scholarly journals COVID-19 Diagnostic Strategies Part II: Protein-Based Technologies

2021 ◽  
Vol 8 (5) ◽  
pp. 54
Author(s):  
Tina Shaffaf ◽  
Ebrahim Ghafar-Zadeh
Keyword(s):  
Nucleic Acid ◽  
Large Scale ◽  
Point Of Care ◽  
Academic Research ◽  
Diagnostic Tools ◽  
Effective Vaccine ◽  
Diagnostic Strategies ◽  
The Future ◽  
Current Outbreak ◽  
Large Scale Screening

After the initiation of the current outbreak, humans’ lives have been profoundly impacted by COVID-19. During the first months, no rapid and reliable detecting tool was readily available to sufficiently respond to the requirement of massive testing. In this situation, when the development of an effective vaccine requires at least a few months, it is crucial to be prepared by developing and commercializing affordable, accurate, rapid and adaptable biosensors not only to fight Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) but also to be armed to avoid the pandemic in the earliest stages in the future. The COVID-19 diagnostic tools are categorized into two main groups of Nucleic Acid (NA)-based and protein-based tests. To date, nucleic acid-based detection has been announced as the gold-standard strategy for coronavirus detection; however, protein-based tests are promising alternatives for rapid and large-scale screening of susceptible groups. In this review, we discuss the current protein-based biosensing tools, the research advances and the potential protein-detecting strategies for COVID-19 detection. This narrative review aims to highlight the importance of the diagnostic tests, encourage the academic research groups and the companies to eliminate the shortcomings of the current techniques and step forward to mass-producing reliable point-of-care (POC) and point-of-need (PON) adaptable diagnostic tools for large-scale screening in the future outbreaks.

scholarly journals High-Accuracy Determination of Microsatellite Instability Compatible with Liquid Biopsies

2020 ◽  
Vol 66 (4) ◽  
pp. 606-613 ◽  
Author(s):  
Amanda Bortolini Silveira ◽  
François-Clément Bidard ◽  
Amélie Kasperek ◽  
Samia Melaabi ◽  
Marie-Laure Tanguy ◽  
...  
Keyword(s):  
Microsatellite Instability ◽  
Large Scale ◽  
Digital Pcr ◽  
Circulating Tumor Dna ◽  
Diagnostic Tools ◽  
Tumor Biomarker ◽  
Analytical Sensitivity ◽  
Liquid Biopsies ◽  
Tumor Dna ◽  
Large Scale Screening

Abstract Background Microsatellite instability (MSI) has recently emerged as a predictive pan-tumor biomarker of immunotherapy efficacy, stimulating the development of diagnostic tools compatible with large-scale screening of patients. In this context, noninvasive detection of MSI from circulating tumor DNA stands as a promising diagnostic and posttreatment monitoring tool. Methods We developed drop-off droplet-digital PCR (ddPCR) assays targeting BAT-26, activin A receptor type 2A (ACVR2A), and defensin beta 105A/B (DEFB105A/B) microsatellite markers. Performances of the assays were measured on reconstitution experiments of various mutant allelic fractions, on 185 tumor samples with known MSI status, and on 72 blood samples collected from 42 patients with advanced colorectal or endometrial cancers before and/or during therapy. Results The 3 ddPCR assays reached analytical sensitivity <0.1% variant allelic frequency and could reliably detect and quantify MSI in both tumor and body fluid samples. High concordance between MSI status determination by the three-marker ddPCR test and the reference pentaplex method were observed (100% for colorectal tumors and 93% for other tumor types). Moreover, the 3 assays showed correlations with r ≥ 0.99 with other circulating tumor DNA markers and their dynamic during treatment correlated well with clinical response. Conclusions This innovative approach for MSI detection provides a noninvasive, cost-effective, and fast diagnostic tool, well suited for large-scale screening of patients that may benefit from immunotherapy agents, as well as for monitoring treatment responses.

scholarly journals CRISPR-Cas Systems for Diagnosing Infectious Diseases

2020 ◽  
Author(s):  
Anastasiya Kostyusheva ◽  
Sergey Brezgin ◽  
Yurii Babin ◽  
Irina Vasil'eva ◽  
Dmitry Kostyushev ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Molecular Diagnostics ◽  
Large Scale ◽  
Point Of Care ◽  
Disease Spread ◽  
Detection Methods ◽  
Epidemiological Surveillance ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Wide Range

Infectious diseases are a global health problem affecting billions of people. Developing rapid and sensitive diagnostic tools is key for successful patient management and curbing disease spread. Currently available diagnostics are very specific and sensitive but time-consuming and require expensive laboratory settings and well-trained personnel; thus, they are not available in resource-limited areas, for the purposes of large-scale screenings and in case of outbreaks and epidemics. Developing new, rapid, and affordable point-of-care diagnostic assays is urgently needed. This review focuses on CRISPR-based technologies and their perspectives to become platforms for point-of-care nucleic acid detection methods and as deployable diagnostic platforms that could help to identify and curb outbreaks and emerging epidemics. We describe the mechanisms and function of different classes and types of CRISPR-Cas systems, including pros and cons for developing molecular diagnostic tests and applications of each type to detect a wide range of infectious agents. Many Cas proteins (Cas9, Cas12, Cas13, Cas14) have been leveraged to create highly accurate and sensitive diagnostic tools combined with technologies of signal amplification and fluorescent, potentiometric, colorimetric, or lateral flow assay detection. In particular, the most advanced platforms -- SHERLOCK/v2, DETECTR, or CRISPR-Chip -- enable detection of attomolar amounts of pathogenic nucleic acids with specificity comparable to that of PCR but with minimal technical settings. Further developing CRISPR-based diagnostic tools promises to dramatically transform molecular diagnostics, making them easily affordable and accessible virtually anywhere in the world. The burden of socially significant diseases, frequent outbreaks, recent epidemics (MERS, SARS and the ongoing coronoviral nCov-2019 infection) urgently need the developing of express-diagnostic tools. Recently devised CRISPR-technologies represent the unprecedented opportunity to reshape epidemiological surveillance and molecular diagnostics.

scholarly journals Point-of-Care Diagnostic Tools for Surveillance of SARS-CoV-2 Infections

2021 ◽  
Vol 9 ◽  
Author(s):  
Dhanasekaran Sakthivel ◽  
David Delgado-Diaz ◽  
Laura McArthur ◽  
William Hopper ◽  
Jack S. Richards ◽  
...  
Keyword(s):  
Large Scale ◽  
Clinical Symptoms ◽  
Point Of Care ◽  
Cost Effective ◽  
Nucleic Acid Amplification ◽  
Diagnostic Tools ◽  
Rt Pcr ◽  
Serological Tests ◽  
Polymerase Chain ◽  
Effective Public Health

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a recently emerged and highly contagious virus that causes coronavirus disease 2019 (COVID-19). As of August 24, 2021, there were more than 212 million confirmed COVID-19 cases and nearly 4.4 million deaths reported globally. Early diagnosis and isolation of infected individuals remains one of the most effective public health interventions to control SARS-CoV-2 spread and for effective clinical management of COVID-19 cases. Currently, SARS-CoV-2 infection is diagnosed presumptively based on clinical symptoms and confirmed by detecting the viral RNA in respiratory samples using reverse transcription polymerase chain reaction (RT-PCR). Standard RT-PCR protocols are time consuming, expensive, and technically demanding, which makes them a poor choice for large scale and point-of-care screening in resource-poor settings. Recently developed isothermal nucleic acid amplification tests (iNAAT), antigen and/or serological tests are cost-effective to scale COVID-19 testing at the point-of-care (PoC) and for surveillance activities. This review discusses the development of rapid PoC molecular tools for the detection and surveillance of SARS-CoV-2 infections.

scholarly journals Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

2021 ◽  
Vol 34 (3) ◽  
Author(s):  
Seyed Hamid Safiabadi Tali ◽  
Jason J. LeBlanc ◽  
Zubi Sadiq ◽  
Oyejide Damilola Oyewunmi ◽  
Carolina Camargo ◽  
...  
Keyword(s):  
Large Scale ◽  
Imaging Techniques ◽  
Point Of Care ◽  
Lessons Learned ◽  
Disease Spread ◽  
Infection Prevention And Control ◽  
Diagnostic Tools ◽  
Specimen Collection ◽  
Recent Developments ◽  
And Control

SUMMARY The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.

scholarly journals Advances in Directly Amplifying Nucleic Acids from Complex Samples

Biosensors ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 117 ◽  
Author(s):  
Faye M. Walker ◽  
Kuangwen Hsieh
Keyword(s):  
Nucleic Acid ◽  
Sample Preparation ◽  
Point Of Care ◽  
Nucleic Acid Amplification ◽  
Current Status ◽  
Diagnostic Tools ◽  
Complex Samples ◽  
Lab On Chip ◽  
On Chip ◽  
Effective Visualization

Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.

scholarly journals Development of an Automated, Non-Enzymatic Nucleic Acid Amplification Test

Micromachines ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1204
Author(s):  
Zackary A. Zimmers ◽  
Alexander D. Boyd ◽  
Hannah E. Stepp ◽  
Nicholas M. Adams ◽  
Frederick R. Haselton
Keyword(s):  
Nucleic Acid ◽  
Internal Control ◽  
Magnetic Beads ◽  
Point Of Care ◽  
Dna Amplification ◽  
Magnetic Bead ◽  
Nucleic Acid Amplification ◽  
Diagnostic Strategies ◽  
Low Resource ◽  
Target Dna

Among nucleic acid diagnostic strategies, non-enzymatic tests are the most promising for application at the point of care in low-resource settings. They remain relatively under-utilized, however, due to inadequate sensitivity. Inspired by a recent demonstration of a highly-sensitive dumbbell DNA amplification strategy, we developed an automated, self-contained assay for detection of target DNA. In this new diagnostic platform, called the automated Pi-powered looping oligonucleotide transporter, magnetic beads capture the target DNA and are then loaded into a microfluidic reaction cassette along with the other reaction solutions. A stepper motor controls the motion of the cassette relative to an external magnetic field, which moves the magnetic beads through the reaction solutions automatically. Real-time fluorescence is used to measure the accumulation of dumbbells on the magnetic bead surface. Left-handed DNA dumbbells produce a distinct signal which reflects the level of non-specific amplification, acting as an internal control. The autoPiLOT assay detected as little as 5 fM target DNA, and was also successfully applied to the detection of S. mansoni DNA. The autoPiLOT design is a novel step forward in the development of a sensitive, user-friendly, low-resource, non-enzymatic diagnostic test.

scholarly journals Effectiveness of Strongyloides Recombinant IgG Immunoreactive Antigen in Detecting IgG and IgG4 Subclass Antibodies for Diagnosis of Human Strongyloidiasis Using Rapid Immunochromatographic Tests

Diagnostics ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 615
Author(s):  
Patcharaporn Boonroumkaew ◽  
Lakkhana Sadaow ◽  
Oranuch Sanpool ◽  
Rutchanee Rodpai ◽  
Tongjit Thanchomnang ◽  
...  
Keyword(s):  
Predictive Value ◽  
Large Scale ◽  
Point Of Care ◽  
Strongyloides Stercoralis ◽  
Diagnostic Tools ◽  
Stool Examination ◽  
Serum Samples ◽  
Diagnostic Efficacy ◽  
Tropical Regions ◽  
Immunosuppressed Patients

Human strongyloidiasis is an important soil-transmitted helminthiasis that affects millions worldwide and can develop into fatal systemic strongyloidiasis in immunosuppressed patients. We have developed two new rapid and simple-to-use immunochromatographic test (ICT) kits for rapid serodiagnosis that support stool examination for clinical diagnosis. Strongyloides stercoralis recombinant IgG immunoreactive antigen (GenBank: AAB97359.1; rSsIR-based ICT kit) was used for detection of IgG and IgG4 antibodies. The diagnostic efficacy of both kits was evaluated using human serum samples from strongyloidiasis patients, healthy individuals, and those with other parasitosis. At a prevalence of infection of 36.4%, the diagnostic sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of the rSsIR-based IgG ICT kit were 91.7%, 83.8%, 76.4%, 94.6%, and 86.7%, respectively, and those of the rSsIR-based IgG4 ICT kit were 78.3%, 84.8%, 74.6%, 87.3%, and 82.4% respectively. The concordance between the two kits was 89.7%. The recombinant antigen can be produced to an unlimited extent and the kits can be used as point-of-care diagnostic tools and in large-scale surveys in endemic areas throughout tropical regions without necessitating additional facilities or ancillary supplies.

scholarly journals Harnessing CRISPR-Cas to Combat COVID-19: From Diagnostics to Therapeutics

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1210
Author(s):  
Kok Gan Chan ◽  
Geik Yong Ang ◽  
Choo Yee Yu ◽  
Chan Yean Yean
Keyword(s):  
Nucleic Acid ◽  
Point Of Care ◽  
Antiviral Agent ◽  
Cost Effective ◽  
Rapid Identification ◽  
Diagnostic Tools ◽  
Nucleic Acid Detection ◽  
Molecular Tests ◽  
Skilled Personnel ◽  
Global Threat

The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global threat with an ever-increasing death toll even after a year on. Hence, the rapid identification of infected individuals with diagnostic tests continues to be crucial in the on-going effort to combat the spread of COVID-19. Viral nucleic acid detection via real-time reverse transcription polymerase chain reaction (rRT-PCR) or sequencing is regarded as the gold standard for COVID-19 diagnosis, but these technically intricate molecular tests are limited to centralized laboratories due to the highly specialized instrument and skilled personnel requirements. Based on the current development in the field of diagnostics, the programmable clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system appears to be a promising technology that can be further explored to create rapid, cost-effective, sensitive, and specific diagnostic tools for both laboratory and point-of-care (POC) testing. Other than diagnostics, the potential application of the CRISPR–Cas system as an antiviral agent has also been gaining attention. In this review, we highlight the recent advances in CRISPR–Cas-based nucleic acid detection strategies and the application of CRISPR–Cas as a potential antiviral agent in the context of COVID-19.

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