Research

9 pages, 622 KiB

Open AccessArticle

Validation of GeneFinder COVID-19 Ag Plus Rapid Test and Its Potential Utility to Slowing Infection Waves: A Single-Center Laboratory Evaluation Study

by Cinzia Peronace, Rossana Tallerico, Manuela Colosimo, Vanessa Sacco, Roberta Talarico, Marco De Fazio, Federica Pasceri, Ilenia Talotta, Giuseppina Panduri, Jung-Hee Kim, Erika Cione and Pasquale Minchella

Diagnostics 2022, 12(5), 1126; https://doi.org/10.3390/diagnostics12051126 - 01 May 2022

Cited by 3 | Viewed by 2500

Abstract

Diagnostic laboratory tools are essential to keep everyone safe and track newly emerging variants; on the other hand, “filter” screening tests recognizing positivity are valuable tools to avoid hectic laboratory work that, besides COVID-19, are also part of the routine. Therefore, complementary assays, [...] Read more.

Diagnostic laboratory tools are essential to keep everyone safe and track newly emerging variants; on the other hand, “filter” screening tests recognizing positivity are valuable tools to avoid hectic laboratory work that, besides COVID-19, are also part of the routine. Therefore, complementary assays, such as rapid antigen tests (RATs), are essential in controlling and monitoring virus spread within the community, especially in the asymptomatic population. A subset of nasopharyngeal swab specimens resulted in SARS-CoV-2 positive and investigated for genomic characterization were used for RAT validation. RATs were performed immediately after sampling, following the manufacturer’s instructions (reading at 15 min). RT-PCRs were carried out within 24 h of specimens’ collection. Out of 603 patients, 145 (24.05%) tested positive by RT-PCR and RAT and 451 (74.79%) tested negative by both methods; discordant results (RT-PCR+/RAT− or RT-PCR−/RAT+) were obtained in 7 patients (1.16%). RATs’ overall specificity and sensitivity were 96.03% (95%CI: 91.55–98.53%) and 99.78% (95%CI: 98.77–99.99%), respectively, taking RT-PCR as the reference. Overall, RAT negative predictive value was 98.69% (95%CI 97.17–99.40%). The GeneFinder COVID-19 Ag Plus Rapid Test performed well as a screening test for early diagnosis of COVID-19, especially in asymptomatic subjects. The data suggested that patients with RT-PCR-proven COVID-19 testing negative by RAT are unlikely to be infectious. GeneFinder COVID-19 Ag Plus Rapid Test also works on variants of concern (VOC) delta and omicron BA.1 and BA.2. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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11 pages, 906 KiB

Open AccessArticle

Evaluation of the Diagnostic Accuracy of Nasal Cavity and Nasopharyngeal Swab Specimens for SARS-CoV-2 Detection via Rapid Antigen Test According to Specimen Collection Timing and Viral Load

by Seungjun Lee, Kristin Widyasari, Hye-Ryun Yang, Jieun Jang, Taejoon Kang and Sunjoo Kim

Diagnostics 2022, 12(3), 710; https://doi.org/10.3390/diagnostics12030710 - 14 Mar 2022

Cited by 15 | Viewed by 3259

Abstract

The rapid diagnosis of SARS-CoV-2 is an essential aspect in the detection and control of the spread of COVID-19. We evaluated the accuracy of the rapid antigen test (RAT) using samples from the nasal cavity and nasopharynx based on sample collection timing and [...] Read more.

The rapid diagnosis of SARS-CoV-2 is an essential aspect in the detection and control of the spread of COVID-19. We evaluated the accuracy of the rapid antigen test (RAT) using samples from the nasal cavity and nasopharynx based on sample collection timing and viral load. We enrolled 175 patients, of which 71 patients and 104 patients had tested positive and negative, respectively, based on real time-PCR. Nasal cavity and nasopharyngeal swab samples were tested using STANDARD Q COVID-19 Ag tests (Q Ag, SD Biosensor, Korea). The sensitivity of the Q Ag test was 77.5% (95% confidence interval [CI], 67.8–87.2%) for the nasal cavity and 81.7% (95% [CI, 72.7–90.7%) for the nasopharyngeal specimens. The RAT results showed a substantial agreement between the nasal cavity and nasopharyngeal specimens (Cohen’s kappa index = 0.78). The sensitivity of the RAT for nasal cavity specimens exceeded 89% for <5 days after symptom onset (DSO) and 86% for Ct of E and RdRp < 25. The Q Ag test performed fairly well, especially in the early DSO when a high viral load was present, and the nasal cavity swab can be considered an alternative site for the rapid diagnosis of COVID-19. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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11 pages, 2501 KiB

Open AccessArticle

Preclinical Validation of a Novel Injection-Molded Swab for the Molecular Assay Detection of SARS-CoV-2

by Chiara E. Ghezzi, Devon R. Hartigan, Justin P. Hardick, Rebecca Gore, Miryam Adelfio, Anyelo R. Diaz, Pamela D. McGuinness, Matthew L. Robinson, Bryan O. Buchholz and Yukari C. Manabe

Diagnostics 2022, 12(1), 206; https://doi.org/10.3390/diagnostics12010206 - 15 Jan 2022

Cited by 3 | Viewed by 2474

Abstract

During the COVID-19 public health emergency, many actions have been undertaken to help ensure that patients and health care providers have timely and continued access to high-quality medical devices to respond effectively. The development and validation of new testing supplies and equipment, including [...] Read more.

During the COVID-19 public health emergency, many actions have been undertaken to help ensure that patients and health care providers have timely and continued access to high-quality medical devices to respond effectively. The development and validation of new testing supplies and equipment, including collection swabs, has helped to expand the availability and capability for various diagnostic, therapeutic, and protective medical devices in high demand during the COVID-19 emergency. Here, we report the initial validation of a new injection-molded anterior nasal swab, ClearTip™, that was experimentally validated in a laboratory setting as well as in independent clinical studies in comparison to gold standard flocked swabs. We have also developed an in vitro anterior nasal tissue model which offers a novel, efficient, and clinically relevant validation tool to replicate the clinical swabbing workflow with high fidelity, while being accessible, safe, reproducible, and time- and cost-effective. ClearTip™ displayed greater inactivated virus release in the benchtop model, confirmed by its greater ability to report positive samples in a small clinical study in comparison to flocked swabs. We also quantified the detection of biological materials, as a proxy for viral material, in multi-center pre-clinical and clinical studies which showed a statistically significant difference in one study and a reduction in performance in comparison to flocked swabs. Taken together, these results emphasize the compelling benefits of non-absorbent injection-molded anterior nasal swabs for COVID-19 detection, comparable to standard flocked swabs. Injection-molded swabs, as ClearTip™, could have the potential to support future swab shortages, due to its manufacturing advantages, while offering benefits in comparison to highly absorbent swabs in terms of comfort, limited volume collection, and potential multiple usage. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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14 pages, 19182 KiB

Open AccessArticle

Recombinant Protein Expression and Purification of N, S1, and RBD of SARS-CoV-2 from Mammalian Cells and Their Potential Applications

by Julio García-Cordero, Juvenal Mendoza-Ramírez, David Fernández-Benavides, Daniela Roa-Velazquez, Jessica Filisola-Villaseñor, Sandra Paola Martínez-Frías, Erik Saul Sanchez-Salguero, Carlos E. Miguel-Rodríguez, Jose L. Maravillas Montero, Jose J. Torres-Ruiz, Diana Gómez-Martín, Leopoldo Santos Argumedo, Edgar Morales-Ríos, Juan M. Alvarado-Orozco and Leticia Cedillo-Barrón

Diagnostics 2021, 11(10), 1808; https://doi.org/10.3390/diagnostics11101808 - 30 Sep 2021

Cited by 13 | Viewed by 6045

Abstract

The coronavirus disease 2019 (COVID-19) pandemic has reached an unprecedented level. There is a strong demand for diagnostic and serological supplies worldwide, making it necessary for countries to establish their own technologies to produce high-quality biomolecules. The two main viral antigens used for [...] Read more.

The coronavirus disease 2019 (COVID-19) pandemic has reached an unprecedented level. There is a strong demand for diagnostic and serological supplies worldwide, making it necessary for countries to establish their own technologies to produce high-quality biomolecules. The two main viral antigens used for the diagnostics for severe acute respiratory syndrome coronavirus (SARS-CoV-2) are the structural proteins spike (S) protein and nucleocapsid (N) protein. The spike protein of SARS-CoV-2 is cleaved into S1 and S2, in which the S1 subunit has the receptor-binding domain (RBD), which induces the production of neutralizing antibodies, whereas nucleocapsid is an ideal target for viral antigen-based detection. In this study, we designed plasmids, pcDNA3.1/S1 and pcDNA3.1/N, and optimized their expression of the recombinant S1 and N proteins from SARS-CoV-2 in a mammalian system. The RBD was used as a control. The antigens were successfully purified from Expi293 cells, with high yields of the S1, N, and RBD proteins. The immunogenic abilities of these proteins were demonstrated in a mouse model. Further, enzyme-linked immunosorbent assays with human serum samples showed that the SARS-CoV-2 antigens are a suitable alternative for serological assays to identify patients infected with COVID-19. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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16 pages, 2929 KiB

Open AccessArticle

Forecasting COVID-19 Severity by Intelligent Optical Fingerprinting of Blood Samples

by Simão P. Faria, Cristiana Carpinteiro, Vanessa Pinto, Sandra M. Rodrigues, José Alves, Filipe Marques, Marta Lourenço, Paulo H. Santos, Angélica Ramos, Maria J. Cardoso, João T. Guimarães, Sara Rocha, Paula Sampaio, David A. Clifton, Mehak Mumtaz and Joana S. Paiva

Diagnostics 2021, 11(8), 1309; https://doi.org/10.3390/diagnostics11081309 - 21 Jul 2021

Cited by 5 | Viewed by 3797

Abstract

Forecasting COVID-19 disease severity is key to supporting clinical decision making and assisting resource allocation, particularly in intensive care units (ICUs). Here, we investigated the utility of time- and frequency-related features of the backscattered signal of serum patient samples to predict COVID-19 disease [...] Read more.

Forecasting COVID-19 disease severity is key to supporting clinical decision making and assisting resource allocation, particularly in intensive care units (ICUs). Here, we investigated the utility of time- and frequency-related features of the backscattered signal of serum patient samples to predict COVID-19 disease severity immediately after diagnosis. ICU admission was the primary outcome used to define disease severity. We developed a stacking ensemble machine learning model including the backscattered signal features (optical fingerprint), patient comorbidities, and age (AUROC = 0.80), which significantly outperformed the predictive value of clinical and laboratory variables available at hospital admission (AUROC = 0.71). The information derived from patient optical fingerprints was not strongly correlated with any clinical/laboratory variable, suggesting that optical fingerprinting brings unique information for COVID-19 severity risk assessment. Optical fingerprinting is a label-free, real-time, and low-cost technology that can be easily integrated as a front-line tool to facilitate the triage and clinical management of COVID-19 patients. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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10 pages, 2618 KiB

Open AccessArticle

Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR

by Agathe Boudet, Robin Stephan, Sophie Bravo, Milène Sasso and Jean-Philippe Lavigne

Diagnostics 2021, 11(7), 1241; https://doi.org/10.3390/diagnostics11071241 - 12 Jul 2021

Cited by 12 | Viewed by 3302

Abstract

Since January 2021, the diffusion of the most propagated SARS-CoV-2 variants in France (UK variant 20I/501Y.V1 (lineage B.1.1.7), 20H/H501Y.V2 (lineage B.1.351) and 20J/H501Y.V3 (lineage P.1)) were urgently screened, needing a surveillance with an RT-PCR screening assay. In this study, we evaluated one RT-PCR [...] Read more.

Since January 2021, the diffusion of the most propagated SARS-CoV-2 variants in France (UK variant 20I/501Y.V1 (lineage B.1.1.7), 20H/H501Y.V2 (lineage B.1.351) and 20J/H501Y.V3 (lineage P.1)) were urgently screened, needing a surveillance with an RT-PCR screening assay. In this study, we evaluated one RT-PCR kit for this screening (ID SARS-CoV-2/UK/SA Variant Triplex^®, ID Solutions, Grabels, France) on 2207 nasopharyngeal samples that were positive for SARS-CoV-2. Using ID Solutions kit, 4.1% (92/2207) of samples were suspected to belonged to B.1.351 or P.1 variants. Next-generation sequencing that was performed on 67.4% (62/92) of these samples confirmed the presence of a B.1.351 variant in only 75.8% of the samples (47/62). Thirteen samples belonged to the UK variant (B.1.1.7), and two to A.27 with N501Y mutation. The thirteen with the UK variant presented one mutation in the S-gene, near the ΔH69/ΔV70 deletion (S71F or A67S), which impacted the detection of ΔH69/ΔV70 deletion. Using another screening kit (PKampVariantDetect SARS-CoV-2 RT-PCR combination 1 and 3^® PerkinElmer, Waltham, MA, USA) on the misidentified samples, we observed that the two mutations, S71F or A67S, did not impact the detection of the UK variant. In conclusion, this study highlights the limitations of the screening strategy based on the detection of few mutations/deletions as well as it not being able to follow the virus evolution. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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9 pages, 572 KiB

Open AccessArticle

SARS-CoV-2 Antigen Detection to Expand Testing Capacity for COVID-19: Results from a Hospital Emergency Department Testing Site

by Giulia Menchinelli, Giulia De Angelis, Margherita Cacaci, Flora Marzia Liotti, Marcello Candelli, Ivana Palucci, Rosaria Santangelo, Maurizio Sanguinetti, Giuseppe Vetrugno, Francesco Franceschi and Brunella Posteraro

Diagnostics 2021, 11(7), 1211; https://doi.org/10.3390/diagnostics11071211 - 05 Jul 2021

Cited by 10 | Viewed by 3664

Abstract

Background: SARS-CoV-2 antigen detection has currently expanded the testing capacity for COVID-19, which yet relies on the SARS-CoV-2 RNA RT-PCR amplification. Objectives: To report on a COVID-19 testing algorithm from a tertiary care hospital emergency department (ED) that combines both antigen (performed on [...] Read more.

Background: SARS-CoV-2 antigen detection has currently expanded the testing capacity for COVID-19, which yet relies on the SARS-CoV-2 RNA RT-PCR amplification. Objectives: To report on a COVID-19 testing algorithm from a tertiary care hospital emergency department (ED) that combines both antigen (performed on the ED) and RT-PCR (performed outside the ED) testing. Methods: Between December 2020 and January 2021, in a priori designated, spatially separated COVID-19 or non-COVID-19 ED areas, respectively, symptomatic or asymptomatic patients received SARS-CoV-2 antigen testing on nasopharyngeal swab samples. Antigen results were promptly accessible to guide subsequent, outside performed confirmatory (RT-PCR) testing. Results: Overall, 1083 (100%) of 1083 samples in the COVID-19 area and 1815 (49.4%) of 3670 samples in the non-COVID-19 area had antigen results that required confirmation by RT-PCR. Antigen positivity rates were 12.4% (134/1083) and 3.7% (66/1815), respectively. Compared to RT-PCR testing results, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of antigen testing were, respectively, 68.0%, 98.3%, 88.8%, and 94.1% in the COVID-19 area, and 41.9%, 97.3%, 27.3%, and 98.6% in non-COVID-19 area. Practically, RT-PCR tests were avoided in 50.6% (1855/3670) of non-COVID-19 area samples (all antigen negative) from patients who, otherwise, would have needed antigen result confirmation. Conclusions: Our algorithm had value to preserve RT-PCR from avoidable usage and, importantly, to save time, which translated into a timely RT-PCR result availability in the COVID-19 area. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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12 pages, 1459 KiB

Open AccessArticle

Sample-Pooling Strategy for SARS-CoV-2 Detection among Students and Staff of the University of Sannio

by Immacolata Polvere, Elena Silvestri, Lina Sabatino, Antonia Giacco, Stefania Iervolino, Teresa Peluso, Rosa Guida, Lucrezia Zerillo, Romualdo Varricchio, Silvia D’Andrea, Serena Voccola, Jessica Raffaella Madera, Alberto Zullo, Romania Stilo, Pasquale Vito and Tiziana Zotti

Diagnostics 2021, 11(7), 1166; https://doi.org/10.3390/diagnostics11071166 - 26 Jun 2021

Cited by 4 | Viewed by 1996

Abstract

Since the beginning of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, it has been clear that testing large groups of the population was the key to stem infection and prevent the effects of the coronavirus disease of 2019, mostly among sensitive [...] Read more.

Since the beginning of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, it has been clear that testing large groups of the population was the key to stem infection and prevent the effects of the coronavirus disease of 2019, mostly among sensitive patients. On the other hand, time and cost-sustainability of virus detection by molecular analysis such as reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) may be a major issue if testing is extended to large communities, mainly asymptomatic large communities. In this context, sample-pooling and test grouping could offer an effective solution. Here we report the screening on 1195 oral-nasopharyngeal swabs collected from students and staff of the Università degli Studi del Sannio (University of Sannio, Benevento, Campania, Italy) and analyzed by an in-house developed multiplex RT-qPCR for SARS-CoV-2 detection through a simple monodimensional sample pooling strategy. Overall, 400 distinct pools were generated and, within 24 h after swab collection, five positive samples were identified. Out of them, four were confirmed by using a commercially available kit suitable for in vitro diagnostic use (IVD). High accuracy, sensitivity and specificity were also determined by comparing our results with a reference IVD assay for all deconvoluted samples. Overall, we conducted 463 analyses instead of 1195, reducing testing resources by more than 60% without lengthening diagnosis time and without significant losses in sensitivity, suggesting that our strategy was successful in recognizing positive cases in a community of asymptomatic individuals with minor requirements of reagents and time when compared to normal testing procedures. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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12 pages, 1314 KiB

Open AccessArticle

Post-Mortem Detection of SARS-CoV-2 RNA in Long-Buried Lung Samples

by Nicolò Musso, Luca Falzone, Stefano Stracquadanio, Dafne Bongiorno, Monica Salerno, Massimiliano Esposito, Francesco Sessa, Massimo Libra, Stefania Stefani and Cristoforo Pomara

Diagnostics 2021, 11(7), 1158; https://doi.org/10.3390/diagnostics11071158 - 24 Jun 2021

Cited by 22 | Viewed by 2923

Abstract

The Coronavirus Disease 19 (COVID-19) pandemic has caused an unexpected death toll worldwide. Even though several guidelines for the management of infectious corpses have been proposed, the limited number of post-mortem analyses during the pandemic has led to inaccuracies in the counting of [...] Read more.

The Coronavirus Disease 19 (COVID-19) pandemic has caused an unexpected death toll worldwide. Even though several guidelines for the management of infectious corpses have been proposed, the limited number of post-mortem analyses during the pandemic has led to inaccuracies in the counting of COVID-19 deaths and contributed to a lack of important information about the pathophysiology of the SARS-CoV-2 infection. Due to the impossibility of carrying out autopsies on all corpses, the scientific community has raised the question of whether confirmatory analyses could be performed on exhumed bodies after a long period of burial to assess the presence of SARS-CoV-2 RNA. Post-mortem lung samples were collected from 16 patients who died from COVID-19 infection and were buried for a long period of time. A custom RNA extraction protocol was developed to enhance extraction of viral RNA from degraded samples and highly sensitive molecular methods, including RT-qPCR and droplet digital PCR (ddPCR), were used to detect the presence of SARS-CoV-2 RNA. The custom extraction protocol developed allowed us to extract total RNA effectively from all lung samples collected. SARS-CoV-2 viral RNA was effectively detected in all samples by both RT-qPCR and ddPCR, regardless of the length of burial. ddPCR results confirmed the persistence of the virus in this anatomical niche and revealed high viral loads in some lung samples, suggesting active infection at the time of death. To the best of our knowledge, this is the first study to demonstrate the persistence of SARS-CoV-2 viral RNA in the lung even after a long post-mortem interval (up to 78 days). The extraction protocol herein described, and the highly sensitive molecular analyses performed, could represent the standard procedures for SARS-CoV-2 detection in degraded lung specimens. Finally, the innovative results obtained encourage post-mortem confirmatory analyses even after a long post-mortem interval. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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11 pages, 2368 KiB

Open AccessArticle

Assay System for Simultaneous Detection of SARS-CoV-2 and Other Respiratory Viruses

by Ho-Jae Lim, Jung-Eun Park, Min-Young Park, Joo-Hwan Baek, Sunkyung Jung, Nackmoon Sung, Jae-Hyun Yang, Min-Woo Lee, Sun-Hwa Lee and Yong-Jin Yang

Diagnostics 2021, 11(6), 1084; https://doi.org/10.3390/diagnostics11061084 - 13 Jun 2021

Cited by 10 | Viewed by 5299

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81–104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland–Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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13 pages, 8670 KiB

Open AccessArticle

Risk Stratification for ECMO Requirement in COVID-19 ICU Patients Using Quantitative Imaging Features in CT Scans on Admission

by Eva Gresser, Jakob Reich, Bastian O. Sabel, Wolfgang G. Kunz, Matthias P. Fabritius, Johannes Rübenthaler, Michael Ingrisch, Dietmar Wassilowsky, Michael Irlbeck, Jens Ricke and Daniel Puhr-Westerheide

Diagnostics 2021, 11(6), 1029; https://doi.org/10.3390/diagnostics11061029 - 03 Jun 2021

Cited by 8 | Viewed by 2293

Abstract

(1) Background: Extracorporeal membrane oxygenation (ECMO) therapy in intensive care units (ICUs) remains the last treatment option for Coronavirus disease 2019 (COVID-19) patients with severely affected lungs but is highly resource demanding. Early risk stratification for the need of ECMO therapy upon admission [...] Read more.

(1) Background: Extracorporeal membrane oxygenation (ECMO) therapy in intensive care units (ICUs) remains the last treatment option for Coronavirus disease 2019 (COVID-19) patients with severely affected lungs but is highly resource demanding. Early risk stratification for the need of ECMO therapy upon admission to the hospital using artificial intelligence (AI)-based computed tomography (CT) assessment and clinical scores is beneficial for patient assessment and resource management; (2) Methods: Retrospective single-center study with 95 confirmed COVID-19 patients admitted to the participating ICUs. Patients requiring ECMO therapy (n = 14) during ICU stay versus patients without ECMO treatment (n = 81) were evaluated for discriminative clinical prediction parameters and AI-based CT imaging features and their diagnostic potential to predict ECMO therapy. Reported patient data include clinical scores, AI-based CT findings and patient outcomes; (3) Results: Patients subsequently allocated to ECMO therapy had significantly higher sequential organ failure (SOFA) scores (p < 0.001) and significantly lower oxygenation indices on admission (p = 0.009) than patients with standard ICU therapy. The median time from hospital admission to ECMO placement was 1.4 days (IQR 0.2–4.0). The percentage of lung involvement on AI-based CT assessment on admission to the hospital was significantly higher in ECMO patients (p < 0.001). In binary logistic regression analyses for ECMO prediction including age, sex, body mass index (BMI), SOFA score on admission, lactate on admission and percentage of lung involvement on admission CTs, only SOFA score (OR 1.32, 95% CI 1.08–1.62) and lung involvement (OR 1.06, 95% CI 1.01–1.11) were significantly associated with subsequent ECMO allocation. Receiver operating characteristic (ROC) curves showed an area under the curve (AUC) of 0.83 (95% CI 0.73–0.94) for lung involvement on admission CT and 0.82 (95% CI 0.72–0.91) for SOFA scores on ICU admission. A combined parameter of SOFA on ICU admission and lung involvement on admission CT yielded an AUC of 0.91 (0.84–0.97) with a sensitivity of 0.93 and a specificity of 0.84 for ECMO prediction; (4) Conclusions: AI-based assessment of lung involvement on CT scans on admission to the hospital and SOFA scoring, especially if combined, can be used as risk stratification tools for subsequent requirement for ECMO therapy in patients with severe COVID-19 disease to improve resource management in ICU settings. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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9 pages, 222 KiB

Open AccessArticle

Clinical Application of a New SARS-CoV-2 Antigen Detection Kit (Colloidal Gold) in the Detection of COVID-19

by Evangelos Terpos, Ioannis Ntanasis-Stathopoulos and Miha Skvarč

Diagnostics 2021, 11(6), 995; https://doi.org/10.3390/diagnostics11060995 - 30 May 2021

Cited by 17 | Viewed by 4544

Abstract

The precise diagnosis of COVID-19 is of outmost importance in order to effectively treat patients and prevent SARS-CoV-2 transmission. Herein, we evaluated the sensitivity and specificity of the COVID-19 Antigen Detection Kit (Colloidal Gold—CG) compared with PCR in nasopharyngeal and nasal samples. A [...] Read more.

The precise diagnosis of COVID-19 is of outmost importance in order to effectively treat patients and prevent SARS-CoV-2 transmission. Herein, we evaluated the sensitivity and specificity of the COVID-19 Antigen Detection Kit (Colloidal Gold—CG) compared with PCR in nasopharyngeal and nasal samples. A total of 114 positive and 244 negative nasopharyngeal specimens confirmed by PCR were used in this comparative study. When the PCR positive Cycle Threshold (Ct) value was ≤25, CG sensitivity was 100%. When the PCR positive Ct value was ≤33, CG sensitivity was 99%. When the PCR positive Ct value was ≤40, CG sensitivity was 89.47%. Regarding nasal swabs, a total of 109 positive and 250 negative specimens confirmed by PCR were used. When the PCR positive Ct value was ≤25, CG sensitivity was 100%. When the PCR positive Ct value was ≤33, CG sensitivity was 96.12%. When the PCR positive Ct value was ≤37, CG sensitivity was 91.74%. Specificity was above 99% regardless of the Ct value of PCR positivity for both nasopharyngeal and nasal specimens. Overall, the CG showed high sensitivity and specificity when the PCR Ct value was less than 33. Therefore, CG can be used for screening early in the disease course. Confirmatory PCR is essential when a false negative result is suspected. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

8 pages, 688 KiB

Open AccessCommunication

Presence of SARS-CoV-2 Nucleoprotein in Cardiac Tissues of Donors with Negative COVID-19 Molecular Tests

by Gianluca Lorenzo Perrucci, Elena Sommariva, Veronica Ricci, Paola Songia, Yuri D’Alessandra, Paolo Poggio, Giulio Pompilio, Gianluca Polvani and Anna Guarino

Diagnostics 2021, 11(4), 731; https://doi.org/10.3390/diagnostics11040731 - 20 Apr 2021

Cited by 5 | Viewed by 2128

Abstract

The 2019 Coronavirus disease (COVID-19) outbreak had detrimental effects on essential medical services such as organ and tissue donation. Lombardy, one of the most active Italian regions in organ/tissue procurement, has been strongly affected by the COVID-19 pandemic. To date, data concerning the [...] Read more.

The 2019 Coronavirus disease (COVID-19) outbreak had detrimental effects on essential medical services such as organ and tissue donation. Lombardy, one of the most active Italian regions in organ/tissue procurement, has been strongly affected by the COVID-19 pandemic. To date, data concerning the risk of SARS-CoV-2 transmission after tissue transplantation are controversial. Here, we aimed to evaluate the presence/absence of SARS-CoV-2 in different cardiac tissues eligible for transplantation obtained from Lombard donors. We used cardiovascular tissues from eight donors potentially suitable for pulmonary valve transplantation. All donor subjects involved in the study returned negative results for the SARS-CoV-2 RNA molecular tests (quantitative real-time reverse-transcription PCR, qRT-PCR, and chip-based digital PCR) in nasopharyngeal swabs (NPS) or bronchoalveolar lavage (BAL). None of the eight donors included in this study revealed the presence of the SARS-CoV-2 viral genome. However, evaluation of the protein content of pulmonary vein wall (PVW) tissue revealed variable levels of SARS-CoV-2 nucleoprotein signal in all donors. Our study demonstrated for the first time, to the best of our knowledge, that viral nucleoprotein but not viral RNA was present in the examined tissue bank specimens, suggesting the need for caution and in-depth investigations on implantable tissue specimens collected during the COVID-19 pandemic period. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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14 pages, 2097 KiB

Open AccessArticle

Safe Management Strategies in Clinical Forensic Autopsies of Confirmed COVID-19 Cases

by Cristoforo Pomara, Monica Salerno, Francesco Sessa, Massimiliano Esposito, Martina Barchitta, Caterina Ledda, Patrizia Grassi, Aldo Liberto, Anna Rita Mattaliano, Venerando Rapisarda, Margherita Ferrante and Antonella Agodi

Diagnostics 2021, 11(3), 457; https://doi.org/10.3390/diagnostics11030457 - 06 Mar 2021

Cited by 20 | Viewed by 3149

Abstract

To date, there is poor evidence on the transmission of infection in individuals handling the bodies of deceased persons infected with SARS-CoV-2 and in particular, during autopsies. The aim of this study was to demonstrate that when appropriate strategies are adopted autopsy is [...] Read more.

To date, there is poor evidence on the transmission of infection in individuals handling the bodies of deceased persons infected with SARS-CoV-2 and in particular, during autopsies. The aim of this study was to demonstrate that when appropriate strategies are adopted autopsy is a safe procedure with a minimal infection risk for all subjects involved (pathologists, technical personnel, and others) when proper strategies are adopted. We performed 16 autopsies on cadavers of persons who had died with confirmed COVID-19 with different post-mortem intervals (PMI). To confirm the presence of SARS-CoV-2 RNA, for each autopsy, 2 swabs were sampled from lungs, while to evaluate environmental contamination, 11 swabs were taken at three different times: T0 (before autopsy), T1 (at the end of the autopsy, without removing the corpse), and T2 (after cleaning and disinfecting the autopsy room). Specifically, 2 swabs were sampled on face shields used by each pathologist, and 4 swabs were collected on the autopsy table; 4 swabs were also collected from walls and 1 from floor. Lung swabs confirmed the presence of SARS-CoV-2 RNA in all cases. Environmental swabs, collected at T0 and T2 were all negative, while swabs sampled at T1 were shown to be positive. Interestingly, no association was shown between PMI length and environmental contamination. Infection control strategies for safe management of clinical forensic autopsies of bodies with suspected or confirmed COVID-19 are also described. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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Review

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17 pages, 1591 KiB

Open AccessReview

Detection of COVID-19 Virus on Surfaces Using Photonics: Challenges and Perspectives

by Bakr Ahmed Taha, Yousif Al Mashhadany, Nur Nadia Bachok, Ahmad Ashrif A Bakar, Mohd Hadri Hafiz Mokhtar, Mohd Saiful Dzulkefly Bin Zan and Norhana Arsad

Diagnostics 2021, 11(6), 1119; https://doi.org/10.3390/diagnostics11061119 - 19 Jun 2021

Cited by 34 | Viewed by 5785

Abstract

The propagation of viruses has become a global threat as proven through the coronavirus disease (COVID-19) pandemic. Therefore, the quick detection of viral diseases and infections could be necessary. This study aims to develop a framework for virus diagnoses based on integrating photonics [...] Read more.

The propagation of viruses has become a global threat as proven through the coronavirus disease (COVID-19) pandemic. Therefore, the quick detection of viral diseases and infections could be necessary. This study aims to develop a framework for virus diagnoses based on integrating photonics technology with artificial intelligence to enhance healthcare in public areas, marketplaces, hospitals, and airfields due to the distinct spectral signatures from lasers’ effectiveness in the classification and monitoring of viruses. However, providing insights into the technical aspect also helps researchers identify the possibilities and difficulties in this field. The contents of this study were collected from six authoritative databases: Web of Science, IEEE Xplore, Science Direct, Scopus, PubMed Central, and Google Scholar. This review includes an analysis and summary of laser techniques to diagnose COVID-19 such as fluorescence methods, surface-enhanced Raman scattering, surface plasmon resonance, and integration of Raman scattering with SPR techniques. Finally, we select the best strategies that could potentially be the most effective methods of reducing epidemic spreading and improving healthcare in the environment. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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13 pages, 1313 KiB

Open AccessReview

Test Groups, Not Individuals: A Review of the Pooling Approaches for SARS-CoV-2 Diagnosis

by Renato Millioni and Cinzia Mortarino

Diagnostics 2021, 11(1), 68; https://doi.org/10.3390/diagnostics11010068 - 04 Jan 2021

Cited by 9 | Viewed by 2774

Abstract

Massive molecular testing for SARS-CoV-2 diagnosis is mandatory to manage the spread of COVID-19. Diagnostic screening should be performed at a mass scale, extended to the asymptomatic population, and repeated over time. An accurate diagnostic pipeline for SARS-CoV-2 that could massively increase the [...] Read more.

Massive molecular testing for SARS-CoV-2 diagnosis is mandatory to manage the spread of COVID-19. Diagnostic screening should be performed at a mass scale, extended to the asymptomatic population, and repeated over time. An accurate diagnostic pipeline for SARS-CoV-2 that could massively increase the laboratory efficiency, while being sustainable in terms of time and costs, should be based on a pooling strategy. In the past few months, researchers from different disciplines had this same idea: test groups, not individuals. This critical review intends to highlight both the general consents—even if the results from different publications have been obtained with different protocols—and the points of disagreement that are creating some interpretative/comprehension difficulties. Different pooling schemes and technical aspects associated to the type of pooling adopted are described and discussed. We hope that this review can consolidate information to support researchers in designing optimized COVID-19 testing protocols based on pooling. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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Other

Jump to: Research, Review

17 pages, 1588 KiB

Open AccessSystematic Review

Diagnostic Performance of Antigen Rapid Diagnostic Tests, Chest Computed Tomography, and Lung Point-of-Care-Ultrasonography for SARS-CoV-2 Compared with RT-PCR Testing: A Systematic Review and Network Meta-Analysis

by Sung Ryul Shim, Seong-Jang Kim, Myunghee Hong, Jonghoo Lee, Min-Gyu Kang and Hyun Wook Han

Diagnostics 2022, 12(6), 1302; https://doi.org/10.3390/diagnostics12061302 - 24 May 2022

Cited by 3 | Viewed by 2865

Abstract

(1) Background: The comparative performance of various diagnostic methods for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection remains unclear. This study aimed to investigate the comparison of the 3 index test performances of rapid antigen diagnostic tests (RDTs), chest computed tomography (CT), and [...] Read more.

(1) Background: The comparative performance of various diagnostic methods for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection remains unclear. This study aimed to investigate the comparison of the 3 index test performances of rapid antigen diagnostic tests (RDTs), chest computed tomography (CT), and lung point-of-care-ultrasonography (US) with reverse transcription-polymerase chain reaction (RT-PCR), the reference standard, to provide more evidence-based data on the appropriate use of these index tests. (2) Methods: We retrieved data from electronic literature searches of PubMed, Cochrane Library, and EMBASE from 1 January 2020, to 1 April 2021. Diagnostic performance was examined using bivariate random-effects diagnostic test accuracy (DTA) and Bayesian network meta-analysis (NMA) models. (3) Results: Of the 3992 studies identified in our search, 118 including 69,445 participants met our selection criteria. Among these, 69 RDT, 38 CT, and 15 US studies in the pairwise meta-analysis were included for DTA with NMA. CT and US had high sensitivity of 0.852 (95% credible interval (CrI), 0.791–0.914) and 0.879 (95% CrI, 0.784–0.973), respectively. RDT had high specificity, 0.978 (95% CrI, 0.960–0.996). In accuracy assessment, RDT and CT had a relatively higher than US. However, there was no significant difference in accuracy between the 3 index tests. (4) Conclusions: This meta-analysis suggests that, compared with the reference standard RT-PCR, the 3 index tests (RDTs, chest CT, and lung US) had similar and complementary performances for diagnosis of SARS-CoV-2 infection. To manage and control COVID-19 effectively, future large-scale prospective studies could be used to obtain an optimal timely diagnostic process that identifies the condition of the patient accurately. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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9 pages, 2639 KiB

Open AccessCase Report

Implementation of a Rapid RT-LAMP Saliva-Based SARS-CoV-2 Testing Program in the Workplace

by Bradley W. M. Cook, Kaitlyn Kobasa, Marielou Tamayo, Natasha Theriault, Diane Gordon Pappas and Steven S. Theriault

Diagnostics 2022, 12(2), 474; https://doi.org/10.3390/diagnostics12020474 - 12 Feb 2022

Cited by 3 | Viewed by 1748

Abstract

Rising SARS-CoV-2 cases, testing delays, and the risk of pre-symptomatic and asymptomatic transmission provided the impetus for an in-house rapid testing program. Employees and their household contacts were encouraged to self-collect saliva samples that were pooled for routine testing using an established colorimetric [...] Read more.

Rising SARS-CoV-2 cases, testing delays, and the risk of pre-symptomatic and asymptomatic transmission provided the impetus for an in-house rapid testing program. Employees and their household contacts were encouraged to self-collect saliva samples that were pooled for routine testing using an established colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. In brief, individual or a maximum of four saliva samples were pooled and heat-inactivated to render microorganisms, especially SARS-CoV-2, non-infectious prior to being added to RT-LAMP assay tubes containing either the human sample control gene, RNase P, or a region of the SARS-CoV-2 gene, ORF1ab. During the second wave of SARS-CoV-2 infections in November 2020, two samples from an employee and a member of their household tested positive via RT-LAMP within two days of each other. A delayed clinical qRT-PCR test confirmation of both individuals 5 days later underscored the power of routine rapid testing with within-the-hour turnaround times. Workplace rapid testing programs using RT-LAMP are flexible in their design, have a reduced cost compared to qRT-PCR, may involve non-invasive self-saliva collection for increased safety for the testing personnel, and can be performed with minimal training. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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8 pages, 206 KiB

Open AccessBrief Report

Prospective Observational COVID-19 Screening and Monitoring of Asymptomatic Cancer Center Health-Care Workers with a Rapid Serological Test

by Angelo Virgilio Paradiso, Simona De Summa, Nicola Silvestris, Stefania Tommasi, Antonio Tufaro, Angela Maria Vittoria Larocca, Vincenzo D’Addabbo, Donata Raffaele, Vito Cafagna, Vito Michele Garrisi and Giuseppe De Palma

Diagnostics 2021, 11(6), 975; https://doi.org/10.3390/diagnostics11060975 - 28 May 2021

Cited by 5 | Viewed by 2156

Abstract

Health-care workers (HCW) are at high risk for SARS-CoV-2 infection and, if asymptomatic, for transmitting the virus to fragile cancer patients. We monitored all asymptomatic HCWs of a cancer institute (94% of all employees agreed to enter the study) with the rapid serological [...] Read more.

Health-care workers (HCW) are at high risk for SARS-CoV-2 infection and, if asymptomatic, for transmitting the virus to fragile cancer patients. We monitored all asymptomatic HCWs of a cancer institute (94% of all employees agreed to enter the study) with the rapid serological test, VivaDiag^TM, identifying SARS-CoV-2 associated-IgM/IgG. The tests were performed at time 0 (n = 606) and after 14 days (n = 393). Overall, the VivaDiag^TM results of nine HCWs (1.5%) were positive, with one confirmed to be SARS-CoV-2-positive after oropharyngeal swab testing by RT-PCR. At time 0, all nine cases showed IgM expression while IgG was detected in only one. After 14 days, IgM persisted in all the cases, while IgG became evident in four. A chemiluminescence immunoassay (CLIA) confirmed IgM positivity in 5/13 VivaDiag^TM positive cases and IgG positivity in 4/5 VivaDiag^TM positive cases. Our study suggests that the VivaDiag^TM test can be of help in identifying SARS-CoV-2 infected people in cohorts of subjects with a high prevalence. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

7 pages, 784 KiB

Open AccessBrief Report

Seroprevalence of Anti-SARS-CoV-2 IgG and IgM among Adults over 65 Years Old in the South of Italy

by Immacolata Polvere, Alfredina Parrella, Giovanna Casamassa, Silvia D’Andrea, Annamaria Tizzano, Gaetano Cardinale, Serena Voccola, Piercarmine Porcaro, Romania Stilo, Pasquale Vito and Tiziana Zotti

Diagnostics 2021, 11(3), 483; https://doi.org/10.3390/diagnostics11030483 - 09 Mar 2021

Cited by 11 | Viewed by 2076

Abstract

SARS-CoV-2 is a zoonotic betacoronavirus associated with worldwide transmission of COVID-19 disease. By the beginning of March, WHO reported about 113,820,000 confirmed cases including more than 2,527,000 deaths all over the world. However, the true extent of virus circulation or its real infection/fatality [...] Read more.

SARS-CoV-2 is a zoonotic betacoronavirus associated with worldwide transmission of COVID-19 disease. By the beginning of March, WHO reported about 113,820,000 confirmed cases including more than 2,527,000 deaths all over the world. However, the true extent of virus circulation or its real infection/fatality ratio is not well-estimated due to the huge portion of asymptomatic infections. In this observational study, we have estimated the prevalence of specific immunoglobulin M and G directed towards SARS-CoV-2 antigen in a cohort of 1383 adult volunteers aged over 65 years old, living in the district of Benevento, in the South of Italy. Serological screening was carried out on capillary blood in September 2020, seven months after pandemic outbreak in Italy, to evaluate virus circulation and antibody response among elderly adults, in which severe symptoms due to viral infection are more common. The overall seroprevalence of anti-SARS-CoV-2 antibodies was 4.70% (CI 3.70%–5.95%) with no statistically significant differences between sexes. Among these, 69.69% (CI 55.61%–77.80%) tested positive to IgM, 23.08% (CI 14.51%–34.64%) to IgG and 9.23% (CI 4.30%–18.71%) was positive for both. All patients that were positive to IgM underwent molecular testing through RT-qPCR on oral-rhino pharyngeal swabs and only one specimen was positive for SARS-CoV-2 RNA detection. Instead, the presence of IgG from screened volunteers was confirmed by re-testing serum samples using both an ELISA assay validated for in vitro diagnostic use (IVD) and a recently published synthetic peptide-based ELISA assay. In conclusion, our report suggests that (1) early restrictions were successful in limiting COVID-19 diffusion in the district of Benevento; (2) rapid serological analysis is an ideal testing for both determining real seroprevalence and massive screening, whereas detection of viral RNA remains a gold standard for identification of infected patients; (3) even among people without COVID-19 related symptoms, the antibody response against SARS-CoV-2 antigens has individual features. Full article

(This article belongs to the Special Issue Surveillance Strategies and Diagnostic Procedures: Integrated Approaches to Manage the COVID-19 Outbreak)

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