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1.
Methods Mol Biol ; 2452: 45-62, 2022.
Article in English | MEDLINE | ID: covidwho-1844259

ABSTRACT

Currently, the most accurate way to diagnose an active SARS-CoV-2 (COVID-19) infection is through detection of viral RNA using reverse transcription polymerase chain reaction (RT-PCR) test. While RT-PCR tests are the most sensitive for identifying infection, there are significant limitations, such as global access to sufficient test kits, turnaround times (TAT) from specimen collection to test result is often greater than 24 h and the need for skilled operators in accredited laboratories requiring specialized equipment. A rapid test performed at the point of care (POC) could provide a result within an approximate time of 30 min post specimen collection, be performed by a health care worker and comprise a simple workflow, improving both turnaround time and potentially decreasing costs (e.g., transport, cold-chain, skilled laboratory staff, complex equipment). Determining the performance of SARS-CoV-2 RT-PCR tests is, however, easier to assess than antigen-based POCT, as residual clinical specimens (swabs in universal transport media [UTM]) are readily available in laboratory environments, and do not require patient informed consent. Evaluating the performance of POCT requires informed-consent driven studies, with patients required to provide a standard of care specimen as well as study evaluation specimens, which is often not acceptable as nasopharyngeal swabbing can be invasive, clinical field trials are costly and time consuming. Many institutions and regulatory bodies also require preliminary data prior to use in field settings. Therefore, we have developed a method to determine the performance of antigen based POCT that can be used by implementers in national healthcare programs, regulators and rapid test developers. The method investigates both quantitative and qualitative parameters, with the latter providing insights into the capability for implementation and national program uptake.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , COVID-19 Testing , Humans , Nasopharynx , Point-of-Care Testing , SARS-CoV-2/genetics , Sensitivity and Specificity
2.
BMJ Open ; 11(10), 2021.
Article in English | ProQuest Central | ID: covidwho-1842937

ABSTRACT

ObjectivesTo identify factors associated with COVID-19 test positivity and assess viral and antibody test concordance.DesignObservational retrospective cohort study.SettingOptum de-identified electronic health records including over 700 hospitals and 7000 clinics in the USA.ParticipantsThere were 891 754 patients who had a COVID-19 test identified in their electronic health record between 20 February 2020 and 10 July 2020.Primary and secondary outcome measuresPer cent of viral and antibody tests positive for COVID-19 (‘positivity rate’);adjusted ORs for factors associated with COVID-19 viral and antibody test positivity;and per cent concordance between positive viral and subsequent antibody test results.ResultsOverall positivity rate was 9% (70 472 of 771 278) and 12% (11 094 of 91 741) for viral and antibody tests, respectively. Positivity rate was inversely associated with the number of individuals tested and decreased over time across regions and race/ethnicities. Antibody test concordance among patients with an initial positive viral test was 91% (71%–95% depending on time between tests). Among tests separated by at least 2 weeks, discordant results occurred in 7% of patients and 9% of immunocompromised patients. Factors associated with increased odds of viral and antibody positivity in multivariable models included: male sex, Hispanic or non-Hispanic black or Asian race/ethnicity, uninsured or Medicaid insurance and Northeast residence. We identified a negative dose effect between the number of comorbidities and viral and antibody test positivity. Paediatric patients had reduced odds (OR=0.60, 95% CI 0.57 to 0.64) of a positive viral test but increased odds (OR=1.90, 95% CI 1.62 to 2.23) of a positive antibody test compared with those aged 18–34 years old.ConclusionsThis study identified sociodemographic and clinical factors associated with COVID-19 test positivity and provided real-world evidence demonstrating high antibody test concordance among viral-positive patients.

3.
BMJ Open ; 11(9), 2021.
Article in English | ProQuest Central | ID: covidwho-1842832

ABSTRACT

ObjectiveThis study aimed to capture key epidemiological data on SARS-CoV-2 infection in Nicaraguan children (≤18 years) seeking medical care, between 6 October and 16 November 2020.DesignIn this cross-sectional study, 418 children were recruited: 319 with symptoms characteristic of COVID-19 and 99 with no symptoms of illness. Children were tested for SARS-CoV-2 RNA using loop-mediated isothermal amplification. A questionnaire was employed to identify symptoms, risk factors, comorbidities and COVID-19 prevention measures.SettingResearch was carried out in four hospitals and two clinics in Managua, Nicaragua, where schools and businesses remained open throughout the COVID-19 pandemic.ParticipantsChildren were enrolled into a possible COVID-19 group if presenting with clinical symptoms. A comparison group included children lacking any COVID-19 symptoms attending routine check-ups or seeking care for issues unrelated to COVID-19.ResultsA high prevalence (43%) of SARS-CoV-2 infection was found, which was relatively equivalent in symptomatic and non-symptomatic children. Age distribution was similar between symptomatic and non-symptomatic children testing positive for SARS-CoV-2. Symptomatic children who tested positive for SARS-CoV-2 were 2.7 times more likely to have diarrhoea (26.7% in positive vs 12.0% in negative;OR=2.7 (95% CI 1.5 to 4.8), p=0.001) and were 2.0 times more likely to have myalgia (17.8% in positive vs 9.8% in negative;OR=2.0 (95% CI 1.0 to 3.8), p=0.04). Children with COVID-19 symptoms, who tested positive for SARS-CoV-2, were more likely to be under age 5 years and to have a pre-existing comorbid condition than children who tested positive but did not have symptoms.ConclusionsThis is the first paediatric study to provide laboratory-confirmed data on SARS-CoV-2 infection in Nicaragua, crucial for paediatric health services planning and a successful COVID-19 response. The high prevalence of the virus suggests widespread and sustained community transmission, underscoring the urgent need for robust data on the true extent of SARS-CoV-2 infection throughout Nicaragua.

4.
Biotechniques ; 2022 May 12.
Article in English | MEDLINE | ID: covidwho-1841240

ABSTRACT

Coronavirus disease 2019 is a public health challenge requiring rapid testing for the detection of infections and transmission. Nucleic acid amplification tests targeting SARS coronavirus 2 (CoV2) are used to detect CoV2 in clinical samples. Real-time reverse transcription quantitative PCR is the standard nucleic acid amplification test for CoV2, although reverse transcription loop-mediated isothermal amplification is used in diagnostics. The authors demonstrate a sequence-specific reverse transcription loop-mediated isothermal amplification-based nucleic acid amplification assay that is finished within 30 min using minimally processed clinical nasal swab samples and describe a fluorescence-quenched reverse transcription loop-mediated isothermal amplification assay using labeled primers and a quencher oligonucleotide. This assay can achieve rapid (30 min) and sensitive (1000 plaque-forming units/ml) fluorescence detection of CoV2 (WA1/2020), B.1.1.7 (Alpha) and variants of concern Delta (B.1.617.2) and Omicron (B.1.1.529) in nasal samples.

5.
International Journal of Environmental Research and Public Health ; 19(9):5172, 2022.
Article in English | ProQuest Central | ID: covidwho-1837070

ABSTRACT

Background: The relevance of growth determination in orthodontics is driving the search for the most precise and least invasive way of tracking the pubertal growth spurt. Objectives: The aim was to explore whether minimally invasive salivary estimation of biomarkers Insulin-like growth factor (IGF-1) and Insulin-like growth factor binding protein-3 (IGFBP-3) could be used to estimate skeletal maturity with diagnostic accuracy, especially in children and adolescent age groups. Subjects and methods: The cross-sectional study was conducted on 105 participants aged 6–25 years from the out-patient Department of Preventive Dental Science at Majmaah University between the period 2 January 2021 and 12 July 2021. Each subject’s lateral cephalogram radiograph was categorized based on skeletal maturity, and saliva samples were estimated for IGF-1 and IGFBP-3 using the respective ELISA kits. Two-way ANOVA with interaction was applied to examine the main effects due to cervical vertebral maturation staging (CVS), Sex and interaction effect due to CVS, and Sex on study parameters. Karl Pearson’s Product Moment Correlation Coefficient was calculated for finding a significant association between IGF, IGFBP3, and the IGF-1/IGFBP3 molar ratio. Results: Highest mean salivary IGF-1 was observed in the pubertal peak stage, which coincides with cervical vertebral maturity stages 3 and 4 (CVS3 and CVS4) for both males (2.57 ng/mL) and females (1.57 ng/mL) and the lowest mean level of IGF-1 for females (0.85 ng/mL) and males (1.22 ng/mL) was observed during the prepubertal stage. There exists a significant variation in IGF-1 between males and females in the pubertal stage (p < 0.01), but the difference is very narrow in the prepubertal and post-pubertal groups (p > 0.05). There was no significant interaction effect of different skeletal stages and gender on the IGFBP3 and the IGF-1/IGFBP3 molar ratio (p > 0.05), but there exists a significant interaction effect on IGF-1 (p < 0.05). Conclusion: Estimation of the IGF-1 and the IGF-1/IGFBP3 molar ratio in saliva, being a non-invasive biological marker, could serve as an adjunctive tool along with radiographic assessment in estimating growth maturity in the adolescence age group. By initiating orthodontic treatment during the mandibular growth peak in adolescence, a positive outcome is ensured in managing skeletal deformities within the craniofacial complex.

6.
Front Public Health ; 10: 852083, 2022.
Article in English | MEDLINE | ID: covidwho-1834649

ABSTRACT

Polymerase chain reaction (PCR) remains the gold standard in disease diagnostics due to its extreme sensitivity and specificity. However, PCR tests are expensive and complex, require skilled personnel and specialized equipment to conduct the tests, and have long turnaround times. On the other hand, lateral flow immunoassay-based antigen tests are rapid, relatively inexpensive, and can be performed by untrained personnel at the point of care or even in the home. However, rapid antigen tests are less sensitive than PCR since they lack the inherent target amplification of PCR. It has been argued that rapid antigen tests are better indicators of infection in public health decision-making processes to test, trace, and isolate infected people to curtail further transmission. Hence, there is a critical need to increase the sensitivity of rapid antigen tests and create innovative solutions to achieve that goal. Herein, we report the development of a low-cost diagnostic platform, enabling rapid detection of SARS-CoV-2 under field or at-home conditions. This platform (Halo™) is a small, highly accurate, consumer-friendly diagnostic reader paired with fluorescently labeled lateral flow assays and custom software for collection and reporting of results. The focus of this study is to compare the analytical performance of HaloTM against comparable tests that use either colloidal gold nanoparticles or fluorescence-based reporters in simulated nasal matrix and not in clinical samples. Live virus data has demonstrated limit of detection performance of 1.9 TCID50/test in simulated nasal matrix for the delta variant, suggesting that single-assay detection of asymptomatic SARS-CoV-2 infections may be feasible. Performance of the system against all tested SARS CoV-2 virus variants showed comparable sensitivities indicating mutations in SARS-CoV-2 variants do not negatively impact the assay.


Subject(s)
COVID-19 , Metal Nanoparticles , COVID-19/diagnosis , Gold , Humans , Proof of Concept Study , SARS-CoV-2
7.
Front Immunol ; 13: 856906, 2022.
Article in English | MEDLINE | ID: covidwho-1834405

ABSTRACT

Tuberculosis (TB) is among the leading causes of death worldwide from a single infectious agent, second only to COVID-19 in 2020. TB is caused by infection with Mycobacterium tuberculosis (Mtb), that results either in a latent or active form of disease, the latter associated with Mtb spread. In the absence of an effective vaccine, epidemiologic modeling suggests that aggressive treatment of individuals with active TB (ATB) may curb spread. Yet, clinical discrimination between latent (LTB) and ATB remains a challenge. While antibodies are widely used to diagnose many infections, the utility of antibody-based tests to diagnose ATB has only regained significant traction recently. Specifically, recent interest in the humoral immune response to TB has pointed to potential differences in both targeted antigens and antibody features that can discriminate latent and active TB. Here we aimed to integrate these observations and broadly profile the humoral immune response across individuals with LTB or ATB, with and without HIV co-infection, to define the most discriminatory humoral properties and diagnose TB disease more easily. Using 209 Mtb antigens, striking differences in antigen-recognition were observed across latently and actively infected individuals that was modulated by HIV serostatus. However, ATB and LTB could be discriminated, irrespective of HIV-status, based on a combination of both antibody levels and Fc receptor-binding characteristics targeting both well characterized (like lipoarabinomannan, 38 kDa or antigen 85) but also novel Mtb antigens (including Rv1792, Rv1528, Rv2435C or Rv1508). These data reveal new Mtb-specific immunologic markers that can improve the classification of ATB versus LTB.


Subject(s)
COVID-19 , HIV Infections , Latent Tuberculosis , Tuberculosis , Antibodies , HIV Infections/complications , Humans
8.
Front Cell Infect Microbiol ; 12: 840210, 2022.
Article in English | MEDLINE | ID: covidwho-1834358

ABSTRACT

In the summer of 2019, DiaSorin Molecular started designing a multiplex respiratory panel with pan-coronavirus detection as one of the planned targets. The R&D team in Gerenzano, Italy was already searching databases, performing alignments and assessing preliminary target regions for common coronavirus RT-PCR, including SARS and MERS-CoV. In December 2019, we were vigilant and following a cluster of pneumonia cases with undetermined etiology in Wuhan, China. As we now know, the cause of the respiratory infections was the new SARS-CoV-2 virus. DiaSorin Molecular swiftly responded in line with our heritage and company history in detecting emerging infectious diseases. Early in the pandemic and in record time, using research and development teams in both Italy and the U.S. together with the U.S. manufacturing team, we were able to develop and commercialize a new diagnostic test, Simplexa™ COVID-19 Direct, to detect SARS-CoV-2. Our unique platform allowed development of a rapid diagnostic test without the need for extraction reagents. Challenges with control materials, quarantines, clinical samples, raw materials and production were overcome and the entire company worked side by side for accelerated delivery of this assay to clinical labs in Europe, the U.S. and Canada.


Subject(s)
COVID-19 , COVID-19/diagnosis , COVID-19 Testing , China , Humans , Pandemics , SARS-CoV-2/genetics , Sensitivity and Specificity
9.
Cell Rep Methods ; 2(3): 100186, 2022 Mar 28.
Article in English | MEDLINE | ID: covidwho-1828185

ABSTRACT

Management of COVID-19 and other epidemics requires large-scale diagnostic testing. The gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains reverse transcription quantitative PCR (qRT-PCR) analysis, which detects viral RNA more sensitively than any other method. However, the resource use and supply-chain requirements of RT-PCR have continued to challenge diagnostic laboratories worldwide. Here, we establish and characterize a low-cost method to detect SARS-CoV-2 in clinical combined nose and throat swabs, allowing for automation in high-throughput settings. This method inactivates virus material with sodium dodecylsulfate (SDS) and uses silicon dioxide as the RNA-binding matrix in combination with sodium chloride (NaCl) and isopropanol. With similar sensitivity for SARS-CoV-2 viral targets but a fraction of time and reagent expenditure compared with commercial kits, our method also enables sample pooling without loss of sensitivity. We suggest that this method will facilitate more economical widespread testing, particularly in resource-limited settings.

10.
Emergent Mater ; 5(2): 249-260, 2022.
Article in English | MEDLINE | ID: covidwho-1827617

ABSTRACT

The deadly novel coronavirus SARS-CoV-2 is responsible for COVID-19, which was first recognized in Wuhan, China, in December 2019. Rapid identification at primary stage of the novel coronavirus, SARS-CoV-2, is important to restrict it and prevent the pandemic. Real-time RT-PCR assays are the best diagnostic tests presently available for SARS-CoV-2 detection, which are highly sensitive, even though expensive equipment and trained technicians are necessary. Furthermore, the method has moderately long time bound. This deadly viral infection can also be detected by applying various spectroscopic techniques as spectroscopy can provide fast, precise identification and monitoring, leading to the overall understanding of its mutation rates, which will further facilitate antiviral drug development as well as vaccine development. It is an innovative and non-invasive technique for combating the spread of novel coronavirus. This review article demonstrates the application of various spectroscopic techniques to detect COVID-19 rapidly. Different spectroscopy-based detection protocols and additional development of new, novel sensors and biosensors along with diagnostic kits had been described here stressing the status of sensitive diagnostic systems to handle with the COVID-19 outbreak. Graphical abstract: Spectroscopy: A versatile sensing tool for cost-effective and rapid detection of novel Coronavirus (COVID-19).

11.
Lecture Notes on Data Engineering and Communications Technologies ; 113:631-642, 2022.
Article in English | Scopus | ID: covidwho-1826253

ABSTRACT

Diagnosis is a critical preventative step in Coronavirus researches. Because of the fast spread of this virus, it is necessary to present a computer-aided diagnostic (CAD) system which is very faster for radiologists. Feature Selection (FS) is a significant technique to obtain an accurate CAD system. This paper presented an effective FS model which based on wrapper approach as evaluator and Particle Swarm Optimization (PSO) as search method for classifying cases of COVID-19 using Computed Tomography (CT). This model was used PSO algorithm to identify the significant features subset within overall features set. Support Vector Machine (SVM), K-nearest neighbor (KNN) classifiers were used as evaluators with 10-fold cross validation and reached accuracy of 99.6% for SVM and 94.27% for KNN respectively. The results were shown that proposed PSO-FS model is an intelligent and outperforms other two traditional FS search methods, Genetic Algorithm (GA) and Greedy Stepwise (GS). © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

12.
Mendel ; 28(1), 2022.
Article in English | Scopus | ID: covidwho-1823664

ABSTRACT

The new Coronavirus or simply Covid-19 causes an acute deadly disease. It has spread rapidly across the world, which has caused serious consequences for health professionals and researchers. This is due to many reasons including the lack of vaccine, shortage of testing kits and resources. Therefore, the main purpose of this study is to present an inexpensive alternative diagnostic tool for the detection of Covid-19 infection by using chest radiographs and Deep Convolutional Neural Network (DCNN) technique. In this paper, we have proposed a reliable and economical solution to detect COVID-19. This will be achieved by using X-rays of patients and an Incremental-DCNN (I-DCNN) based on ResNet-101 architec-ture. The datasets used in this study were collected from publicly available chest radiographs on medical repositories. The proposed I-DCNN method will help in diagnosing the positive Covid-19 patient by utilising three chest X-ray imagery groups, these will be: Covid-19, viral pneumonia, and healthy cases. Furthermore, the main contribution of this paper resides on the use of incremental learning in order to accommodate the detection system. This has high computational energy requirements, time consuming challenges, while working with large-scale and reg-ularly evolving images. The incremental learning process will allow the recognition system to learn new datasets, while keeping the convolutional layers learned pre-viously. The overall Covid-19 detection rate obtained using the proposed I-DCNN was of 98.70% which undeniably can contribute effectively to the detection of COVID-19 infection. © 2022, Brno University of Technology. All rights reserved.

13.
Chemical Engineering Journal ; : 136864, 2022.
Article in English | ScienceDirect | ID: covidwho-1821170

ABSTRACT

Synthetic biology enabling technologies have been harnessed to create new diagnostic technologies. However, most strategies involve error-prone amplification steps and limitations of accuracy in RNA detection. Here, a cell-free synthetic biology-powered biosensing strategy, termed as SHARK (Synthetic Enzyme Shift RNA Signal Amplifier Related Cas13a Knockdown Reaction), could efficiently and accurately amplify RNA signal by leveraging the collateral cleavage of activated Cas13a to regulate cell-free enzyme synthesis. Based on cascade amplification and tailored enzyme output, SHARK behaves broad compatibility in different scenarios. The portable device based on SHARK was successfully used as SARS-CoV-2 biosensors with high sensitivity and selectivity, and the results were highly consistent with Ct values of qRT-PCR. In addition, when combined with machine learning, SHARK performs bio-computations and thus for cancer diagnosis and staging based on 64 clinical samples. SHARK shows characteristics of precise recognition, cascade amplification and tailored signal outputting comparisons with established assays, presenting significant potential in developing next-generation RNA detection technology.

14.
Cell Rep Methods ; : 100222, 2022 May 03.
Article in English | MEDLINE | ID: covidwho-1819464

ABSTRACT

During the COVID-19 pandemic, the development of point-of-care (POC) diagnostic testing accelerated in an unparalleled fashion. As a result, there has been an increased need for accurate, robust, and easy to use POC testing in a variety of non-traditional settings (i.e. pharmacies, drive-thru sites, schools). While stakeholders often express the desire for POC technologies that are "as simple as digital pregnancy tests," there is little discussion of what this means in regards to device design, development, and assessment. The design of POC technologies and systems should take into account the capabilities and limitations of the users and their environments. Such "human factors" are important tenets that can help technology developers create POC technologies that are effective for end-users in a multitude of settings. Here, we review the core principles of human factors and discuss lessons learned during the evaluation process of SARS-CoV-2 POC testing.

15.
ChemMedChem ; 2022 May 01.
Article in English | MEDLINE | ID: covidwho-1819344

ABSTRACT

Aptamers that can recognize the spike (S) protein of SARS-CoV-2 with high affinity and specificity are useful molecules towards the development of diagnostics and therapeutics to fight COVID-19. However, this S protein is constantly mutating, producing variants of concern (VoCs) that can significantly weaken the binding by aptamers initially engineered to recognize the S protein of the wildtype virus or a specific VoC. One strategy to overcome this problem is to develop universal aptamers that are insensitive to all or most of the naturally emerging mutations in the protein. We have recently demonstrated this concept by subjecting a pool of S protein-binding DNA aptamers for one-round parallel-SELEX experiments targeting 5 different S protein variants for binding-based sequence enrichment, followed by bioinformatic analysis of the enriched pools. This effort has led to the identification of a universal aptamer that recognizes 8 different variants of the spike protein with equally excellent affinity.

16.
ACS Appl Bio Mater ; 5(5): 2046-2068, 2022 May 16.
Article in English | MEDLINE | ID: covidwho-1815472

ABSTRACT

Recent advances in microfluidics-based point-of-care testing (POCT) technology such as paper, array, and beads have shown promising results for diagnosing various infectious diseases. The fast and timely detection of viral infection has proven to be a critical step for deciding the therapeutic outcome in the current COVID-19 pandemic, which in turn not only enhances the patient survival rate but also reduces the disease-associated comorbidities. In the present scenario, rapid, noninvasive detection of the virus using low cost and high throughput microfluidics-based POCT devices embraces the advantages over existing diagnostic technologies, for which a centralized lab facility, expensive instruments, sample pretreatment, and skilled personnel are required. Microfluidic-based multiplexed POCT devices can be a boon for clinical diagnosis in developing countries that lacks a centralized health care system and resources. The microfluidic devices can be used for disease diagnosis and exploited for the development and testing of drug efficacy for disease treatment in model systems. The havoc created by the second wave of COVID-19 led several countries' governments to the back front. The lack of diagnostic kits, medical devices, and human resources created a huge demand for a technology that can be remotely operated with single touch and data that can be analyzed on a phone. Recent advancements in information technology and the use of smartphones led to a paradigm shift in the development of diagnostic devices, which can be explored to deal with the current pandemic situation. This review sheds light on various approaches for the development of cost-effective microfluidics POCT devices. The successfully used microfluidic devices for COVID-19 detection under clinical settings along with their pros and cons have been discussed here. Further, the integration of microfluidic devices with smartphones and wireless network systems using the Internet-of-things will enable readers for manufacturing advanced POCT devices for remote disease management in low resource settings.


Subject(s)
COVID-19 , Microfluidics , COVID-19/diagnosis , Humans , Lab-On-A-Chip Devices , Pandemics , Point-of-Care Testing
17.
J Theor Biol ; 545: 111145, 2022 Apr 29.
Article in English | MEDLINE | ID: covidwho-1814839

ABSTRACT

The many respiratory viruses that cause influenza-like illness (ILI) are reported and tracked as one entity, defined by the CDC as a group of symptoms that include a fever of 100 degrees Fahrenheit, a cough, and/or a sore throat. In the United States alone, ILI impacts 9-49 million people every year. While tracking ILI as a single clinical syndrome is informative in many respects, the underlying viruses differ in parameters and outbreak properties. Most existing models treat either a single respiratory virus or ILI as a whole. However, there is a need for models capable of comparing several individual viruses that cause respiratory illness, including ILI. To address this need, here we present a flexible model and simulations of epidemics for influenza, RSV, rhinovirus, seasonal coronavirus, adenovirus, and SARS/MERS, parameterized by a systematic literature review and accompanied by a global sensitivity analysis. We find that for these biological causes of ILI, their parameter values, timing, prevalence, and proportional contributions differ substantially. These results demonstrate that distinguishing the viruses that cause ILI will be an important aspect of future work on diagnostics, mitigation, modeling, and preparation for future pandemics.

18.
Zhurnal Mikrobiologii Epidemiologii i Immunobiologii ; 99(1):126-138, 2022.
Article in Russian | Scopus | ID: covidwho-1812155

ABSTRACT

In this review, methods for isothermal amplification of nucleic acids are considered and analyzed, in particular, loop isothermal amplification of DNA and RNA (LAMP/RT-LAMP), helicase-dependent amplification (HDA) and recombinase polymerase amplification (RPA). The advantages and disadvantages of each of the techniques are described. The possibility of their application in the molecular diagnostics of infectious diseases is evaluated. A brief review of the literature on the use of LAMP, HDA, RPA in the diagnostics of viral, bacterial infections and diseases of protozoal etiology was conducted. It has been shown that the LAMP method has a number of advantages over other diagnostic methods: High efficiency, specificity, simplicity, turnaround time and minimum requirements for instrument equipment. As a result, it is concluded that loop isothermal amplification is a promising method for detecting the DNA/RNA of various pathogens. The data on the introduction of the LAMP method in the diagnostics of particularly dangerous bacterial and viral infections, including for the detection of RNA of a new coronavirus infection (SARS-CoV-2) in clinical samples, are presented. © 2022, Central Research Institute for Epidemiology. All rights reserved.

19.
Viruses ; 14(4)2022 Mar 29.
Article in English | MEDLINE | ID: covidwho-1810313

ABSTRACT

Surface plasmon resonance and biolayer interferometry are two common real-time and label-free assays that quantify binding events by providing kinetic parameters. There is increased interest in using these techniques to characterize whole virus-ligand interactions, as the methods allow for more accurate characterization than that of a viral subunit-ligand interaction. This review aims to summarize and evaluate the uses of these technologies specifically in virus-ligand and virus-like particle-ligand binding cases to guide the field towards studies that apply these robust methods for whole virus-based studies.


Subject(s)
Biosensing Techniques , Surface Plasmon Resonance , Biological Assay , Interferometry/methods , Kinetics , Ligands
20.
BMJ Open ; 12(4): e053912, 2022 Apr 21.
Article in English | MEDLINE | ID: covidwho-1807404

ABSTRACT

BACKGROUND: Accurate detection of SARS-CoV-2 is necessary to mitigate the COVID-19 pandemic. However, the test reagents and assay platforms are varied and may not be sufficiently robust to diagnose COVID-19. METHODS: We reviewed 85 studies (21 530 patients), published from five regions of the world, to highlight issues involved in the diagnosis of COVID-19 in the early phase of the pandemic. All relevant articles, published up to 31 May 2020, in PubMed, BioRiXv, MedRiXv and Google Scholar, were included. We evaluated the qualitative (9749 patients) and quantitative (10 355 patients) performance of RT-PCR and serologic diagnostic tests for real-world samples, and assessed the concordance (5538 patients) between test performance in meta-analyses. Synthesis of results was done using random effects modelling and bias was evaluated according to QUADAS-2 guidelines. RESULTS: The RT-PCR tests exhibited heterogeneity in the primers and reagents used. Of 1957 positive RT-PCR COVID-19 participants, 1585 had positive serum antibody (IgM±IgG) tests (sensitivity 0.81, 95% CI 0.66 to 0.90). While 3509 of 3581 participants RT-PCR negative for COVID-19 were found negative by serology testing (specificity 0.98, 95% CI 0.94 to 0.99). The chemiluminescent immunoassay exhibited the highest sensitivity, followed by ELISA and lateral flow immunoassays. Serology tests had higher sensitivity and specificity for laboratory approval than for real-world reporting data. DISCUSSION: The robustness of the assays/platforms is influenced by variability in sampling and reagents. Serological testing complements and may minimise false negative RT-PCR results. Lack of standardised assay protocols in the early phase of pandemic might have contributed to the spread of COVID-19.


Subject(s)
COVID-19 , Antibodies, Viral , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing , Humans , Pandemics , SARS-CoV-2 , Sensitivity and Specificity
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