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Virus Diagnostic Methods and Techniques: Learning from the COVID-19 Global...
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Virus Diagnostic Methods and Techniques: Learning from the COVID-19 Global Outbreak

A topical collection in Diagnostics (ISSN 2075-4418). This collection belongs to the section "Diagnostic Microbiology and Infectious Disease".

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Editors

Dr. Chao-Min Cheng

E-Mail Website
Guest Editor
Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu City 300, Taiwan
Interests: biomedical engineering; diagnostic methods; vaccines
Special Issues, Collections and Topics in MDPI journals
Dr. Sandeep K. Vashist

E-Mail Website
Guest Editor
Fapon Biotech Inc., Reuterweg 48, 52080 Aachen, Germany
Interests: immunoassays; IVD; POC technologies; molecular diagnostics; next-generation sequencing; mobile healthcare
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Carmen de Mendoza

E-Mail Website
Guest Editor
Pharmaceutical & Health Science Department, Universidad San Pablo-CEU, Madrid, Spain
Interests: human retroviruses (HIV-1, HIV-2 & HTLV); viral hepatitis (HBV, HCV, and HDV); resistance to antiretrovirals; molecular epidemiology for HTLV-1, HIV-2 subtypes
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

The spread of COVID-19 has become a global healthcare issue around the world. With recent technological advances in multiple research fields, such as materials science, micro-/nanotechnology, molecular biology, and bioengineering, much attention is shifting toward the development of new virus-based detection tools that not only address the needs for high sensitivity and specificity but also fulfil economic objectives in addition to the need for rapid point-of-care for groups and individuals with constrained resources and, possibly, limited training. These new detection technologies are also potentially applicable to different healthcare issues since they are disposable, inexpensive, portable, and easy to use—especially when their manufacture is based on low-cost materials. The topics in this Special Issue would cover point-of-care detection devices, microfluidic or paper-based detection devices, new materials for making detection devices, and others, with a particular focus on the precise diagnosis of COVID-19.

Dr. Chao-Min Cheng
Dr. Sandeep K. Vashist
Prof. Dr. Carmen de Mendoza
Guest Editors

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Keywords

COVID-19

 

Published Papers (46 papers)

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2024

Jump to: 2022, 2021, 2020

13 pages, 1263 KiB  
Article
COVID-19 and Tuberculosis: Mathematical Modeling of Infection Spread Taking into Account Reduced Screening
by Anna Starshinova, Nikolay Osipov, Irina Dovgalyk, Anastasia Kulpina, Ekaterina Belyaeva and Dmitry Kudlay
Diagnostics 2024, 14(7), 698; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics14070698 - 26 Mar 2024
Viewed by 368
Abstract
The COVID-19 pandemic resulted in the cessation of many tuberculosis (TB) support programs and reduced screening coverage for TB worldwide. We propose a model that demonstrates, among other things, how undetected cases of TB affect the number of future M. tuberculosis (M. [...] Read more.
The COVID-19 pandemic resulted in the cessation of many tuberculosis (TB) support programs and reduced screening coverage for TB worldwide. We propose a model that demonstrates, among other things, how undetected cases of TB affect the number of future M. tuberculosis (M. tb) infections. The analysis of official statistics on the incidence of TB, preventive examination coverage of the population, and the number of patients with bacterial excretion of M. tb in the Russian Federation from 2008 to 2021 is carried out. The desired model can be obtained due to the fluctuation of these indicators in 2020, when the COVID-19 pandemic caused a dramatic reduction in TB interventions. Statistical analysis is carried out using R v.4.2.1. The resulting model describes the dependence of the detected incidence and prevalence of TB with bacterial excretion in the current year on the prevalence of TB with bacterial excretion in the previous year and on the coverage of preventive examinations in the current and previous years. The adjusted coefficient of model determination (adjusted R-squared) is 0.9969, indicating that the model contains almost no random component. It clearly shows that TB cases missed due to low screening coverage and left uncontrolled will lead to a significant increase in the number of new infections in the future. We may conclude that the obtained results clearly demonstrate the need for mass screening of the population in the context of the spread of TB infection, which makes it possible to timely identify patients with TB with bacterial excretion. Full article
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2022

Jump to: 2024, 2021, 2020

12 pages, 876 KiB  
Article
Development of in House ELISAs to Detect Antibodies to SARS-CoV-2 in Infected and Vaccinated Humans by Using Recombinant S, S1 and RBD Proteins
by Aysun Yilmaz, Nuri Turan, Bekir Sami Kocazeybek, Harika Oyku Dinc, Hasan Emre Tali, Ozge Aydin, Hamid Besim Tali, Semaha Gul Yilmaz, Dildar Konukoglu, Sermin Borekci, Dashzeveg Bold, Gleyder Roman Sosa, Nejdiye Gungordu, Ilgim Vardaloglu, Nesrin Gareayaghi, Mine Guzel, Ebru Guner, Jean-Remy Sadeyen, Pengxiang Chang, Munir Iqbal, Juergen A. Richt and Huseyin Yilmazadd Show full author list remove Hide full author list
Diagnostics 2022, 12(12), 3085; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12123085 - 07 Dec 2022
Viewed by 1651
Abstract
(1) Background: The aim of this study was to produce in-house ELISAs which can be used to determine SARS-CoV-2-specific antibody levels directed against the spike protein (S), the S1 subunit of S and the receptor binding domain (RBD) of S in SARS-CoV-2 vaccinated [...] Read more.
(1) Background: The aim of this study was to produce in-house ELISAs which can be used to determine SARS-CoV-2-specific antibody levels directed against the spike protein (S), the S1 subunit of S and the receptor binding domain (RBD) of S in SARS-CoV-2 vaccinated and infected humans. (2) Methods: Three in-house ELISAs were developed by using recombinant proteins of SARS-CoV-2, namely the S, S1 and RBD proteins. Specificity and sensitivity evaluations of these tests were performed using sera from SARS-CoV-2-infected (n = 70) and SARS-CoV-2-vaccinated (n = 222; CoronaVac vaccine) humans in Istanbul, Turkey. The analyses for the presence of SARS-CoV-2-specific antibodies were performed using the in-house ELISAs, a commercial ELISA (Abbott) and a commercial surrogate virus neutralization test (sVNT). We also analyzed archival human sera (n = 50) collected before the emergence of COVID-19 cases in Turkey. (3) Results: The sensitivity of the in-house S, S1 and RBD ELISAs was found to be 88.44, 90.17 and 95.38%, while the specificity was 72.27, 89.08 and 89.92%, respectively, when compared to the commercial SARS-CoV-2 antibody test kit. The area under curve (AUC) values were 0.777 for the in-house S ELISA, 0.926 for the S1 ELISA, and 0.959 for the RBD ELISA. The kappa values were 0.62, 0.79 and 0.86 for the S, S1 and RBD ELISAs, respectively. (4) Conclusions: The in-house S1 and RBD ELISAs developed in this study have acceptable performance characteristics in terms of sensitivity, specificity, AUC and kappa values. In particular, the RBD ELISA seems viable to determine SARS-CoV-2-specific antibody levels, both in infected and vaccinated people, and help mitigate SARS-CoV-2 outbreaks and spread. Full article
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11 pages, 1572 KiB  
Article
Construction and Validation of Mortality Risk Nomograph Model for Severe/Critical Patients with COVID-19
by Li Cheng, Wen-Hui Bai, Jing-Jing Yang, Peng Chou, Wan-Shan Ning, Qiang Cai and Chen-Liang Zhou
Diagnostics 2022, 12(10), 2562; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12102562 - 21 Oct 2022
Cited by 3 | Viewed by 1165
Abstract
Objective: A nomograph model of mortality risk for patients with coronavirus disease 2019 (COVID-19) was established and validated. Methods: We collected the clinical medical records of patients with severe/critical COVID-19 admitted to the eastern campus of Renmin Hospital of Wuhan University from January [...] Read more.
Objective: A nomograph model of mortality risk for patients with coronavirus disease 2019 (COVID-19) was established and validated. Methods: We collected the clinical medical records of patients with severe/critical COVID-19 admitted to the eastern campus of Renmin Hospital of Wuhan University from January 2020 to May 2020 and to the north campus of Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, from April 2022 to June 2022. We assigned 254 patients to the former group, which served as the training set, and 113 patients were assigned to the latter group, which served as the validation set. The least absolute shrinkage and selection operator (LASSO) and multivariable logistic regression were used to select the variables and build the mortality risk prediction model. Results: The nomogram model was constructed with four risk factors for patient mortality following severe/critical COVID-19 (≥3 basic diseases, APACHE II score, urea nitrogen (Urea), and lactic acid (Lac)) and two protective factors (percentage of lymphocyte (L%) and neutrophil-to-platelets ratio (NPR)). The area under the curve (AUC) of the training set was 0.880 (95% confidence interval (95%CI), 0.837~0.923) and the AUC of the validation set was 0.814 (95%CI, 0.705~0.923). The decision curve analysis (DCA) showed that the nomogram model had high clinical value. Conclusion: The nomogram model for predicting the death risk of patients with severe/critical COVID-19 showed good prediction performance, and may be helpful in making appropriate clinical decisions for high-risk patients. Full article
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9 pages, 683 KiB  
Article
Clinical Added Value of SARS-CoV-2 Antigen Detection in Blood Samples
by Saoussen Oueslati, Melek Manai Bouokazi, Ikrame Ramdhani, Lélia Escaut, Tài Pham, Souad Ouzani, Nadia Anguel, Sophie Bulifon, Christelle Vauloup-Fellous, Audrey Coilly, Laurence Legros, Magali Guichardon, Nicolas Fortineau, Laurent Dortet, Anne-Marie Roque-Afonso and Thierry Naas
Diagnostics 2022, 12(10), 2427; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12102427 - 07 Oct 2022
Cited by 3 | Viewed by 1304
Abstract
This study evaluated the performances of immunoassays (LFIA and ELISA) designed for SARS-CoV-2 Antigen (Ag)-detection in nasopharyngeal (NP) and serum samples in comparison to RT-PCR. NP samples from patients with respiratory symptoms (183 RT-PCR-positive and 74 RT-PCR-negative samples) were collected from March to [...] Read more.
This study evaluated the performances of immunoassays (LFIA and ELISA) designed for SARS-CoV-2 Antigen (Ag)-detection in nasopharyngeal (NP) and serum samples in comparison to RT-PCR. NP samples from patients with respiratory symptoms (183 RT-PCR-positive and 74 RT-PCR-negative samples) were collected from March to April and November to December 2020. Seroconversion and antigen dynamics were assessed by symptom onset and day of RT-PCR diagnosis. Serum samples from 87 COVID-19 patients were used to investigate the added value of Ag quantification, at diagnosis and during follow-up. The sensitivity of COVID-VIRO-LFIA on samples with Ct ≤ 33, considered as the contagious threshold, was 86% on NPs (CI 95%: 79–90.5) and 76% on serum samples (CI 95%: 59.4–88), with a specificity of 100%. Serum N-Ag was detected during active infection as early as day two from symptom onset, with a diagnostic sensitivity of 81.5%. Within one week of symptom onset, diagnostic sensitivity and specificity reached 90.9% (95% CI, 85.1%–94.6%) and 98.3% (95% CI, 91.1%–99.9%), respectively. Serum N-Ag concentration closely correlated with disease severity. Longitudinal analysis revealed the simultaneous increase of antibodies and decrease of N-Ag. Sensitivities of COVID-VIRO-LFIA and COV-QUANTO-ELISA tests on NP and serum samples were close to 80%. They are suitable COVID-19-laboratory diagnostic tests, particularly when blood samples are available, thus reducing the requirement for NP sampling, and subsequent PCR analysis. ELISA titers may help to identify patients at risk of poor outcomes. Full article
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18 pages, 2167 KiB  
Review
COVID-19 Diagnosis: A Comprehensive Review of the RT-qPCR Method for Detection of SARS-CoV-2
by Debashis Dutta, Sarah Naiyer, Sabanaz Mansuri, Neeraj Soni, Vandana Singh, Khalid Hussain Bhat, Nishant Singh, Gunjan Arora and M. Shahid Mansuri
Diagnostics 2022, 12(6), 1503; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12061503 - 20 Jun 2022
Cited by 29 | Viewed by 7094
Abstract
The world is grappling with the coronavirus disease 2019 (COVID-19) pandemic, the causative agent of which is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 symptoms are similar to the common cold, including fever, sore throat, cough, muscle and chest pain, brain fog, [...] Read more.
The world is grappling with the coronavirus disease 2019 (COVID-19) pandemic, the causative agent of which is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 symptoms are similar to the common cold, including fever, sore throat, cough, muscle and chest pain, brain fog, dyspnoea, anosmia, ageusia, and headache. The manifestation of the disease can vary from being asymptomatic to severe life-threatening conditions warranting hospitalization and ventilation support. Furthermore, the emergence of mutecated variants of concern (VOCs) is paramount to the devastating effect of the pandemic. This highly contagious virus and its emergent variants challenge the available advanced viral diagnostic methods for high-accuracy testing with faster result yields. This review is to shed light on the natural history, pathology, molecular biology, and efficient diagnostic methods of COVID-19, detecting SARS-CoV-2 in collected samples. We reviewed the gold standard RT-qPCR method for COVID-19 diagnosis to confer a better understanding and application to combat the COVID-19 pandemic. This comprehensive review may further develop awareness about the management of the COVID-19 pandemic. Full article
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16 pages, 354 KiB  
Review
Biomarkers during COVID-19: Mechanisms of Change and Implications for Patient Outcomes
by Cheng-Han Chen, Sheng-Wen Lin, Ching-Fen Shen, Kai-Sheng Hsieh and Chao-Min Cheng
Diagnostics 2022, 12(2), 509; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12020509 - 16 Feb 2022
Cited by 18 | Viewed by 4240
Abstract
As the COVID-19 (Coronavirus disease 19) pandemic spreads worldwide, the massive numbers of COVID-19 patients have created a considerable healthcare burden for every country. The clinical spectrum of SARS-CoV-2 infection is broad, ranging from asymptomatic to mild, moderate, severe, and critical. Most COVID-19 [...] Read more.
As the COVID-19 (Coronavirus disease 19) pandemic spreads worldwide, the massive numbers of COVID-19 patients have created a considerable healthcare burden for every country. The clinical spectrum of SARS-CoV-2 infection is broad, ranging from asymptomatic to mild, moderate, severe, and critical. Most COVID-19 patients present with no or mild symptoms, but nearly one-fifth of all patients develop severe or life-threatening complications. In addition to localized respiratory manifestations, severe COVID-19 cases also show extra-pulmonary complications or induce multiorgan failure. Identifying, triaging, and treating patients at risk early is essential and urgent. This article reviews the potential prognostic value of various biomarkers at different clinical spectrum stages of COVID-19 infection and includes information on fundamental prognostic mechanisms as well as potential clinical implications. Biomarkers are measurable biochemical substances used to recognize and indicate disease severity or response to therapeutic interventions. The information they provide is objective and suitable for delivering healthcare providers with a means of stratifying disease state in COVID-19 patients. This, in turn, can be used to help select and guide intervention efforts as well as gauge the efficacy of therapeutic approaches. Here, we review a number of potential biomarkers that may be used to guide treatment, monitor treatment efficacy, and form individualized therapeutic guidance based on patient response. Implementation of the COVID-19 biomarkers discussed here may lead to significantly improved quality of care and patient outcomes for those infected with SARS-CoV-2 worldwide. Full article
21 pages, 7362 KiB  
Article
COVID-19 Detection in Chest X-ray Images Using a New Channel Boosted CNN
by Saddam Hussain Khan, Anabia Sohail, Asifullah Khan and Yeon-Soo Lee
Diagnostics 2022, 12(2), 267; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12020267 - 21 Jan 2022
Cited by 42 | Viewed by 3764
Abstract
COVID-19 is a respiratory illness that has affected a large population worldwide and continues to have devastating consequences. It is imperative to detect COVID-19 at the earliest opportunity to limit the span of infection. In this work, we developed a new CNN architecture [...] Read more.
COVID-19 is a respiratory illness that has affected a large population worldwide and continues to have devastating consequences. It is imperative to detect COVID-19 at the earliest opportunity to limit the span of infection. In this work, we developed a new CNN architecture STM-RENet to interpret the radiographic patterns from X-ray images. The proposed STM-RENet is a block-based CNN that employs the idea of split–transform–merge in a new way. In this regard, we have proposed a new convolutional block STM that implements the region and edge-based operations separately, as well as jointly. The systematic use of region and edge implementations in combination with convolutional operations helps in exploring region homogeneity, intensity inhomogeneity, and boundary-defining features. The learning capacity of STM-RENet is further enhanced by developing a new CB-STM-RENet that exploits channel boosting and learns textural variations to effectively screen the X-ray images of COVID-19 infection. The idea of channel boosting is exploited by generating auxiliary channels from the two additional CNNs using Transfer Learning, which are then concatenated to the original channels of the proposed STM-RENet. A significant performance improvement is shown by the proposed CB-STM-RENet in comparison to the standard CNNs on three datasets, especially on the stringent CoV-NonCoV-15k dataset. The good detection rate (97%), accuracy (96.53%), and reasonable F-score (95%) of the proposed technique suggest that it can be adapted to detect COVID-19 infected patients. Full article
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2021

Jump to: 2024, 2022, 2020

12 pages, 1675 KiB  
Article
Seven-Month Analysis of Five SARS-CoV-2 Antibody Assay Results after ChAdOx1 nCoV-19 Vaccination: Significant Decrease in SARS-CoV-2 Antibody Titer
by Seri Jeong, Nuri Lee, Su-Kyung Lee, Eun-Jung Cho, Jungwon Hyun, Min-Jeong Park, Wonkeun Song, Eun-Ju Jung, Heungjeong Woo, Yu-Bin Seo, Jin-Ju Park and Hyun-Soo Kim
Diagnostics 2022, 12(1), 85; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12010085 - 30 Dec 2021
Cited by 1 | Viewed by 1753
Abstract
We investigated the longevity rates of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after a complete ChAdOx1 nCoV-19 vaccination, which are rare and important to estimate their efficacy and establish a vaccination strategy. We assessed the positivity rates and changes of [...] Read more.
We investigated the longevity rates of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after a complete ChAdOx1 nCoV-19 vaccination, which are rare and important to estimate their efficacy and establish a vaccination strategy. We assessed the positivity rates and changes of titers before (T0) and at one month (T1), four months (T2), and seven months (T3) after a ChAdOx1 nCoV-19 vaccination using five SARS-CoV-2 antibody assays. A total of 874 serum samples were obtained from 228 (T0 and T1), 218 (T2), and 200 (T3) healthcare workers. The positive rates for all five assays were 0.0–0.9% at T0, 66.2–92.5% at T1, 98.2–100.0% at T2, and 66.0–100.0% at T3. The positive rates at T3 were decreased compared to those at T2. The median antibody titers of all the assays at T3 were significantly decreased compared to those at T2 (860.5 to 232.0 U/mL for Roche total, 1041.5 to 325.5 AU/mL for Abbott IgG, 10.9 to 2.3 index for Siemens IgG, 99.5% to 94.7% for SD Biosensor V1, and 88.5% to 38.2% for GenScript). A third-dose scheme can be considered based on our data generated from five representative assays. Our findings contribute insights into SARS-CoV-2 antibody assays and appropriate vaccination strategies. Full article
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13 pages, 13837 KiB  
Article
In-House Immunofluorescence Assay for Detection of SARS-CoV-2 Antigens in Cells from Nasopharyngeal Swabs as a Diagnostic Method for COVID-19
by Athene Hoi-Ying Lam, Jian-Piao Cai, Ka-Yi Leung, Ricky-Ruiqi Zhang, Danlei Liu, Yujing Fan, Anthony Raymond Tam, Vincent Chi-Chung Cheng, Kelvin Kai-Wang To, Kwok-Yung Yuen, Ivan Fan-Ngai Hung and Kwok-Hung Chan
Diagnostics 2021, 11(12), 2346; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11122346 - 13 Dec 2021
Cited by 3 | Viewed by 3714
Abstract
Immunofluorescence is a traditional diagnostic method for respiratory viruses, allowing rapid, simple and accurate diagnosis, with specific benefits of direct visualization of antigens-of-interest and quality assessment. This study aims to evaluate the potential of indirect immunofluorescence as an in-house diagnostic method for SARS-CoV-2 [...] Read more.
Immunofluorescence is a traditional diagnostic method for respiratory viruses, allowing rapid, simple and accurate diagnosis, with specific benefits of direct visualization of antigens-of-interest and quality assessment. This study aims to evaluate the potential of indirect immunofluorescence as an in-house diagnostic method for SARS-CoV-2 antigens from nasopharyngeal swabs (NPS). Three primary antibodies raised from mice were used for immunofluorescence staining, including monoclonal antibody against SARS-CoV nucleocapsid protein, and polyclonal antibodies against SARS-CoV-2 nucleocapsid protein and receptor-binding domain of SARS-CoV-2 spike protein. Smears of cells from NPS of 29 COVID-19 patients and 20 non-infected individuals, and cells from viral culture were stained by the three antibodies. Immunofluorescence microscopy was used to identify respiratory epithelial cells with positive signals. Polyclonal antibody against SARS-CoV-2 N protein had the highest sensitivity and specificity among the three antibodies tested, detecting 17 out of 29 RT-PCR-confirmed COVID-19 cases and demonstrating no cross-reactivity with other tested viruses except SARS-CoV. Detection of virus-infected cells targeting SARS-CoV-2 N protein allow identification of infected individuals, although accuracy is limited by sample quality and number of respiratory epithelial cells. The potential of immunofluorescence as a simple diagnostic method was demonstrated, which could be applied by incorporating antibodies targeting SARS-CoV-2 into multiplex immunofluorescence panels used clinically, such as for respiratory viruses, thus allowing additional routine testing for diagnosis and surveillance of SARS-CoV-2 even after the epidemic has ended with low prevalence of COVID-19. Full article
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14 pages, 860 KiB  
Article
Spectrum Bias and Individual Strengths of SARS-CoV-2 Serological Tests—A Population-Based Evaluation
by Sebastian Einhauser, David Peterhoff, Hans Helmut Niller, Stephanie Beileke, Felix Günther, Philipp Steininger, Ralph Burkhardt, Iris M. Heid, Annette B. Pfahlberg, Klaus Überla, Olaf Gefeller and Ralf Wagner
Diagnostics 2021, 11(10), 1843; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11101843 - 06 Oct 2021
Cited by 14 | Viewed by 2318
Abstract
Antibody testing for determining the SARS-CoV-2 serostatus was rapidly introduced in early 2020 and since then has been gaining special emphasis regarding correlates of protection. With limited access to representative samples with known SARS-CoV-2 infection status during the initial period of test development [...] Read more.
Antibody testing for determining the SARS-CoV-2 serostatus was rapidly introduced in early 2020 and since then has been gaining special emphasis regarding correlates of protection. With limited access to representative samples with known SARS-CoV-2 infection status during the initial period of test development and validation, spectrum bias has to be considered when moving from a “test establishment setting” to population-based settings, in which antibody testing is currently implemented. To provide insights into the presence and magnitude of spectrum bias and to estimate performance measures of antibody testing in a population-based environment, we compared SARS-CoV-2 neutralization to a battery of serological tests and latent class analyses (LCA) in a subgroup (n = 856) of the larger population based TiKoCo-19 cohort (n = 4185). Regarding spectrum bias, we could proof notable differences in test sensitivities and specificities when moving to a population-based setting, with larger effects visible in earlier registered tests. While in the population-based setting the two Roche ELECSYS anti-SARS-CoV-2 tests outperformed every other test and even LCA regarding sensitivity and specificity in dichotomous testing, they didn’t provide satisfying quantitative correlation with neutralization capacity. In contrast, our in-house anti SARS-CoV-2-Spike receptor binding domain (RBD) IgG-ELISA (enzyme-linked-immunosorbant assay) though inferior in dichotomous testing, provided satisfactory quantitative correlation and may thus represent a better correlate of protection. In summary, all tests, led by the two Roche tests, provided sufficient accuracy for dichotomous identification of neutralizing sera, with increasing spectrum bias visible in earlier registered tests, while the majority of tests, except the RBD-ELISA, didn’t provide satisfactory quantitative correlations. Full article
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13 pages, 2065 KiB  
Review
RT-LAMP CRISPR-Cas12/13-Based SARS-CoV-2 Detection Methods
by Kasturi Selvam, Mohamad Ahmad Najib, Muhammad Fazli Khalid, Suharni Mohamad, Fahreddin Palaz, Mehmet Ozsoz and Ismail Aziah
Diagnostics 2021, 11(9), 1646; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11091646 - 08 Sep 2021
Cited by 20 | Viewed by 7593
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has attracted public attention. The gold standard for diagnosing COVID-19 is reverse transcription–quantitative polymerase chain reaction (RT-qPCR). However, RT-qPCR can only be performed in centralized laboratories due to the [...] Read more.
Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has attracted public attention. The gold standard for diagnosing COVID-19 is reverse transcription–quantitative polymerase chain reaction (RT-qPCR). However, RT-qPCR can only be performed in centralized laboratories due to the requirement for advanced laboratory equipment and qualified workers. In the last decade, clustered regularly interspaced short palindromic repeats (CRISPR) technology has shown considerable promise in the development of rapid, highly sensitive, and specific molecular diagnostic methods that do not require complicated instrumentation. During the current COVID-19 pandemic, there has been growing interest in using CRISPR-based diagnostic techniques to develop rapid and accurate assays for detecting SARS-CoV-2. In this work, we review and summarize reverse-transcription loop-mediated isothermal amplification (RT-LAMP) CRISPR-based diagnostic techniques for detecting SARS-CoV-2. Full article
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8 pages, 517 KiB  
Communication
Sample Adequacy Control (SAC) Lowers False Negatives and Increases the Quality of Screening: Introduction of “Non-Competitive” SAC for qPCR Assays
by Ivan Brukner, Alex Resendes, Shaun Eintracht, Andreas I. Papadakis and Matthew Oughton
Diagnostics 2021, 11(7), 1133; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11071133 - 22 Jun 2021
Cited by 1 | Viewed by 3000
Abstract
Sample Adequacy Control (SAC) has critical analytical, clinical and epidemiological value that increases confidence in a negative test result. The SAC is an integral qPCR assay control, which ensures that all pre-analytical and analytical steps are adequate for accurate testing and reporting. As [...] Read more.
Sample Adequacy Control (SAC) has critical analytical, clinical and epidemiological value that increases confidence in a negative test result. The SAC is an integral qPCR assay control, which ensures that all pre-analytical and analytical steps are adequate for accurate testing and reporting. As such, a negative SAC with a negative result on pathogen screen specifies that the result should be reported as inconclusive instead of negative. Despite this, many regulatory approved tests do not incorporate SAC into their assay design. Herein, we emphasize the universal value of SAC and offer for the first time, a simple technical strategy to introduce non-competitive SAC which does not interfere with the limit of detection for the screened pathogen. Integration of SAC can provide key benefits towards identifying, isolating, quarantining and contact tracing infected individuals and in turn can improve worldwide efforts in infection control. Full article
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18 pages, 838 KiB  
Review
Viral Dynamics and Real-Time RT-PCR Ct Values Correlation with Disease Severity in COVID-19
by Ali A. Rabaan, Raghavendra Tirupathi, Anupam A Sule, Jehad Aldali, Abbas Al Mutair, Saad Alhumaid, Muzaheed, Nitin Gupta, Thoyaja Koritala, Ramesh Adhikari, Muhammad Bilal, Manish Dhawan, Ruchi Tiwari, Saikat Mitra, Talha Bin Emran and Kuldeep Dhama
Diagnostics 2021, 11(6), 1091; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11061091 - 15 Jun 2021
Cited by 122 | Viewed by 18972
Abstract
Real-time RT-PCR is considered the gold standard confirmatory test for coronavirus disease 2019 (COVID-19). However, many scientists disagree, and it is essential to understand that several factors and variables can cause a false-negative test. In this context, cycle threshold (Ct) values are being [...] Read more.
Real-time RT-PCR is considered the gold standard confirmatory test for coronavirus disease 2019 (COVID-19). However, many scientists disagree, and it is essential to understand that several factors and variables can cause a false-negative test. In this context, cycle threshold (Ct) values are being utilized to diagnose or predict SARS-CoV-2 infection. This practice has a significant clinical utility as Ct values can be correlated with the viral load. In addition, Ct values have a strong correlation with multiple haematological and biochemical markers. However, it is essential to consider that Ct values might be affected by pre-analytic, analytic, and post-analytical variables such as collection technique, specimen type, sampling time, viral kinetics, transport and storage conditions, nucleic acid extraction, viral RNA load, primer designing, real-time PCR efficiency, and Ct value determination method. Therefore, understanding the interpretation of Ct values and other influential factors could play a crucial role in interpreting viral load and disease severity. In several clinical studies consisting of small or large sample sizes, several discrepancies exist regarding a significant positive correlation between the Ct value and disease severity in COVID-19. In this context, a revised review of the literature has been conducted to fill the knowledge gaps regarding the correlations between Ct values and severity/fatality rates of patients with COVID-19. Various databases such as PubMed, Science Direct, Medline, Scopus, and Google Scholar were searched up to April 2021 by using keywords including “RT-PCR or viral load”, “SARS-CoV-2 and RT-PCR”, “Ct value and viral load”, “Ct value or COVID-19”. Research articles were extracted and selected independently by the authors and included in the present review based on their relevance to the study. The current narrative review explores the correlation of Ct values with mortality, disease progression, severity, and infectivity. We also discuss the factors that can affect these values, such as collection technique, type of swab, sampling method, etc. Full article
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9 pages, 867 KiB  
Article
Evaluation of a Pseudovirus Neutralization Assay for SARS-CoV-2 and Correlation with Live Virus-Based Micro Neutralization Assay
by Ahmed Majdi K. Tolah, Sayed S. Sohrab, Khaled Majdi K. Tolah, Ahmed M. Hassan, Sherif A. El-Kafrawy and Esam I. Azhar
Diagnostics 2021, 11(6), 994; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11060994 - 30 May 2021
Cited by 16 | Viewed by 3192
Abstract
The unusual cases of pneumonia outbreak were reported from Wuhan city in late December 2019. Serological testing provides a powerful tool for the identification of prior infection and for epidemiological studies. Pseudotype virus neutralization assays are widely used for many viruses and applications [...] Read more.
The unusual cases of pneumonia outbreak were reported from Wuhan city in late December 2019. Serological testing provides a powerful tool for the identification of prior infection and for epidemiological studies. Pseudotype virus neutralization assays are widely used for many viruses and applications in the fields of serology. The accuracy of pseudotype neutralizing assay allows for its use in low biosafety lab and provides a safe and effective alternative to the use of wild-type viruses. In this study, we evaluated the performance of this assay compared to the standard microneutralization assay as a reference. The lentiviral pseudotype particles were generated harboring the Spike gene of SARS-CoV-2. The generated pseudotype particles assay was used to evaluate the activity of neutralizing antibodies in 300 human serum samples from a COVID-19 sero-epidemiological study. Testing of these samples resulted in 55 positive samples and 245 negative samples by pseudotype viral particles assay while microneutralization assay resulted in 64 positive and 236 negative by MN assay. Compared to the MN, the pseudotyped viral particles assay showed a sensitivity of 85.94% and a specificity of 100%. Based on the data generated from this study, the pseudotype-based neutralization assay showed a reliable performance for the detection of neutralizing antibodies against SARS-CoV-2 and can be used safely and efficiently as a diagnostic tool in a biosafety level 2 laboratory. Full article
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3 pages, 562 KiB  
Editorial
How Smart Manufacturing Can Help Combat the COVID-19 Pandemic
by Yun-Siang Lin, Chao-Min Cheng and Chen-Fu Chien
Diagnostics 2021, 11(5), 885; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11050885 - 17 May 2021
Cited by 5 | Viewed by 4233
Abstract
The coronavirus pandemic (COVID-19) caused by severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) has threatened public health and caused tremendous social and economic losses [...] Full article
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3 pages, 348 KiB  
Interesting Images
Immune Response Visualized In Vivo by [18F]-FDG PET/CT after COVID-19 Vaccine
by Romain-David Seban, Laurence Champion, Nicolas Deleval, Capucine Richard and Claire Provost
Diagnostics 2021, 11(4), 676; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11040676 - 09 Apr 2021
Cited by 11 | Viewed by 2701
Abstract
Worldwide deployment of COVID-19 vaccines is in progress. Recent immune activation following vaccination can sometimes be seen in fluorine-18-fluorodeoxyglucose positron emission tomography/computed tomography ([18F]-FDG PET/CT). As previously evidenced, FDG-avid axillary lymph node(s) are common in patients receiving vaccines against SARS-CoV-2, influenza virus, or [...] Read more.
Worldwide deployment of COVID-19 vaccines is in progress. Recent immune activation following vaccination can sometimes be seen in fluorine-18-fluorodeoxyglucose positron emission tomography/computed tomography ([18F]-FDG PET/CT). As previously evidenced, FDG-avid axillary lymph node(s) are common in patients receiving vaccines against SARS-CoV-2, influenza virus, or human papillomavirus, and reflect a regional immune response. In addition, these findings may also be accompanied by an increased spleen glucose metabolism after the COVID-19 vaccine, which captures a systemic immune response. Hence, we provide here a clinical example demonstrating that immune response could be associated with increased glucose metabolism in lymphoid organs such as lymph nodes and the spleen, which are critical modulators of T cell immunity. We believe that it is of paramount importance that nuclear physicians should be able to recognize clinical and imaging features of such immune responses upon vaccination for COVID-19 and beyond. Full article
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11 pages, 237 KiB  
Review
Mini-Review Discussing the Reliability and Efficiency of COVID-19 Vaccines
by Bogdan Doroftei, Alin Ciobica, Ovidiu-Dumitru Ilie, Radu Maftei and Ciprian Ilea
Diagnostics 2021, 11(4), 579; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11040579 - 24 Mar 2021
Cited by 112 | Viewed by 22095
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 is a novel strain of human beta-coronavirus that has produced over two million deaths and affected one hundred million individuals worldwide. As all the proposed drugs proved to be unstable, inducing side effects, the need to develop [...] Read more.
Severe Acute Respiratory Syndrome Coronavirus 2 is a novel strain of human beta-coronavirus that has produced over two million deaths and affected one hundred million individuals worldwide. As all the proposed drugs proved to be unstable, inducing side effects, the need to develop a vaccine crystallized in a short time. As a result, we searched the databases for articles in which the authors reported the efficacy and safety of the use of several vaccines vaccines by sex, age group, and frequency of adverse reactions. We identified a total of 19 relevant articles that were discussed throughout this manuscript. We concluded that from all eleven vaccines, three had an efficacy >90% (Pfizer–BioNTech (~95%), Moderna (~94%), and Sputnik V (~92%)) except for Oxford–AstraZeneca (~81%). However, Moderna, Sputnik V, and Oxford–AstraZeneca also alleviate severe adverse reactions, whereas in Pfizer–BioNTech this was not revealed. The remaining five (Convidicea (AD5-nCOV); Johnson & Johnson (Ad26.COV2.S); Sinopharm (BBIBP-CorV); Covaxin (BBV152), and Sinovac (CoronaVac)) were discussed based on their immunogenicity, and safety reported by the recipients since only phases 1 and 2 were conducted without clear evidence published regarding their efficacy. CoviVac and EpiVacCorona have just been approved, which is why no published article could be found. All adverse events reported following the administration of one of the four vaccines ranged from mild to moderate; limited exceptions in which the patients either developed severe forms or died, because most effects were dose-dependent. It can be concluded that aforementioned vaccines are efficient and safe, regardless of age and sex, being well-tolerated by the recipients. Full article
17 pages, 599 KiB  
Communication
Comparative Assessment of Sera from Individuals after S-Gene RNA-Based SARS-CoV-2 Vaccination with Spike-Protein-Based and Nucleocapsid-Based Serological Assays
by Anja Dörschug, Hagen Frickmann, Julian Schwanbeck, Elif Yilmaz, Kemal Mese, Andreas Hahn, Uwe Groß and Andreas E. Zautner
Diagnostics 2021, 11(3), 426; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11030426 - 03 Mar 2021
Cited by 28 | Viewed by 3239
Abstract
Due to the beginning of vaccination against COVID-19, serological discrimination between vaccine-associated humoral response and serology-based surveillance of natural SARS-CoV-2 infections as well as breakthrough infections becomes an issue of relevance. Here, we assessed the differentiated effects of the application of an RNA [...] Read more.
Due to the beginning of vaccination against COVID-19, serological discrimination between vaccine-associated humoral response and serology-based surveillance of natural SARS-CoV-2 infections as well as breakthrough infections becomes an issue of relevance. Here, we assessed the differentiated effects of the application of an RNA vaccine using SARS-CoV-2 spike protein epitopes on the results of both anti-spike protein–based serology (EUROIMMUN) and anti-nucleocapsid-based serology (VIROTECH). A total of 80 serum samples from vaccinees acquired at different time points after vaccination was assessed. While positive or borderline serological response in the anti-spike protein assay was observed for all samples (90% both IgG and IgA, 6.3% IgA only, 3.8% borderline IgG only), only a single case of a falsely positive IgM was observed for the anti-nucleocapsid assay as expected due to this assay’s specificity. Positive anti-spike protein antibodies were already detectable in the second week after the first dose of vaccination, with higher titers after the second dose of the vaccine. In conclusion, the combined application of anti-spike protein–based serology and anti-nucleocapsid-based serology will provide a useful option for the discrimination of vaccination response and natural infection. Full article
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18 pages, 1403 KiB  
Article
SARS-CoV-2 Subgenomic N (sgN) Transcripts in Oro-Nasopharyngeal Swabs Correlate with the Highest Viral Load, as Evaluated by Five Different Molecular Methods
by Massimo Zollo, Veronica Ferrucci, Barbara Izzo, Fabrizio Quarantelli, Carmela Di Domenico, Marika Comegna, Carmela Paolillo, Felice Amato, Roberto Siciliano, Giuseppe Castaldo and Ettore Capoluongo
Diagnostics 2021, 11(2), 288; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11020288 - 12 Feb 2021
Cited by 22 | Viewed by 3746
Abstract
The COVID-19 pandemic has forced diagnostic laboratories to focus on the early diagnostics of SARS-CoV-2. The positivity of a molecular test cannot respond to the question regarding the viral capability to replicate, spread, and give different clinical effects. Despite the fact that some [...] Read more.
The COVID-19 pandemic has forced diagnostic laboratories to focus on the early diagnostics of SARS-CoV-2. The positivity of a molecular test cannot respond to the question regarding the viral capability to replicate, spread, and give different clinical effects. Despite the fact that some targets are covered by commercially-available assays, the identification of new biomarkers is desired in order to improve the quality of the information given by these assays. Therefore, since the subgenomic transcripts (sgN and sgE) are considered markers of viral activity, we evaluated these subgenomic transcripts in relation to the genomic amplification obtained using five different commercial CE-IVD tools. Methods: Five CE-IVD kits were compared in terms of their capability to detect both synthetic SARS-CoV-2 viral constructs (spiked in TMB or PBS medium) and targets (N, E, RdRp and Orf1ab genes) in twenty COVID-19–positive patients’ swabs. The sgN and sgE were assayed by real-time RT-qPCR and digital PCR. Results: None of the diagnostic kits missed the viral target genes when they were applied to targets spiked in TMB or PBS (at dilutions ranging from 100 pg to 0.1 pg). Nevertheless, once they were applied to RNA extracted from the patients’ swabs, the superimposability ranged from 50% to 100%, regardless of the extraction procedure. The sgN RNA transcript was detected only in samples with a higher viral load (Ct ≤ 22.5), while sgE was within all of the Ct ranges. Conclusions: The five kits show variable performances depending on the assay layout. It is worthy of note that the detection of the sgN transcript is associated with a higher viral load, thus representing a new marker of early and more severe infection. Full article
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15 pages, 1254 KiB  
Communication
Serological Test to Determine Exposure to SARS-CoV-2: ELISA Based on the Receptor-Binding Domain of the Spike Protein (S-RBDN318-V510) Expressed in Escherichia coli
by Alan Roberto Márquez-Ipiña, Everardo González-González, Iram Pablo Rodríguez-Sánchez, Itzel Montserrat Lara-Mayorga, Luis Alberto Mejía-Manzano, Mónica Gabriela Sánchez-Salazar, José Guillermo González-Valdez, Rocio Ortiz-López, Augusto Rojas-Martínez, Grissel Trujillo-de Santiago and Mario Moisés Alvarez
Diagnostics 2021, 11(2), 271; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11020271 - 10 Feb 2021
Cited by 15 | Viewed by 4629
Abstract
Massive worldwide serological testing for SARS-CoV-2 is needed to determine the extent of virus exposure in a particular region, the ratio of symptomatic to asymptomatic infected persons, and the duration and extent of immunity after infection. To achieve this, the development and production [...] Read more.
Massive worldwide serological testing for SARS-CoV-2 is needed to determine the extent of virus exposure in a particular region, the ratio of symptomatic to asymptomatic infected persons, and the duration and extent of immunity after infection. To achieve this, the development and production of reliable and cost-effective SARS-CoV-2 antigens is critical. We report the bacterial production of the peptide S-RBDN318-V510, which contains the receptor-binding domain of the SARS-CoV-2 spike protein (region of 193 amino acid residues from asparagine-318 to valine-510) of the SARS-CoV-2 spike protein. We purified this peptide using a straightforward approach involving bacterial lysis, his-tag-mediated affinity chromatography, and imidazole-assisted refolding. The antigen performances of S-RBDN318-V510 and a commercial full-length spike protein were compared in ELISAs. In direct ELISAs, where the antigen was directly bound to the ELISA surface, both antigens discriminated sera from non-exposed and exposed individuals. However, the discriminating resolution was better in ELISAs that used the full-spike antigen than the S-RBDN318-V510. Attachment of the antigens to the ELISA surface using a layer of anti-histidine antibodies gave equivalent resolution for both S-RBDN318-V510 and the full-length spike protein. Results demonstrate that ELISA-functional SARS-CoV-2 antigens can be produced in bacterial cultures, and that S-RBDN318-V510 may represent a cost-effective alternative to the use of structurally more complex antigens in serological COVID-19 testing. Full article
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13 pages, 3539 KiB  
Review
SARS-CoV-2 in Mexico: Beyond Detection Methods, Scope and Limitations
by Cynthia Martinez-Liu, Natalia Martínez-Acuña, Daniel Arellanos-Soto, Kame Galan-Huerta, Sonia Lozano-Sepulveda, María del Carmen Martínez-Guzmán and Ana Maria Rivas-Estilla
Diagnostics 2021, 11(1), 124; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11010124 - 14 Jan 2021
Cited by 5 | Viewed by 5740
Abstract
The new coronavirus that was first identified in December 2019 in Wuhan China, now called SARS-CoV-2, which causes the disease called COVID-19, has spread from China to the entire world in a few months. Due to its contagious potential (R0: 5.7) and because [...] Read more.
The new coronavirus that was first identified in December 2019 in Wuhan China, now called SARS-CoV-2, which causes the disease called COVID-19, has spread from China to the entire world in a few months. Due to its contagious potential (R0: 5.7) and because there is still no effective treatment to stop the infection, and a vaccine for prevention it is not yet available to the general population, COVID-19 is currently considered a global health problem. The need to implement sensitive methods for the identification of individuals with COVID-19 has led to the development of different molecular and immunological tests. The importance of a timely and accurate diagnosis is essential to determine the course of the pandemic. The interpretation of the results obtained by each test as well as the factors that affect these results have not been fully described. In this review, we describe and analyze the different SARS-CoV-2 detection methods that have been performed in Mexico and are available worldwide, outlining their strengths and weaknesses. Further, a broader perspective of the correct use and interpretation of the results obtained with these diagnostic tools is proposed to improve the containment strategy and identify the true impact of the pandemic. Full article
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12 pages, 8220 KiB  
Review
COVID-19 Point-of-Care Diagnostics That Satisfy Global Target Product Profiles
by Abdi Ghaffari, Robyn Meurant and Ali Ardakani
Diagnostics 2021, 11(1), 115; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11010115 - 12 Jan 2021
Cited by 17 | Viewed by 7187
Abstract
COVID-19 pandemic will continue to pose a major public health threat until vaccination-mediated herd immunity is achieved. Most projections predict vaccines will reach a large subset of the population late in 2021 or early 2022. In the meantime, countries are exploring options to [...] Read more.
COVID-19 pandemic will continue to pose a major public health threat until vaccination-mediated herd immunity is achieved. Most projections predict vaccines will reach a large subset of the population late in 2021 or early 2022. In the meantime, countries are exploring options to remove strict lockdown measures and allow society and the economy to return to normal function. One possibility is to expand on existing COVID-19 testing strategies by including large-scale rapid point-of-care diagnostic tests (POCTs). Currently, there is significant variability in performance and features of available POCTs, making selection and procurement of an appropriate test for specific use case difficult. In this review, we have used the World Health Organization’s (WHO) recently published target product profiles (TPPs) for specific use cases of COVID-19 diagnostic tests to screen for top-performing POCTs on the market. Several POCTs, based on clinical sensitivity/specificity, the limit of detection, and time to results, which meet WHO TPP criteria for direct detection of SARS-CoV-2 (acute infection) or indirect diagnosis of past infection (host antibodies), are highlighted here. Full article
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11 pages, 276 KiB  
Article
Comparison of Five Serological Assays for the Detection of SARS-CoV-2 Antibodies
by Anja Dörschug, Julian Schwanbeck, Andreas Hahn, Anke Hillebrecht, Sabine Blaschke, Kemal Mese, Uwe Groß, Sascha Dierks, Hagen Frickmann and Andreas E. Zautner
Diagnostics 2021, 11(1), 78; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11010078 - 06 Jan 2021
Cited by 12 | Viewed by 2791
Abstract
Serological assays can contribute to the estimation of population proportions with previous immunologically relevant contact with the Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) virus. In this study, we compared five commercially available diagnostic assays for the diagnostic identification of SARS-CoV-2-specific antibodies. [...] Read more.
Serological assays can contribute to the estimation of population proportions with previous immunologically relevant contact with the Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) virus. In this study, we compared five commercially available diagnostic assays for the diagnostic identification of SARS-CoV-2-specific antibodies. Depending on the assessed immunoglobulin subclass, recorded sensitivity ranged from 17.0% to 81.9% with best results for immunoglobulin G. Specificity with blood donor sera ranged from 90.2% to 100%, with sera from EBV patients it ranged from 84.3% to 100%. Agreement from fair to nearly perfect was recorded depending on the immunoglobulin class between the assays, the with best results being found for immunoglobulin G. Only for this immunoglobulin class was the association between later sample acquisition times (about three weeks after first positive PCR results) and positive serological results in COVID-19 patients confirmed. In conclusion, acceptable and comparable reliability for the assessed immunoglobulin G-specific assays could be shown, while there is still room for improvement regarding the reliability of the assays targeting the other immunoglobulin classes. Full article
37 pages, 1298 KiB  
Review
Nucleic Acid-Based Diagnostic Tests for the Detection SARS-CoV-2: An Update
by Choo Yee Yu, Kok Gan Chan, Chan Yean Yean and Geik Yong Ang
Diagnostics 2021, 11(1), 53; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11010053 - 01 Jan 2021
Cited by 63 | Viewed by 13057
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began as a cluster of pneumonia cases in Wuhan, China before spreading to over 200 countries and territories on six continents in less than six months. Despite rigorous global [...] Read more.
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began as a cluster of pneumonia cases in Wuhan, China before spreading to over 200 countries and territories on six continents in less than six months. Despite rigorous global containment and quarantine efforts to limit the transmission of the virus, COVID-19 cases and deaths have continued to increase, leaving devastating impacts on the lives of many with far-reaching effects on the global society, economy and healthcare system. With over 43 million cases and 1.1 million deaths recorded worldwide, accurate and rapid diagnosis continues to be a cornerstone of pandemic control. In this review, we aim to present an objective overview of the latest nucleic acid-based diagnostic tests for the detection of SARS-CoV-2 that have been authorized by the Food and Drug Administration (FDA) under emergency use authorization (EUA) as of 31 October 2020. We systematically summarize and compare the principles, technologies, protocols and performance characteristics of amplification- and sequencing-based tests that have become alternatives to the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel. We highlight the notable features of the tests including authorized settings, along with the advantages and disadvantages of the tests. We conclude with a brief discussion on the current challenges and future perspectives of COVID-19 diagnostics. Full article
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2020

Jump to: 2024, 2022, 2021

15 pages, 2760 KiB  
Article
Prognostic Value of Admission Chest CT Findings for Invasive Ventilation Therapy in COVID-19 Pneumonia
by Eva Gresser, Johannes Rueckel, Daniel Puhr-Westerheide, Vincent Schwarze, Nicola Fink, Wolfgang G. Kunz, Dietmar Wassilowsky, Michael Irlbeck, Jens Ricke, Michael Ingrisch and Bastian O. Sabel
Diagnostics 2020, 10(12), 1108; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10121108 - 19 Dec 2020
Cited by 7 | Viewed by 2935
Abstract
(1) Background: To assess the value of chest CT imaging features of COVID-19 disease upon hospital admission for risk stratification of invasive ventilation (IV) versus no or non-invasive ventilation (non-IV) during hospital stay. (2) Methods: A retrospective single-center study was conducted including all [...] Read more.
(1) Background: To assess the value of chest CT imaging features of COVID-19 disease upon hospital admission for risk stratification of invasive ventilation (IV) versus no or non-invasive ventilation (non-IV) during hospital stay. (2) Methods: A retrospective single-center study was conducted including all patients admitted during the first three months of the pandemic at our hospital with PCR-confirmed COVID-19 disease and admission chest CT scans (n = 69). Using clinical information and CT imaging features, a 10-point ordinal risk score was developed and its diagnostic potential to differentiate a severe (IV-group) from a more moderate course (non-IV-group) of the disease was tested. (3) Results: Frequent imaging findings of COVID-19 pneumonia in both groups were ground glass opacities (91.3%), consolidations (53.6%) and crazy paving patterns (31.9%). Characteristics of later stages such as subpleural bands were observed significantly more often in the IV-group (52.2% versus 26.1%, p = 0.032). Using information directly accessible during a radiologist’s reporting, a simple risk score proved to reliably differentiate between IV- and non-IV-groups (AUC: 0.89 (95% CI 0.81–0.96), p < 0.001). (4) Conclusions: Information accessible from admission CT scans can effectively and reliably be used in a scoring model to support risk stratification of COVID-19 patients to improve resource and allocation management of hospitals. Full article
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25 pages, 5193 KiB  
Review
Prevalence of COVID-19 Diagnostic Output with Chest Computed Tomography: A Systematic Review and Meta-Analysis
by Temitope Emmanuel Komolafe, John Agbo, Ebenezer Obaloluwa Olaniyi, Kayode Komolafe and Xiaodong Yang
Diagnostics 2020, 10(12), 1023; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10121023 - 28 Nov 2020
Cited by 2 | Viewed by 2639
Abstract
Background: The pooled prevalence of chest computed tomography (CT) abnormalities and other detailed analysis related to patients’ biodata like gender and different age groups have not been previously described for patients with coronavirus disease 2019 (COVID-19), thus necessitating this study. Objectives: To perform [...] Read more.
Background: The pooled prevalence of chest computed tomography (CT) abnormalities and other detailed analysis related to patients’ biodata like gender and different age groups have not been previously described for patients with coronavirus disease 2019 (COVID-19), thus necessitating this study. Objectives: To perform a meta-analysis to evaluate the diagnostic performance of chest CT, common CT morphological abnormalities, disease prevalence, biodata information, and gender prevalence of patients. Methods: Studies were identified by searching PubMed and Science Direct libraries from 1 January 2020 to 30 April 2020. Pooled CT positive rate of COVID-19 and RT-PCR, CT-imaging features, history of exposure, and biodata information were estimated using the quality effect (QE) model. Results: Out of 36 studies included, the sensitivity was 89% (95% CI: 80–96%) and 98% (95% CI: 90–100%) for chest CT and reverse transcription-polymerase chain reaction (RT-PCR), respectively. The pooled prevalence across lesion distribution were 72% (95% CI: 62–80%), 92% (95% CI: 84–97%) for lung lobe, 88% (95% CI: 81–93%) for patients with history of exposure, and 91% (95% CI: 85–96%) for patients with all categories of symptoms. Seventy-six percent (95% CI: 67–83%) had age distribution across four age groups, while the pooled prevalence was higher in the male with 54% (95% CI: 50–57%) and 46% (95% CI: 43–50%) in the female. Conclusions: The sensitivity of RT-PCR was higher than chest CT, and disease prevalence appears relatively higher in the elderly and males than children and females, respectively. Full article
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7 pages, 509 KiB  
Communication
Evaluation of SARS-CoV-2 Serological Testing in Patients with Multiple Myeloma and Other Hematologic Malignancies on Monoclonal Antibody Therapies
by Lenin Mahimainathan, Madhusudhanan Narasimhan, Rolando Corchado, Hetalkumari Patel, Ankit Kansagra, Sridevi Devaraj, Praveen Ramakrishnan Geethakumari and Alagarraju Muthukumar
Diagnostics 2020, 10(12), 992; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10120992 - 24 Nov 2020
Cited by 1 | Viewed by 2310
Abstract
Background: Patients with hematological malignancies (HM), including multiple myeloma (MM), frequently suffer from immune deficiency-associated infectious complications because of both the disease and the treatment. Alarming results from China and the UK confirm the vulnerability of HM patients to severe acute respiratory syndrome [...] Read more.
Background: Patients with hematological malignancies (HM), including multiple myeloma (MM), frequently suffer from immune deficiency-associated infectious complications because of both the disease and the treatment. Alarming results from China and the UK confirm the vulnerability of HM patients to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection-driven coronavirus disease 2019 (COVID-19). Given that the immunoassay interference from the endogenous monoclonal immunoglobulin (M paraprotein) and treatment antibodies continually challenges the MM management, it is critical to evaluate the SARS-CoV-2 serology tests for suspected interference/cross-reactivity. Methods: We compared the degree of interference in three SARS-CoV-2 serology assay platforms in HM patients with and without COVID-19 and on various therapeutic monoclonal antibody (t-mAb) treatments. Further, we confirmed the cross-reactivity in pooled samples from normal and COVID-19 + samples spiked with respective antibodies in vitro. Results: None of the 93 HM patient samples with or without t-MAbs showed cross-reactivity on any of the three serology platforms tested. Conclusions: The tested three serologic assays for SARS-CoV-2 are specific and do not have cross-reactivity with M-components or t-MAbs indicating that they can be used safely in oncology practice and in research exploring the immunologic response to COVID-19 in patients with HM. Full article
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14 pages, 3234 KiB  
Article
Peptide Nucleic Acid (PNA)-Enhanced Specificity of a Dual-Target Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR) Assay for the Detection and Differentiation of SARS-CoV-2 from Related Viruses
by Won-Suk Choi, Ju Hwan Jeong, Halcyon Dawn G. Nicolas, Sol Oh, Khristine Joy C. Antigua, Ji-Hyun Park, Beomkyu Kim, Sun-Woo Yoon, Kyeong Seob Shin, Young Ki Choi, Yun Hee Baek and Min-Suk Song
Diagnostics 2020, 10(10), 775; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10100775 - 30 Sep 2020
Cited by 6 | Viewed by 3790
Abstract
The threat posed by coronaviruses to human health has necessitated the development of a highly specific and sensitive viral detection method that could differentiate between the currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-related coronaviruses (SARSr-CoVs). In this study, [...] Read more.
The threat posed by coronaviruses to human health has necessitated the development of a highly specific and sensitive viral detection method that could differentiate between the currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-related coronaviruses (SARSr-CoVs). In this study, we developed a peptide nucleic acid (PNA)-based real-time quantitative polymerase chain reaction (RT-qPCR) assay targeting the N gene to efficiently discriminate SARS-CoV-2 from other SARSr-CoVs in human clinical samples. Without compromising the sensitivity, this method significantly enhanced the specificity of SARS-CoV-2 detection by 100-fold as compared to conventional RT-qPCR. In addition, we designed an RT-qPCR method for the sensitive and universal detection of ORF3ab-E genes of SARSr-CoV with a limit of detection (LOD) of 3.3 RNA copies per microliter. Thus, the developed assay serves as a confirmative dual-target detection method. Our PNA-mediated dual-target RT-qPCR assay can detect clinical SARS-CoV-2 samples in the range of 18.10–35.19 Ct values with an 82.6–100% detection rate. Furthermore, our assay showed no cross-reactions with other coronaviruses such as human coronaviruses (229E, NL63, and OC43) and Middle East respiratory syndrome coronavirus, influenza viruses (Type B, H1N1, H3N2, HPAI H5Nx, and H7N9), and other respiratory disease-causing viruses (MPV, RSV A, RSV B, PIV, AdV, and HRV). We, thus, developed a PNA-based RT-qPCR assay that differentiates emerging pathogens such as SARS-CoV-2 from closely related viruses such as SARSr-CoV and allows diagnosis of infections related to already identified or new coronavirus strains. Full article
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12 pages, 1471 KiB  
Communication
Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome Analysis
by Petr Klempt, Petr Brož, Martin Kašný, Adam Novotný, Kateřina Kvapilová and Petr Kvapil
Diagnostics 2020, 10(10), 769; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10100769 - 29 Sep 2020
Cited by 13 | Viewed by 3882
Abstract
Single next-generation sequencing (NGS) proved to be an important tool for monitoring the SARS-CoV-2 outbreak at the global level Until today, thousands of SARS-CoV-2 genome sequences have been published at GISAID (Global Initiative on Sharing All Influenza Data) but only a portion are [...] Read more.
Single next-generation sequencing (NGS) proved to be an important tool for monitoring the SARS-CoV-2 outbreak at the global level Until today, thousands of SARS-CoV-2 genome sequences have been published at GISAID (Global Initiative on Sharing All Influenza Data) but only a portion are suitable for reliable variant analysis. Here we report on the comparison of three commercially available NGS library preparation kits. We discuss advantages and limitations from the perspective of required input sample quality and data quality for advanced SARS-CoV-2 genome analysis. Full article
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14 pages, 2129 KiB  
Article
A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings
by Arunkumar Arumugam, Matthew L. Faron, Peter Yu, Cole Markham, Michelle Wu and Season Wong
Diagnostics 2020, 10(10), 739; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10100739 - 24 Sep 2020
Cited by 13 | Viewed by 5215
Abstract
Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection. However, it generally requires expensive equipment such as RNA isolation instruments and real-time PCR thermal cyclers. As a pandemic, COVID-19 has spread indiscriminately, and [...] Read more.
Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection. However, it generally requires expensive equipment such as RNA isolation instruments and real-time PCR thermal cyclers. As a pandemic, COVID-19 has spread indiscriminately, and many low resource settings and developing countries do not have the means for fast and accurate COVID-19 detection to control the outbreak. Additionally, long assay times, in part caused by slow sample preparation steps, have created a large backlog when testing patient samples suspected of COVID-19. With many PCR-based molecular assays including an extraction step, this can take a significant amount of time and labor, especially if the extraction is performed manually. Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. If RNA extraction steps can be omitted without significantly affecting clinical sensitivity, the turn-around time of COVID-19 tests, and the backlog we currently experience can be reduced drastically. Furthermore, our data suggest that rapid RT-PCR can be implemented for sensitive and specific molecular diagnosis of COVID-19 in locations where sophisticated laboratory instruments are not available. Our USD 300 set up achieved rapid RT-PCR using thin-walled PCR tubes and a water bath setup using sous vide immersion heaters, a Raspberry Pi computer, and a single servo motor that can process up to 96 samples at a time. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. These findings can help rapid COVID-19 testing to become more accessible and attainable across the globe. Full article
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13 pages, 2690 KiB  
Article
Sensitivity, Specificity and Predictive Values of Molecular and Serological Tests for COVID-19: A Longitudinal Study in Emergency Room
by Zeno Bisoffi, Elena Pomari, Michela Deiana, Chiara Piubelli, Niccolò Ronzoni, Anna Beltrame, Giulia Bertoli, Niccolò Riccardi, Francesca Perandin, Fabio Formenti, Federico Gobbi, Dora Buonfrate and Ronaldo Silva
Diagnostics 2020, 10(9), 669; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10090669 - 03 Sep 2020
Cited by 27 | Viewed by 10722
Abstract
Background: We assessed the sensitivity, specificity and positive and negative predictive value (PPV and NPV) of molecular and serological tests for the diagnosis of SARS-CoV-2 infection. Methods: A total of 346 patients were enrolled in the emergency room. We evaluated three Reverse Transcriptase-real [...] Read more.
Background: We assessed the sensitivity, specificity and positive and negative predictive value (PPV and NPV) of molecular and serological tests for the diagnosis of SARS-CoV-2 infection. Methods: A total of 346 patients were enrolled in the emergency room. We evaluated three Reverse Transcriptase-real time PCRs (RT-PCRs) including six different gene targets, five serologic rapid diagnostic tests (RDT) and one ELISA. The final classification of infected/non-infected patients was performed using Latent Class Analysis combined with clinical re-assessment of incongruous cases. Results: Out of these, 24.6% of patients were classified as infected. The molecular test RQ-SARS-nCoV-2 showed the highest performance with 91.8% sensitivity, 100% specificity, 100.0% PPV and 97.4% NPV respectively. Considering the single gene targets, S and RdRp of RQ-SARS-nCoV-2 had the highest sensitivity (94.1%). The in-house RdRp presented the lowest sensitivity (62.4%). The specificity ranged from 99.2% for in-house RdRp and N2 to 95.0% for E. The PPV ranged from 97.1% of N2 to 85.4% of E and the NPV from 98.1% of S to 89.0% of in-house RdRp. All serological tests had < 50% sensitivity and low PPV and NPV. VivaDiag IgM (RDT) had 98.5% specificity, with 84.0% PPV, but 24.7% sensitivity. Conclusion: Molecular tests for SARS-CoV-2 infection showed excellent specificity, but significant differences in sensitivity. Serological tests have limited utility in a clinical context. Full article
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12 pages, 4367 KiB  
Article
Evaluation of the Usefulness of CO-RADS for Chest CT in Patients Suspected of Having COVID-19
by Tomoyuki Fujioka, Marie Takahashi, Mio Mori, Junichi Tsuchiya, Emi Yamaga, Toshihiro Horii, Hirofumi Yamada, Mizuki Kimura, Koichiro Kimura, Yoshio Kitazume, Mitsuhiro Kishino and Ukihide Tateishi
Diagnostics 2020, 10(9), 608; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10090608 - 19 Aug 2020
Cited by 40 | Viewed by 6806
Abstract
The purpose of this study was to use the Coronavirus Disease 2019 (COVID-19) Reporting and Data System (CO-RADS) to evaluate the chest computed tomography (CT) images of patients suspected of having COVID-19, and to investigate its diagnostic performance and interobserver agreement. The Dutch [...] Read more.
The purpose of this study was to use the Coronavirus Disease 2019 (COVID-19) Reporting and Data System (CO-RADS) to evaluate the chest computed tomography (CT) images of patients suspected of having COVID-19, and to investigate its diagnostic performance and interobserver agreement. The Dutch Radiological Society developed CO-RADS as a diagnostic indicator for assessing suspicion of lung involvement of COVID-19 on a scale of 1 (very low) to 5 (very high). We investigated retrospectively 154 adult patients with clinically suspected COVID-19, between April and June 2020, who underwent chest CT and reverse transcription-polymerase chain reaction (RT-PCR). The patients’ average age was 61.3 years (range, 21–93), 101 were male, and 76 were RT-PCR positive. Using CO-RADS, four radiologists evaluated the chest CT images. Sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were calculated. Interobserver agreement was calculated using the intraclass correlation coefficient (ICC) by comparing the individual reader’s score to the median of the remaining three radiologists. The average sensitivity was 87.8% (range, 80.2–93.4%), specificity was 66.4% (range, 51.3–84.5%), and AUC was 0.859 (range, 0.847–0.881); there was no significant difference between the readers (p > 0.200). In 325 (52.8%) of 616 observations, there was absolute agreement among observers. The average ICC of readers was 0.840 (range, 0.800–0.874; p < 0.001). CO-RADS is a categorical taxonomic evaluation scheme for COVID-19 pneumonia, using chest CT images, that provides outstanding performance and from substantial to almost perfect interobserver agreement for predicting COVID-19. Full article
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10 pages, 1517 KiB  
Article
Direct-RT-qPCR Detection of SARS-CoV-2 without RNA Extraction as Part of a COVID-19 Testing Strategy: From Sample to Result in One Hour
by Eva Kriegova, Regina Fillerova and Petr Kvapil
Diagnostics 2020, 10(8), 605; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10080605 - 18 Aug 2020
Cited by 31 | Viewed by 8228
Abstract
Due to the lack of protective immunity in the general population and the absence of effective antivirals and vaccines, the Coronavirus disease 2019 (COVID-19) pandemic continues in some countries, with local epicentres emerging in others. Due to the great demand for effective COVID-19 [...] Read more.
Due to the lack of protective immunity in the general population and the absence of effective antivirals and vaccines, the Coronavirus disease 2019 (COVID-19) pandemic continues in some countries, with local epicentres emerging in others. Due to the great demand for effective COVID-19 testing programmes to control the spread of the disease, we have suggested such a testing programme that includes a rapid RT-qPCR approach without RNA extraction. The Direct-One-Step-RT-qPCR (DIOS-RT-qPCR) assay detects severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in less than one hour while maintaining the high sensitivity and specificity required of diagnostic tools. This optimised protocol allows for the direct use of swab transfer media (14 μL) without the need for RNA extraction, achieving comparable sensitivity to the standard method that requires the time-consuming and costly step of RNA isolation. The limit of detection for DIOS-RT-qPCR was lower than seven copies/reaction, which translates to 550 virus copies/mL of swab. The speed, ease of use and low price of this assay make it suitable for high-throughput screening programmes. The use of fast enzymes allows RT-qPCR to be performed under standard laboratory conditions within one hour, making it a potential point-of-care solution on high-speed cycling instruments. This protocol also implements the heat inactivation of SARS-CoV-2 (75 °C for 10 min), which renders samples non-infectious, enabling testing in BSL-2 facilities. Moreover, we discuss the critical steps involved in developing tests for the rapid detection of COVID-19. Implementing rapid, easy, cost-effective methods can help control the worldwide spread of the COVID-19 infection. Full article
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8 pages, 1614 KiB  
Article
Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples
by Vlad Petrovan, Virgil Vrajmasu, Ana Cristina Bucur, Dan Sebastian Soare, Eugen Radu, Paula Dimon and Mihaela Zaulet
Diagnostics 2020, 10(7), 472; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10070472 - 11 Jul 2020
Cited by 12 | Viewed by 5044
Abstract
Due to the current pandemic, a global shortage of reagents has drawn interest in developing alternatives to increase the number of coronavirus tests. One such alternative is sample pooling. We compared commercial kits that are used in COVID-19 diagnostics in terms of their [...] Read more.
Due to the current pandemic, a global shortage of reagents has drawn interest in developing alternatives to increase the number of coronavirus tests. One such alternative is sample pooling. We compared commercial kits that are used in COVID-19 diagnostics in terms of their sensitivity and feasibility for use in pooling. In this preliminary study, we showed that pooling of up to 80 samples did not affect the efficacy of the kits. Additionally, the RNA-dependent RNA polymerase (RdRp) gene is a more suitable target in pooled samples than the envelope (E) gene. This approach could provide an easy method of screening a large number of samples and help adjust different governmental regulations. Full article
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10 pages, 1846 KiB  
Article
Rapid Large-Scale COVID-19 Testing during Shortages
by Christian Beetz, Volha Skrahina, Toni M. Förster, Hanaa Gaber, Jefri J. Paul, Filipa Curado, Arndt Rolfs, Peter Bauer, Stephan Schäfer, Volkmar Weckesser, Vivi Lieu, Mandy Radefeldt, Claudia Pöppel, Susann Krake, Krishna K. Kandaswamy, Katja Bruesehafer and Florian Vogel
Diagnostics 2020, 10(7), 464; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10070464 - 08 Jul 2020
Cited by 21 | Viewed by 7180
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in economic and social lockdowns in most countries all over the globe. Early identification of infected individuals is regarded as one of the most important prerequisites [...] Read more.
The Coronavirus disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in economic and social lockdowns in most countries all over the globe. Early identification of infected individuals is regarded as one of the most important prerequisites for fighting the pandemic and for returning to a ‘New Normal’. Large-scale testing is therefore crucial, but is facing several challenges including shortage of sample collection tools and of molecular biological reagents, and the need for safe electronic communication of medical reports. We present the successful establishment of a holistic SARS-CoV-2 testing platform that covers proband registration, sample collection and shipment, sample testing, and report issuing. The RT-PCR-based virus detection, being central to the platform, was extensively validated: sensitivity and specificity were defined as 96.8% and 100%, respectively; intra-run and inter-run precision were <3%. A novel type of sample swab and an in-house-developed RNA extraction system were shown to perform as good as commercially available products. The resulting flexibility guarantees independence from the current bottlenecks in SARS-CoV-2 testing. Based on our technology, we offered testing at local, national, and global levels. In the present study, we report the results from approx. 18,000 SARS-CoV-2 tests in almost 10,000 individuals from a low-frequency SARS-CoV-2 pandemic area in a homogenous geographical region in north-eastern Germany for a period of 10 weeks (21 March to 31 May 2020). Among the probands, five SARS-CoV-2 positive cases were identified. Comparative analysis of corresponding virus genomes revealed a diverse origin from three of the five currently recognized SARS-CoV-2 phylogenetic clades. Our study exemplifies how preventive SARS-CoV-2 testing can be set up in a rapid and flexible manner. The application of our test has enabled a safe maintenance/resume of critical local infrastructure, e.g., nursing homes where more than 5000 elderlies and caretakers got tested. The strategy outlined by the present study may serve as a blueprint for the implementation of large-scale preventive SARS-CoV-2 testing elsewhere. Full article
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14 pages, 2780 KiB  
Review
COVID-19 Serological Tests: How Well Do They Actually Perform?
by Abdi Ghaffari, Robyn Meurant and Ali Ardakani
Diagnostics 2020, 10(7), 453; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10070453 - 04 Jul 2020
Cited by 117 | Viewed by 39462
Abstract
In only a few months after initial discovery in Wuhan, China, SARS-CoV-2 and the associated coronavirus disease 2019 (COVID-19) have become a global pandemic causing significant mortality and morbidity and implementation of strict isolation measures. In the absence of vaccines and effective therapeutics, [...] Read more.
In only a few months after initial discovery in Wuhan, China, SARS-CoV-2 and the associated coronavirus disease 2019 (COVID-19) have become a global pandemic causing significant mortality and morbidity and implementation of strict isolation measures. In the absence of vaccines and effective therapeutics, reliable serological testing must be a key element of public health policy to control further spread of the disease and gradually remove quarantine measures. Serological diagnostic tests are being increasingly used to provide a broader understanding of COVID-19 incidence and to assess immunity status in the population. However, there are discrepancies between claimed and actual performance data for serological diagnostic tests on the market. In this study, we conducted a review of independent studies evaluating the performance of SARS-CoV-2 serological tests. We found significant variability in the accuracy of marketed tests and highlight several lab-based and point-of-care rapid serological tests with high levels of performance. The findings of this review highlight the need for ongoing independent evaluations of commercialized COVID-19 diagnostic tests. Full article
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20 pages, 888 KiB  
Review
Molecular and Serological Tests for COVID-19. A Comparative Review of SARS-CoV-2 Coronavirus Laboratory and Point-of-Care Diagnostics
by Robert Kubina and Arkadiusz Dziedzic
Diagnostics 2020, 10(6), 434; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10060434 - 26 Jun 2020
Cited by 177 | Viewed by 32070
Abstract
Validated and accurate laboratory testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a crucial part of the timely management of Coronavirus Disease 2019 (COVID-19) disease, supporting the clinical decision-making process for infection control at the healthcare level and detecting asymptomatic cases. [...] Read more.
Validated and accurate laboratory testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a crucial part of the timely management of Coronavirus Disease 2019 (COVID-19) disease, supporting the clinical decision-making process for infection control at the healthcare level and detecting asymptomatic cases. This would facilitate an appropriate treatment, a prompt isolation and consequently deceleration of the pandemic. Various laboratory tests can identify the genetic material of SARS-CoV-2 that causes COVID-19 in specimens, or specific anti-viral antibodies in blood/serum. Due to the current pandemic situation, a development of point-of-care diagnostics (POCD) allows us to substantially accelerate taking clinical decisions and implement strategic planning at the national level of preventative measures. This review summarizes and compares the available POCD and those currently under development, including quantitative reverse transcription PCR (RT-qPCR), serology immunoassays (SIAs) and protein microarray method (PMM) designed for standard and rapid COVID-19 diagnosis. Full article
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33 pages, 5047 KiB  
Review
COVID-19 Diagnostics, Tools, and Prevention
by Mayar Allam, Shuangyi Cai, Shambavi Ganesh, Mythreye Venkatesan, Saurabh Doodhwala, Zexing Song, Thomas Hu, Aditi Kumar, Jeremy Heit, COVID-19 Study Group and Ahmet F. Coskun
Diagnostics 2020, 10(6), 409; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10060409 - 16 Jun 2020
Cited by 57 | Viewed by 23695
Abstract
The Coronavirus Disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), outbreak from Wuhan City, Hubei province, China in 2019 has become an ongoing global health emergency. The emerging virus, SARS-CoV-2, causes coughing, fever, muscle ache, and shortness of breath [...] Read more.
The Coronavirus Disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), outbreak from Wuhan City, Hubei province, China in 2019 has become an ongoing global health emergency. The emerging virus, SARS-CoV-2, causes coughing, fever, muscle ache, and shortness of breath or dyspnea in symptomatic patients. The pathogenic particles that are generated by coughing and sneezing remain suspended in the air or attach to a surface to facilitate transmission in an aerosol form. This review focuses on the recent trends in pandemic biology, diagnostics methods, prevention tools, and policies for COVID-19 management. To meet the growing demand for medical supplies during the COVID-19 era, a variety of personal protective equipment (PPE) and ventilators have been developed using do-it-yourself (DIY) manufacturing. COVID-19 diagnosis and the prediction of virus transmission are analyzed by machine learning algorithms, simulations, and digital monitoring. Until the discovery of a clinically approved vaccine for COVID-19, pandemics remain a public concern. Therefore, technological developments, biomedical research, and policy development are needed to decipher the coronavirus mechanism and epidemiological characteristics, prevent transmission, and develop therapeutic drugs. Full article
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15 pages, 2073 KiB  
Review
COVID-19 Infection Diagnosis: Potential Impact of Isothermal Amplification Technology to Reduce Community Transmission of SARS-CoV-2
by Ameh S. James and John I. Alawneh
Diagnostics 2020, 10(6), 399; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10060399 - 11 Jun 2020
Cited by 68 | Viewed by 9808
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic is largely driven by community transmission, after 2019 novel Coronavirus (2019-nCoV or SARS-CoV-2) crosses the borders. To stop the spread, rapid testing is required at community clinics and hospitals. These rapid tests should be comparable with [...] Read more.
The current coronavirus disease 2019 (COVID-19) pandemic is largely driven by community transmission, after 2019 novel Coronavirus (2019-nCoV or SARS-CoV-2) crosses the borders. To stop the spread, rapid testing is required at community clinics and hospitals. These rapid tests should be comparable with the standard PCR technology. Isothermal amplification technology provides an excellent alternative that is highly amenable to resource limited settings, where expertise and infrastructure to support PCR are not available. In this review, we provide a brief description of isothermal amplification technology, its potential and the gaps that need to be considered for SARS-CoV-2 detection. Among this emerging technology, loop-mediated amplification (LAMP), recombinase polymerase amplification (RPA) and Nicking enzyme-assisted reaction (NEAR) technologies have been identified as potential platforms that could be implemented at community level, without samples referral to a centralized laboratory and prolonged turnaround time associated with the standard COVID-19 RT-PCR test. LAMP, for example, has recently been shown to be comparable with PCR and could be performed in less than 30 min by non-laboratory staff, without RNA extractions commonly associated with PCR. Interestingly, NEAR (ID NOW™ COVID-19 (Abbott, IL, USA) was able to detect the virus in 5 min. More so, isothermal platforms are cost effective and could easily be scaled up to resource limited settings. Diagnostics developers, scientific community and commercial companies could consider this alternative method to help stop the spread of COVID-19. Full article
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12 pages, 313 KiB  
Article
Group Testing-Based Robust Algorithm for Diagnosis of COVID-19
by Jin-Taek Seong
Diagnostics 2020, 10(6), 396; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10060396 - 11 Jun 2020
Cited by 4 | Viewed by 3032
Abstract
At the time of writing, the COVID-19 infection is spreading rapidly. Currently, there is no vaccine or treatment, and researchers around the world are attempting to fight the infection. In this paper, we consider a diagnosis method for COVID-19, which is characterized by [...] Read more.
At the time of writing, the COVID-19 infection is spreading rapidly. Currently, there is no vaccine or treatment, and researchers around the world are attempting to fight the infection. In this paper, we consider a diagnosis method for COVID-19, which is characterized by a very rapid rate of infection and is widespread. A possible method for avoiding severe infections is to stop the spread of the infection in advance by the prompt and accurate diagnosis of COVID-19. To this end, we exploit a group testing (GT) scheme, which is used to find a small set of confirmed cases out of a large population. For the accurate detection of false positives and negatives, we propose a robust algorithm (RA) based on the maximum a posteriori probability (MAP). The key idea of the proposed RA is to exploit iterative detection to propagate beliefs to neighbor nodes by exchanging marginal probabilities between input and output nodes. As a result, we show that our proposed RA provides the benefit of being robust against noise in the GT schemes. In addition, we demonstrate the performance of our proposal with a number of tests and successfully find a set of infected samples in both noiseless and noisy GT schemes with different COVID-19 incidence rates. Full article
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6 pages, 4900 KiB  
Communication
Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis
by Chao-Ju Chen, Li-Ling Hsieh, Shu-Kai Lin, Chu-Feng Wang, Yi-Hui Huang, Shang-Yi Lin and Po-Liang Lu
Diagnostics 2020, 10(5), 333; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10050333 - 21 May 2020
Cited by 13 | Viewed by 6849
Abstract
Coronavirus disease 2019 (COVID-19), the current uncontrolled outbreak of infectious disease, has caused significant challenges throughout the world. A reliable rapid diagnostic test for COVID-19 is demanded worldwide. The real-time reverse transcriptase polymerase chain was one of the most quickly established methods in [...] Read more.
Coronavirus disease 2019 (COVID-19), the current uncontrolled outbreak of infectious disease, has caused significant challenges throughout the world. A reliable rapid diagnostic test for COVID-19 is demanded worldwide. The real-time reverse transcriptase polymerase chain was one of the most quickly established methods in the novel viral pandemic and was considered as the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this report, we illustrate our experience of applying a protocol from the Taiwan CDC and achieving assay optimization in the immediate circumstances to meet the urgent medical and public health needs. Full article
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15 pages, 1388 KiB  
Article
Antibody Tests in Detecting SARS-CoV-2 Infection: A Meta-Analysis
by Panagiota I. Kontou, Georgia G. Braliou, Niki L. Dimou, Georgios Nikolopoulos and Pantelis G. Bagos
Diagnostics 2020, 10(5), 319; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10050319 - 19 May 2020
Cited by 183 | Viewed by 15098
Abstract
The emergence of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 made imperative the need for diagnostic tests that can identify the infection. Although Nucleic Acid Test (NAT) is considered to be the gold standard, serological tests based on antibodies could be very helpful. [...] Read more.
The emergence of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 made imperative the need for diagnostic tests that can identify the infection. Although Nucleic Acid Test (NAT) is considered to be the gold standard, serological tests based on antibodies could be very helpful. However, individual studies are usually inconclusive, thus, a comparison of different tests is needed. We performed a systematic review and meta-analysis in PubMed, medRxiv and bioRxiv. We used the bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities. We evaluated IgM and IgG tests based on Enzyme-linked immunosorbent assay (ELISA), Chemiluminescence Enzyme Immunoassays (CLIA), Fluorescence Immunoassays (FIA), and the Lateral Flow Immunoassays (LFIA). We identified 38 studies containing data from 7848 individuals. Tests using the S antigen are more sensitive than N antigen-based tests. IgG tests perform better compared to IgM ones and show better sensitivity when the samples were taken longer after the onset of symptoms. Moreover, a combined IgG/IgM test seems to be a better choice in terms of sensitivity than measuring either antibody alone. All methods yield high specificity with some of them (ELISA and LFIA) reaching levels around 99%. ELISA- and CLIA-based methods perform better in terms of sensitivity (90%–94%) followed by LFIA and FIA with sensitivities ranging from 80% to 89%. ELISA tests could be a safer choice at this stage of the pandemic. LFIA tests are more attractive for large seroprevalence studies but show lower sensitivity, and this should be taken into account when designing and performing seroprevalence studies. Full article
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12 pages, 2228 KiB  
Review
Saliva—Friend and Foe in the COVID-19 Outbreak
by Pingping Han and Sašo Ivanovski
Diagnostics 2020, 10(5), 290; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10050290 - 09 May 2020
Cited by 66 | Viewed by 14260
Abstract
The coronavirus disease 2019 (COVID-19) outbreak, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global ongoing pandemic. Timely, accurate and non-invasive SARS-CoV-2 detection in both symptomatic and asymptomatic patients, as well as determination of their immune status, [...] Read more.
The coronavirus disease 2019 (COVID-19) outbreak, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global ongoing pandemic. Timely, accurate and non-invasive SARS-CoV-2 detection in both symptomatic and asymptomatic patients, as well as determination of their immune status, will facilitate effective large-scale pandemic control measures to prevent the spread of COVID-19. Saliva is a biofluid whose anatomical source and location is of particularly strategic relevance to COVID-19 transmission and monitoring. This review focuses on the role of saliva as both a foe (a common mode of viral transmission via salivary droplets and potentially aerosols) and a friend (as a non-invasive diagnostic tool for viral detection and immune status surveillance) in combating COVID-19. Full article
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3 pages, 581 KiB  
Editorial
Combining Point-of-Care Diagnostics and Internet of Medical Things (IoMT) to Combat the COVID-19 Pandemic
by Ting Yang, Mattia Gentile, Ching-Fen Shen and Chao-Min Cheng
Diagnostics 2020, 10(4), 224; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10040224 - 16 Apr 2020
Cited by 81 | Viewed by 10723
Abstract
The current standard testing method for screening coronavirus disease 2019 (COVID-19) is through reverse real-time PCR assay (rRT-PCR), a common molecular-based assay that requires an average of four to six hours to provide results [...] Full article
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7 pages, 426 KiB  
Editorial
In Vitro Diagnostic Assays for COVID-19: Recent Advances and Emerging Trends
by Sandeep Kumar Vashist
Diagnostics 2020, 10(4), 202; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10040202 - 05 Apr 2020
Cited by 237 | Viewed by 29901
Abstract
There have been tremendous advances in in vitro diagnostic (IVD) assays for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main IVD assays used for COVID-19 employ real-time reverse transcriptase polymerase chain reaction (RT-PCR) that takes a [...] Read more.
There have been tremendous advances in in vitro diagnostic (IVD) assays for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main IVD assays used for COVID-19 employ real-time reverse transcriptase polymerase chain reaction (RT-PCR) that takes a few hours. But the assay duration has been shortened to 45 min by Cepheid. Of interest is the point-of-care (POC) molecular assay by Abbott that decreased the assay duration to just 5 min. Most molecular tests have been approved by the United States Food and Drug Administration (FDA) under emergency use authorization (EUA) and are Conformité Européenne (CE) marked. A wide range of serology immunoassays (IAs) have also been developed that complement the molecular assays for the diagnosis of COVID-19. The most prominent IAs are automated chemiluminescent IA (CLIA), manual ELISA, and rapid lateral flow IA (LFIA), which detect the immunoglobulin M (IgM) and immunoglobulin G (IgG) produced in persons in response to SARS-CoV-2 infection. The ongoing research efforts and advances in complementary technologies will pave the way to new POC IVD assays in the coming months. However, the performance of IVD assays needs to be critically evaluated before they are employed for the clinical diagnosis of COVID-19. Full article
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3 pages, 392 KiB  
Editorial
Point-of-Care RNA-Based Diagnostic Device for COVID-19
by Ting Yang, Yung-Chih Wang, Ching-Fen Shen and Chao-Min Cheng
Diagnostics 2020, 10(3), 165; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10030165 - 18 Mar 2020
Cited by 104 | Viewed by 20962
Abstract
At the end of 2019, the novel coronavirus disease (COVID-19), a fast-spreading respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was reported in Wuhan, China and has now affected over 123 countries globally [...] Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

"Technologies for COVID-19 Diagnosis and Pandemic Response" Planned Book Chapter:

Chapters

Title

(MDPI Publication in COVID-19 Special Issue)

Authors

1.

SARS-CoV-2 infection & pathophysiology

Recruiting

2.

Role of diagnostics in the COVID-19 pandemic response

Dr. Sandeep Kumar Vashist

3.

Biomarkers during COVID-19: Mechanisms of Change and Implications for Patient Outcomes

(https://0-www-mdpi-com.brum.beds.ac.uk/2075-4418/12/2/509)

Dr. Chao-Min Cheng

4.

In Vitro Diagnostic Assays for COVID-19: Recent Advances and Emerging Trends

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10040202)

Sandeep Kumar Vashist

5.

Nucleic Acid-Based Diagnostic Tests for the Detection SARS-CoV-2: An Update

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11010053)

Choo Yee Yu, Kok Gan Chan, Chan Yean Yean

& Geik Yong Ang

 

6.

Viral Dynamics and Real-Time RT-PCR Ct Values Correlation with Disease Severity in COVID-19

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11061091)

Ali A. Rabaan, Raghavendra Tirupathi, Anupam A Sule, Jehad Aldali, Abbas Al Mutair, Saad Alhumaid, Muzaheed, Nitin Gupta, Thoyaja Koritala, Ramesh Adhikari, Muhammad Bilal, Manish Dhawan, Ruchi Tiwari, Saikat Mitra, Talha Bin Emran & Kuldeep Dhama

7.

Prevalence of COVID-19 Diagnostic Output with Chest Computed Tomography: A Systematic Review and Meta-Analysis

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10121023)

Temitope Emmanuel Komolafe, John Agbo, Ebenezer Obaloluwa Olaniyi, Kayode Komolafe

& Xiaodong Yang

8.

COVID-19 Point-of-Care Diagnostics That Satisfy Global Target Product Profiles

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11010115)

Abdi Ghaffari, Robyn Meurant & Ali Ardakani

 

9.

Antibody Tests in Detecting SARS-CoV-2 Infection: A Meta-Analysis

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10050319)

Panagiota I. Kontou,

Georgia G. Braliou, Niki L. Dimou, Georgios Nikolopoulos & Pantelis G. Bagos

10.

COVID-19 Serological Tests: How Well Do They Actually Perform?

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10070453)

Abdi Ghaffari, Robyn Meurant & Ali Ardakani

11.

Molecular and Serological Tests for COVID-19. A Comparative Review of SARS-CoV-2 Coronavirus Laboratory and Point-of-Care Diagnostics

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10060434)

Robert Kubina & Arkadiusz Dziedzic

 

12.

COVID-19 Diagnostics, Tools, and Prevention

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10060409)

Mayar Allam, Shuangyi Cai, Shambavi Ganesh, Mythreye Venkatesan, Saurabh Doodhwala, Zexing Song, Thomas Hu, Aditi Kumar, Jeremy Heit, COVID-19 Study Group &

Ahmet F. Coskun

13.

COVID-19 Infection Diagnosis: Potential Impact of Isothermal Amplification Technology to Reduce Community Transmission of SARS-CoV-2

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10060399)

Ameh S. James & John I. Alawneh

 

14.

Saliva—Friend and Foe in the COVID-19 Outbreak

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10050290)

Pingping Han & Sašo Ivanovski

 

15.

Combining Point-of-Care Diagnostics and Internet of Medical Things (IoMT) to Combat the COVID-19 Pandemic

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics10040224)

Ting Yang, Mattia Gentile,

Ching-Fen Shen &

Chao-Min Cheng

 

16.

Electrochemical biosensors for COVID-19

Recruiting

17.

How Smart Manufacturing Can Help Combat the COVID-19 Pandemic

(https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11050885)

Yun-Siang Lin, Chao-Min Cheng & Chen-Fu Chien

 

18.

COVID-19 self-tests and their role in pandemic response

Dr. Sandeep Kumar Vashist

19.

Role of mobile healthcare technologies, digital healthcare, artificial intelligence and telemedicine in COVID-19 pandemic response

Recruiting

20.

Impact of COVID-19 on IVD industry and healthcare and how it will influence future pandemic response

Recruiting

 

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