scholarly journals Different Laboratory Diagnosis methods of COVID-19: A Systematic Review

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Navid Omidifar ◽  
Kamran Bagheri Lankarani ◽  
Mohsen Moghadami ◽  
Mansoureh Shokripour ◽  
Mostafa Chashmpoosh ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Laboratory Diagnosis ◽  
Diagnostic Techniques ◽  
Disease Spread ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Laboratory Equipment ◽  
Reactive Protein ◽  
Pcr Method ◽  
Conferences And Congresses

: The virus causing COVID-19 disease is known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease spread rapidly and was transmitted like a contagious disease throughout China, and then it gradually spread in other parts of the world. Accordingly, the rapid and accurate detection of the SARS-CoV-2 virus plays an essential role in selecting timely treatments, saving lives, and preventing the spread of the disease. This study summarizes the methods used to identify coronavirus nucleic acid. The effectiveness of coronavirus nucleic acid detection kits by different samples and the performance of other diagnostic techniques are also addressed in this study. We searched Embase, Google Scholar, MEDLINE, Web of Science, Scopus, and PubMed databases as well as the references of all relevant articles in English published during 2019 - 2020 using keywords related to COVID-19, detection kits, and respiratory failure and proceedings from relevant conferences and congresses. The authors collected the relevant reports, and each of the authors independently reviewed the data published in different studies. The results of previous studies indicated that the diagnosis methods of the COVID-19 disease are the RT-PCR method, ELISA kits, quick tests, white blood cell count, C-reactive protein (CRP) levels, other laboratory factors and antigenic detection methods. Given the sensitivity and specificity of these methods at different periods using different samples, the disease interpretation can be performed accurately. The findings showed that proper laboratory equipment and appropriate laboratory kits are necessary for the rapid and precise identification of COVID-19.

scholarly journals Advanced CRISPR-Cas Effector Enzyme-Based Diagnostics for Infectious Diseases, Including COVID-19

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1356
Author(s):  
Sangha Kwon ◽  
Ha Youn Shin
Keyword(s):  
Nucleic Acid ◽  
Infectious Diseases ◽  
Pathogen Detection ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Nucleic Acid Amplification ◽  
Detection Methods ◽  
Molecular Diagnostic ◽  
Nucleic Acid Detection ◽  
Time Accuracy

Rapid and precise diagnostic tests can prevent the spread of diseases, including worldwide pandemics. Current commonly used diagnostic methods include nucleic-acid-amplification-based detection methods and immunoassays. These techniques, however, have several drawbacks in diagnosis time, accuracy, and cost. Nucleic acid amplification methods are sensitive but time-consuming, whereas immunoassays are more rapid but relatively insensitive. Recently developed CRISPR-based nucleic acid detection methods have been found to compensate for these limitations. In particular, the unique collateral enzymatic activities of Cas12 and Cas13 have dramatically reduced the diagnosis times and costs, while improving diagnostic accuracy and sensitivity. This review provides a comprehensive description of the distinct enzymatic features of Cas12 and Cas13 and their applications in the development of molecular diagnostic platforms for pathogen detection. Moreover, it describes the current utilization of CRISPR-Cas-based diagnostic techniques to identify SARS-CoV-2 infection, as well as recent progress in the development of CRISPR-Cas-based detection strategies for various infectious diseases. These findings provide insights into designing effective molecular diagnostic platforms for potential pandemics.

scholarly journals The Laboratory Diagnosis ofNeisseria gonorrhoeae

2005 ◽  
Vol 16 (1) ◽  
pp. 15-25 ◽  
Author(s):  
Lai-King Ng ◽  
Irene E Martin
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Testing ◽  
Laboratory Diagnosis ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Biochemical Tests ◽  
Culture Methods ◽  
Gene Target ◽  
Clinical Specimens ◽  
Confirmatory Tests

The present article describes the laboratory diagnosis ofNeisseria gonorrhoeaeby culturing of the organism from different types of clinical specimens followed by confirmatory tests. The success of culture methods requires good quality collection and transport of clinical specimens. The present guide describes the media requirements and cultural conditions forN gonorrhoeaegrowth and the characteristics for a presumptive identification ofN gonorrhoeae. Confirmatory tests include biochemical tests, chromogenic enzyme substrate tests, immunoassays and nucleic acid methods. Nucleic acid detection methods include either amplification-based methods or nonamplification tests, and are increasingly used in clinical laboratories where a viable culture is not possible to obtain. Nucleic acid methods can also be used to detect the presence of low numbers in a specimen. Nucleic acid detection methods need confirmation with another amplification method or gene target. Controls must be included to ensure true positive and negative results, and to rule out nucleic acid contamination. Monitoring of antimicrobial susceptibilities ofN gonorrhoeaeis important to investigate treatment failure and to evaluate the efficacy of currently recommended therapies. Many methods for the characterization ofN gonorrhoeaerequire cultures. The useful typing methods for determining strain relatedness include auxotyping, serotyping, plasmid profile analysis, DNA sequencing of theporBgene and pulsed-field gel electrophoresis. Quality assurance programs for diagnostic testing and antimicrobial susceptibility testing is reviewed.

scholarly journals Development and detection of genetically modified crops

2020 ◽  
Vol 145 ◽  
pp. 01013
Author(s):  
Zhao Yu-jia ◽  
Fan Pei-lei ◽  
Liang Liang ◽  
Liu Yin-yin ◽  
Zhao Hai-bo ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Genetically Modified ◽  
Genetically Modified Crops ◽  
Detection Methods ◽  
Social Benefits ◽  
Nucleic Acid Detection ◽  
Genetically Modified Crop ◽  
The World ◽  
The Difference

Genetically modified crops (GMCs) have been known for the excellent qualities. The commercializing of GMCs has taken great economic and social benefits. However, the bio-security of GMCs was still an issue. To solve this problem, countries around the world were constantly strengthening regulations on planting, processing and detecting of GMCs. This paper reviewed the development of commercialization and detection of GMCs. The difference between protein and nucleic acid detection methods of genetically modified crop was further discussed. This paper will provide new insights for the application of genetically modified crops.

scholarly journals Optimize Clinical Laboratory Diagnosis of COVID-19 from Suspect Cases by Likelihood Ratio of SARS-CoV-2 IgM and IgG antibody

2020 ◽  
Author(s):  
Feng Yangchun
Keyword(s):  
Nucleic Acid ◽  
Likelihood Ratio ◽  
Posterior Probability ◽  
Clinical Laboratory ◽  
Laboratory Diagnosis ◽  
Antibody Detection ◽  
Nucleic Acid Detection ◽  
Igg Antibodies ◽  
Igg Antibody ◽  
Antibody Tests

ObjectiveTo optimize clinical laboratory diagnosis of COVID-19 from suspect cases by Likelihood Ratio of SARS-CoV-2 IgM and IgG antibody.MethodsBy reinterpreting the data in the article “Diagnostic Value of Combined Detection of Serum 2019 novel coronavirus IgM and IgG Antibodies in novel coronavirusin Infection”, the positive likelihood ratio of IgM and IgG antibody in diagnosis of COVID-19 (nucleic acid positive patients) was calculated, and the posterior probability of IgM and IgG antibodies and their tandem detection to diagnose was finally calculated.ResultsThe positive likelihood ratios of single IgM and IgG antibody were 18.50 and 12.65 respectively, and the posterior probabilities were 90.18% and 86.26% respectively. However, the posterior probability of the two antibodies tandem detection is 99.15%, which can give clinicians quantitative confidence in the diagnosis of COVID-19 from suspected cases. According to the results of this study, combining the advantages and disadvantages of nucleic acid detection and antibody detection, the clinical pathway for clinicians to diagnose COVID-19 is found.ConclusionFor suspected cases, IgM and IgG antibody tests should be firstly done at the same time. If the antibody tests are all positive, COVID-19 can be confirmed. If not, nucleic acid detection (one or more times) is performed, and in extreme cases, high-throughput viral genome sequencing is performed.

scholarly journals Evaluation of seven different rapid methods for nucleic acid detection of SARS-COV-2 virus

2021 ◽  
Author(s):  
Sally Mahmoud ◽  
Esra Ibrahim ◽  
Subhashini Ganesan ◽  
Bhagyashree Thakre ◽  
Juliet Teddy ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Gold Standard ◽  
Large Scale ◽  
Virus Detection ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Test Accuracy ◽  
Rt Pcr ◽  
Rapid Methods ◽  
Kappa Value

Background In the current COVID-19 pandemic there is mass screening of SARS-CoV-2 happening round the world due to the extensive spread of the infections. There is a high demand for rapid diagnostic tests to expedite identification of cases and to facilitate early isolation and control spread. Hence this study evaluates seven different rapid nucleic acid detection assays that are commercially available for SARS- CoV- 2 virus detection. Methods Nasopharyngeal samples were collected from 4859 participants and were tested for SARS-CoV-2 virus by the gold standard RT-PCR method along with one of these seven rapid methods of detection. Evaluation of the rapid nucleic acid detection assays was done by comparing the results of these rapid methods with the gold standard RT-qPCR results for SARS-COV-2 detection. Results AQ-TOP had the highest sensitivity (98%) and strong kappa value of 0.943 followed by Genechecker and Abbot ID NOW. The POCKIT (ii RT-PCR) assay had the highest test accuracy of 99.29% followed by Genechecker and Cobas Liat. Atila iAMP showed the highest percentage of invalid reports (35.5%) followed by AQ-TOP with 6% and POCKIT with 3.7% of invalid reports. Conclusion Genechecker system, Abbott ID NOW and Cobas Liat, were found to have best performance and agreement when compared to the standard RT-PCR for COVID-19 detection. With further research, these rapid tests have the potential to be employed in large scale screening of COVID-19.

scholarly journals Assessment of the Diagnostic Ability of Four Detection Methods Using Three Sample Types of COVID-19 Patients

2021 ◽  
Vol 11 ◽  
Author(s):  
Fei Yu ◽  
Guoliang Xie ◽  
Shufa Zheng ◽  
Dongsheng Han ◽  
Jiaqi Bao ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Reverse Transcription ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Sample Type ◽  
Rt Pcr ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Oropharyngeal Swab ◽  
And Control

BackgroundViral nucleic acid detection is considered the gold standard for the diagnosis of coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2 infection. However, unsuitable sample types and laboratory detection kits/methods lead to misdiagnosis, which delays the prevention and control of the pandemic.MethodsWe compared four nucleic acid detection methods [two kinds of reverse transcription polymerase chain reactions (RT-PCR A: ORF1ab and N testing; RT-PCRB: only ORF1ab testing), reverse transcription recombinase aided amplification (RT-RAA) and droplet digital RT-PCR (dd-RT-PCR)] using 404 samples of 72 hospitalized COVID-19 patients, including oropharyngeal swab (OPS), nasopharyngeal swabs (NPS) and saliva after deep cough, to evaluate the best sample type and method for SARS-CoV-2 detection.ResultsAmong the four methods, dd-RT-PCR exhibited the highest positivity rate (93.0%), followed by RT-PCR B (91.2%) and RT-RAA (91.2%), while the positivity rate of RT-PCR A was only 71.9%. The viral load in OPS [24.90 copies/test (IQR 15.58-129.85)] was significantly lower than that in saliva [292.30 copies/test (IQR 20.20-8628.55)] and NPS [274.40 copies/test (IQR 33.10-2836.45)]. In addition, if OPS samples were tested alone by RT-PCR A, only 21.4% of the COVID-19 patients would be considered positive. The accuracy of all methods reached nearly 100% when saliva and NPS samples from the same patient were tested simultaneously.ConclusionsSARS-CoV-2 nucleic acid detection methods should be fully evaluated before use. High-positivity rate methods such as RT-RAA and dd-RT-PCR should be considered when possible. Furthermore, saliva after deep cough and NPS can greatly improve the accuracy of the diagnosis, and testing OPS alone is not recommended.

scholarly journals Analytical Ancestry: “Firsts” in Fluorescent Labeling of Nucleosides, Nucleotides, and Nucleic Acids

2009 ◽  
Vol 55 (4) ◽  
pp. 670-683 ◽  
Author(s):  
Larry J Kricka ◽  
Paolo Fortina
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Fluorescent Dyes ◽  
Fluorescent Labeling ◽  
Covalent Attachment ◽  
Detection Methods ◽  
Fluorescent Label ◽  
Nucleic Acid Detection ◽  
Fluorescent Labels ◽  
Fluorescent Properties

Abstract Background: The inherent fluorescent properties of nucleosides, nucleotides, and nucleic acids are limited, and thus the need has arisen for fluorescent labeling of these molecules for a variety of analytical applications. Content: This review traces the analytical ancestry of fluorescent labeling of nucleosides, nucleotides, and nucleic acids, with an emphasis on the first to publish or patent. The scope of labeling includes (a) direct labeling by covalent labeling of nucleic acids with a fluorescent label or noncovalent binding or intercalation of a fluorescent dye to nucleic acids and (b) indirect labeling via covalent attachment of a secondary label to a nucleic acid, and then binding this to a fluorescently labeled ligand binder. An alternative indirect strategy involves binding of a nucleic acid to a nucleic acid binder molecule (e.g., antibody, antibiotic, histone, antibody, nuclease) that is labeled with a fluorophore. Fluorescent labels for nucleic acids include organic fluorescent dyes, metal chelates, carbon nanotubes, quantum dots, gold particles, and fluorescent minerals. Summary: Fluorescently labeled nucleosides, nucleotides, and nucleic acids are important types of reagents for biological assay methods and underpin current methods of chromosome analysis, gel staining, DNA sequencing and quantitative PCR. Although these methods use predominantly organic fluorophores, new types of particulate fluorophores in the form of nanoparticles, nanorods, and nanotubes may provide the basis of a new generation of fluorescent labels and nucleic acid detection methods.

Advances in Nucleic Acid Detection and Quantification

2009 ◽  
Vol 37 (2) ◽  
pp. e1-e4 ◽  
Author(s):  
Ian C. Kavanagh ◽  
Simon C. Baker
Keyword(s):  
Nucleic Acid ◽  
Molecular Biology ◽  
Single Molecule ◽  
Single Cells ◽  
Genetic Research ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
British Library ◽  
Introductory Session ◽  
Detection And Quantification

The last decade has seen many changes in molecular biology at the bench, as we have moved away from a primary goal of cataloguing genes and mRNA towards techniques that detect and quantify nucleic acid molecules even within single cells. With the invention of the polymerase chain reaction (PCR), a nucleic acid sequence could now be amplified to generate a large number of identical copies, and this launched a new era in genetic research. PCR has developed in parallel to fluorescent hybridization probing to provide low-, medium- and high-throughput detection methods. However, PCR and hybridization detection have significant drawbacks as long-term solutions for routine research and diagnostics assays. Therefore many novel methods are being developed independently, but as yet no one technique has emerged as a clear replacement for PCR, microarrays or even sequencing. In order to examine the technological horizon in this area, around 90 delegates assembled at Hinxton Hall, Cambridge, U.K. on 28 and 29 October 2008 for a Biochemical Society/Wellcome Trust Focused Meeting sponsored by Thermo Fisher Scientific and the British Library. The title of the meeting was ‘Advances in Nucleic Acid Detection and Quantification’, and the primary aim was to bring together scientists from different disciplines who nevertheless are trying to develop reliable methods for the quantification or detection of RNA and DNA molecules. This meant that physical and organic chemists, microbial ecologists and clinicians appeared alongside molecular biologists. An introductory session on general nucleic acid detection technologies was initiated with a fascinating insight into single-molecule, singlecell hybridization from Professor Sir Edwin Southern. This served as an ideal base for sessions on single-cell molecular biology and an examination of current applications of emerging technology. This issue of Biochemical Society Transactions contains some of the papers prepared by speakers at the meeting, and highlights not only how PCR and microarrays are already being replaced, but also which methods are likely to replace them.

scholarly journals Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods

2021 ◽  
Vol 8 ◽  
Author(s):  
A. Cassedy ◽  
A. Parle-McDermott ◽  
R. O’Kennedy
Keyword(s):  
Nucleic Acid ◽  
Virus Detection ◽  
High Sensitivity ◽  
High Volume ◽  
Detection Methods ◽  
Immunological Methods ◽  
Nucleic Acid Detection ◽  
Viral Genomes ◽  
Diagnostic Measures ◽  
Point Of Use

Viruses are ubiquitous in the environment. While many impart no deleterious effects on their hosts, several are major pathogens. This risk of pathogenicity, alongside the fact that many viruses can rapidly mutate highlights the need for suitable, rapid diagnostic measures. This review provides a critical analysis of widely used methods and examines their advantages and limitations. Currently, nucleic-acid detection and immunoassay methods are among the most popular means for quickly identifying viral infection directly from source. Nucleic acid-based detection generally offers high sensitivity, but can be time-consuming, costly, and require trained staff. The use of isothermal-based amplification systems for detection could aid in the reduction of results turnaround and equipment-associated costs, making them appealing for point-of-use applications, or when high volume/fast turnaround testing is required. Alternatively, immunoassays offer robustness and reduced costs. Furthermore, some immunoassay formats, such as those using lateral-flow technology, can generate results very rapidly. However, immunoassays typically cannot achieve comparable sensitivity to nucleic acid-based detection methods. Alongside these methods, the application of next-generation sequencing can provide highly specific results. In addition, the ability to sequence large numbers of viral genomes would provide researchers with enhanced information and assist in tracing infections.

scholarly journals Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays

2021 ◽  
Author(s):  
Sri Gowtham Thakku ◽  
Cheri M Ackerman ◽  
Cameron Myhrvold ◽  
Roby P Bhattacharyya ◽  
Jonathan Livny ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Sensitivity And Specificity ◽  
Health Management ◽  
Point Of Care ◽  
Bacterial Species ◽  
Bacterial Pathogen ◽  
Antibiotic Resistance Genes ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Multiplexed Detection

Rapid and accurate diagnosis of infections is fundamental to individual patient care and public health management. Nucleic acid detection methods are critical to this effort, but are limited either in the breadth of pathogens targeted or by the expertise and infrastructure required. We present here a high-throughput system that enables rapid identification of bacterial pathogens, bCARMEN, which utilizes: (1) modular CRISPR-Cas13-based nucleic acid detection with enhanced sensitivity and specificity; and (2) a droplet microfluidic system that enables thousands of simultaneous, spatially multiplexed detection reactions at nanoliter volumes; and (3) a novel pre-amplification strategy that further enhances sensitivity and specificity. We demonstrate bCARMEN is capable of detecting and discriminating 52 clinically relevant bacterial species and several key antibiotic resistance genes. We further develop a proof of principle system for use with stabilized reagents and a simple workflow with optical readout using a cell phone camera, opening up the possibility of a rapid point-of-care multiplexed bacterial pathogen identification and antibiotic susceptibility testing.

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