a commercial RT-PCR test in terms of test duration, sensitivity, and specificity. Our results show that the samples with higher fluorescence levels correspond to those with low Ct values, suggesting a correlation between viral load and increased MB fluorescence. The proposed assay represents a fast (total duration of 2 h 20 min including amplification and fluorescence reading stages) and simple way of detecting SARS-CoV-2 in clinical samples from the upper respiratory tract.

scholarly journals Molecular beacon assay development for Severe Acute Respiratory Syndrome Coronavirus 2 detection

2021 ◽  
Author(s):  
Josué Carvalho ◽  
Jéssica Lopes Nunes ◽  
Joana Figueiredo ◽  
Tiago Santos ◽  
André Miranda ◽  
...  
Keyword(s):  
Molecular Beacon ◽  
Point Of Care ◽  
Total Duration ◽  
Fluorescence Analysis ◽  
Population Level ◽  
Clinical Samples ◽  
Test Duration ◽  
Upper Respiratory Tract ◽  
Testing Strategy ◽  
Two Stage

The fast spread of SARS-CoV-2 has led to a global pandemic, calling for fast and accurate assays to allow infection diagnosis and prevention of transmission. We aimed to develop a molecular beacon (MB)-based detection assay for SARS-CoV-2, designed to, detect the ORF1ab and S genes, proposing a two-stage COVID-19 testing strategy, using MBs to detect the presence of target amplicons by fluorescence analysis. Two MBs were designed, optimized in terms of concentration, fluorescence plateaus of hybridization, reaction temperature and best real-time results. A total of 450 nasopharyngel and throat swab samples (418 positive and 32 negative) were tested with the MB assay and the fluorescence levels compared with the cycle threshold (Ct) values obtained from a commercial RT-PCR test in terms of test duration, sensitivity and specificity. Our results show that the samples with higher fluorescence levels correspond to those with low Ct values, suggesting a correlation between viral load and increased MB fluorescence. The proposed assay represents a fast (total duration of 2 h 20 min including amplification and fluorescence reading stages) and simple way of detecting SARS-CoV-2 in clinical samples from the upper respiratory tract. Our two-stage testing strategy is suitable for further development into a point-of-care assay and potentially scalable to population level.

scholarly journals MRFGRO: a hybrid meta-heuristic feature selection method for screening COVID-19 using deep features

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arijit Dey ◽  
Soham Chattopadhyay ◽  
Pawan Kumar Singh ◽  
Ali Ahmadian ◽  
Massimiliano Ferrara ◽  
...  
Keyword(s):  
Feature Selection ◽  
Golden Ratio ◽  
Medical Image Analysis ◽  
Feature Selection Method ◽  
World Health ◽  
Significant Feature ◽  
Feature Subset ◽  
Upper Respiratory Tract ◽  
Global Pandemic ◽  
Health Organization

AbstractCOVID-19 is a respiratory disease that causes infection in both lungs and the upper respiratory tract. The World Health Organization (WHO) has declared it a global pandemic because of its rapid spread across the globe. The most common way for COVID-19 diagnosis is real-time reverse transcription-polymerase chain reaction (RT-PCR) which takes a significant amount of time to get the result. Computer based medical image analysis is more beneficial for the diagnosis of such disease as it can give better results in less time. Computed Tomography (CT) scans are used to monitor lung diseases including COVID-19. In this work, a hybrid model for COVID-19 detection has developed which has two key stages. In the first stage, we have fine-tuned the parameters of the pre-trained convolutional neural networks (CNNs) to extract some features from the COVID-19 affected lungs. As pre-trained CNNs, we have used two standard CNNs namely, GoogleNet and ResNet18. Then, we have proposed a hybrid meta-heuristic feature selection (FS) algorithm, named as Manta Ray Foraging based Golden Ratio Optimizer (MRFGRO) to select the most significant feature subset. The proposed model is implemented over three publicly available datasets, namely, COVID-CT dataset, SARS-COV-2 dataset, and MOSMED dataset, and attains state-of-the-art classification accuracies of 99.15%, 99.42% and 95.57% respectively. Obtained results confirm that the proposed approach is quite efficient when compared to the local texture descriptors used for COVID-19 detection from chest CT-scan images.

Clinical applications of spectroscopic techniques in conjunction with multivariate analysis in virus diagnosis

2021 ◽  
pp. 1-27
Author(s):  
Marfran C. D. Santos ◽  
João V. M. Mariz ◽  
Raissa V. O. Silva ◽  
Camilo L. M. Morais ◽  
Kássio M. G. Lima
Keyword(s):  
Multivariate Analysis ◽  
Near Infrared ◽  
Low Cost ◽  
Diagnostic Techniques ◽  
Clinical Samples ◽  
Spectroscopic Techniques ◽  
Global Pandemic ◽  
Molecular Fluorescence ◽  
Viral Diagnosis ◽  
Near Future

In view of the global pandemic that started in 2020, caused by COVID-19, the importance of the existence of fast, reliable, cheap diagnostic techniques capable of detecting the virus even in the first days of infection became evident. This review discusses studies involving the use of spectroscopic techniques in the detection of viruses in clinical samples. Techniques based on mid-infrared, near-infrared, Raman, and molecular fluorescence are explained and it was demonstrated how they can be used in conjunction with computational tools of multivariate analysis to build models capable of detecting viruses. Studies that used real clinical samples from 2011 to 2021 were analyzed. The results demonstrate the potential of the techniques in detecting viruses. Spectroscopic techniques, as well as chemometric techniques, were also explained. Viral diagnosis based on spectroscopy has interesting advantages compared to standard techniques such as: fast results, no need for reagents, non-destructiveness for the sample, no need for sample preparation, relatively low cost, among others. Several studies have corroborated the real possibility that, in the near future, we may have spectroscopic tools being successfully applied in viral diagnosis.

NEW CORONOVIRUS INFECTION: CLINICAL AND PATHOGENETIC ASPECTS OF COVID-19 IN PREGNANT WOMEN

2021 ◽  
pp. 57-62
Author(s):  
Allakhyarov D.Z. ◽  
Petrov Yu.A. ◽  
Chernavsky V.V.
Keyword(s):  
Pregnant Women ◽  
The Body ◽  
World Health ◽  
Upper Respiratory Tract ◽  
Global Pandemic ◽  
High Prevalence ◽  
Coronavirus Infection ◽  
The Moment ◽  
Health Organization ◽  
The Impact

This article presents reviews of literature sources on the clinical and pathogenetic aspects of the course of a new coronovirus infection in pregnant women, in order to analyze the features of the course of COVID-19 in pregnant women and to assess the impact of infection on the body of a woman and a fetus. Pregnancy is a special physiological condition, during which a number of changes occur in the body, not only in the hormonal status, but also in the immune system. The urgency of this problem is due to the high prevalence of new coronavirus infection among the population. On March 12, 2020, the World Health Organization (WHO), as a result of the dynamic development of the epidemic in many countries and continents, declared a global pandemic of the contagious disease COVID-19 caused by the SARS-CoV-2 virus. According to available studies, pregnant women are more susceptible to a more severe course of infectious diseases affecting the upper respiratory tract. According to various studies, a new coronavirus infection can lead to premature birth, miscarriage, and preeclampsia. Separate studies show increased mortality in pregnant women diagnosed with COVID-19. The SARS-CoV-2 virus does not have a direct teratogenic effect on the fetus, but it can indirectly lead to harmful effects on the developing organism. Special attention should be paid to the issue of vaccination of pregnant women against a new coronavirus infection, at the moment there is no accurate data on the effect of the vaccine on the body of the pregnant woman and the fetus. In this regard, the question of the impact of a new coronavirus infection on the course of pregnancy has become relevant.

scholarly journals Luminescence switch-on detection of protein tyrosine kinase-7 using a G-quadruplex-selective probe

2015 ◽  
Vol 6 (7) ◽  
pp. 4284-4290 ◽  
Author(s):  
Sheng Lin ◽  
Wei Gao ◽  
Zeru Tian ◽  
Chao Yang ◽  
Lihua Lu ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Protein Tyrosine Kinase ◽  
Protein Tyrosine ◽  
Detection Assay ◽  
G Quadruplex ◽  
Protein Tyrosine Kinase 7

A novel luminescent G-quadruplex-selective iridium(iii) complex was employed in a G-quadruplex-based detection assay for PTK7.

scholarly journals Humoral immune response and prolonged PCR positivity in a cohort of 1343 SARS-CoV 2 patients in the New York City region

2020 ◽  
Author(s):  
Ania Wajnberg ◽  
Mayce Mansour ◽  
Emily Leven ◽  
Nicole M. Bouvier ◽  
Gopi Patel ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Viral Genome ◽  
Enzyme Linked Immunosorbent Assay ◽  
Upper Respiratory Tract ◽  
City Region ◽  
Symptom Resolution ◽  
Humoral Immune ◽  
Global Pandemic

AbstractBackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. The percentage of infected individuals who seroconvert is still an open question. In addition, it has been shown in some individuals that viral genome can still be detected at considerable time post symptom resolution. Here we investigated both seroconversion and PCR-positivity in a large cohort of convalescent serum donors in New York City.MethodsIndividuals with confirmed or suspected SARS-CoV-2 infection were screened via PCR for presence of viral genome and via enzyme-linked immunosorbent assay for presence of anti SARS-CoV-2 spike antibodies.ResultsAll but three confirmed SARS-CoV-2 patients seroconverted to the SARS-CoV-2 spike while only 37.4% of suspected SARS-CoV-2 patients seroconverted. PCR-positivity was detected up to 28 days from symptom resolution.ConclusionsHere we show that the vast majority of confirmed COVID19 patients seroconvert, potentially providing immunity to reinfection. We also report that in a large proportion of individuals, viral genome can be detected via PCR in the upper respiratory tract for weeks post symptom resolution, but it is unclear if this signal represents infectious virus.

scholarly journals A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).

2021 ◽  
Author(s):  
Andrew T Rajczewski ◽  
Subina T Mehta ◽  
Dinh Duy An Ngyuen ◽  
Björn Andreas Grüning ◽  
James E Johnson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Direct Detection ◽  
Clinical Diagnostics ◽  
Clinical Proteomics ◽  
Clinical Samples ◽  
P Value ◽  
Upper Respiratory Tract ◽  
Proteomics Data ◽  
High Throughput Analysis

The Coronavirus Disease 2019 (COVID19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.

Indirect Fluorescence Detection of Non Fluorescent Analytes Using Isotachophoretic Mobility Markers

2008 ◽  
Author(s):  
Tarun K. Khurana ◽  
Moran Bercovici ◽  
Juan G. Santiago
Keyword(s):  
Numerical Simulation ◽  
Amino Acids ◽  
Fluorescence Detection ◽  
Indirect Detection ◽  
Fluorescent Marker ◽  
Fluorescent Signal ◽  
Design And Optimization ◽  
Detection Assay ◽  
Environmental Toxin ◽  
Simulation Results

We have developed a method to detect non-fluorescent analytes on standard microfluidic chip platforms equipped with fluorescence detection. We leverage isotachophoresis (ITP) to electrophoretically segregate both analytes and fluorescent species termed mobility markers into distinct zones. The fluorescent marker zones bound analyte zones, so that gaps in the fluorescent signal indicate the presence and concentration of analytes. We here demonstrate separation and indirect detection of amino acids, serine and phenylalanine and organic acids, acetic acid and phenylpropionic acid (∼10 μM) using this technique. We also present an indirect detection of the environmental toxin phenol [1][2] (∼10 μM) using two mobility markers. We show preliminary numerical simulation results that provide useful guidelines in design and optimization of our indirect detection assay.

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