SARS-CoV-2 Identification by Diagnostic/Medical Laboratory: Methods, Statistics, Interesting Cases

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Diagnostic Microbiology and Infectious Disease".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 147548

Special Issue Editor

Department of Biomedical Research, Molecular Diagnostics Laboratory, National Medicines Institute, Warsaw, Poland
Interests: SARS-CoV-2; enterobacterales; antibiotic resistance; ß-lactamases; carbapenemases

Special Issue Information

Dear Colleagues,

The global spread of a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes severe upper respiratory tract infection, coronavirus disease 2019 (COVID-19) is a public health problem of great concern. This virus was initially identified in China in December 2019 and soon thereafter, in March 2020, the World Health Organization declared COVID-19 a pandemic. The detection of viral RNA by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) is considered the gold standard for screening and diagnosing this infection in humans. New serological tests are also helpful as a complementary COVID-19 diagnostic tool and/or may play a significant role in post-vaccine immune response studies. The introduction of effective vaccines against SARS-CoV-2 is expected to prevent the incidence of this disease, ultimately leading to community protection. Recently, various vaccines have become available to protect against COVID-19; an important question is whether these vaccines will also prevent transmission of the virus.

The purpose of this Special Issue is to publish studies on the diagnostic methods of SARS-CoV-2, identification of new variants of the virus, results of laboratory statistics, and interesting cases of patients with COVID-19. Original research, case reports and review articles summarizing the state of the knowledge on SARS-CoV-2 are welcome.

Prof. Dr. Anna Baraniak
Guest Editor

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Published Papers (64 papers)

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15 pages, 2246 KiB  
Article
Investigating the Use of SARS-CoV-2 (COVID-19) Odor Expression as a Non-Invasive Diagnostic Tool—Pilot Study
by Janet Crespo-Cajigas, Vidia A. Gokool, Andrea Ramírez Torres, Liam Forsythe, Benjamin S. Abella, Howard K. Holness, Alan T. Charlie Johnson, Richard Postrel and Kenneth G. Furton
Diagnostics 2023, 13(4), 707; https://doi.org/10.3390/diagnostics13040707 - 13 Feb 2023
Cited by 2 | Viewed by 1767
Abstract
Since the beginning of the COVID-19 pandemic, there has been enormous interest in the development of measures that would allow for the swift detection of the disease. The rapid screening and preliminary diagnosis of SARS-CoV-2 infection allow for the instant identification of possibly [...] Read more.
Since the beginning of the COVID-19 pandemic, there has been enormous interest in the development of measures that would allow for the swift detection of the disease. The rapid screening and preliminary diagnosis of SARS-CoV-2 infection allow for the instant identification of possibly infected individuals and the subsequent mitigation of the disease spread. Herein, the detection of SARS-CoV-2-infected individuals was explored using noninvasive sampling and low-preparatory-work analytical instrumentation. Hand odor samples were obtained from SARS-CoV-2-positive and -negative individuals. The volatile organic compounds (VOCs) were extracted from the collected hand odor samples using solid phase microextraction (SPME) and analyzed using gas chromatography coupled with mass spectrometry (GC-MS). Sparse partial least squares discriminant analysis (sPLS-DA) was used to develop predictive models using the suspected variant sample subsets. The developed sPLS-DA models performed moderately (75.8% (±0.4) accuracy, 81.8% sensitivity, 69.7% specificity) at distinguishing between SARS-CoV-2-positive and negative -individuals based on the VOC signatures alone. Potential markers for distinguishing between infection statuses were preliminarily acquired using this multivariate data analysis. This work highlights the potential of using odor signatures as a diagnostic tool and sets the groundwork for the optimization of other rapid screening sensors such as e-noses or detection canines. Full article
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8 pages, 1025 KiB  
Communication
SARS-CoV-2 Detection via RT-PCR in Matched Saliva and Nasopharyngeal Samples Reveals High Concordance in Different Commercial Assays
by Karoline Almeida Felix de Sousa, Carolina Kymie Vasques Nonaka, Renata Naves de Ávila Mendonça, Verena Neiva Mascarenhas, Thamires Gomes Lopes Weber, Carlos Gustavo Regis Silva, Ana Verena Almeida Mendes, Ricardo Khouri, Bruno Solano Freitas Souza and Clarissa Araújo Gurgel Rocha
Diagnostics 2023, 13(2), 329; https://doi.org/10.3390/diagnostics13020329 - 16 Jan 2023
Cited by 2 | Viewed by 1333
Abstract
Background: Self-collected saliva samples can increase the diagnostic efficiency and benefit healthcare workers, patient care, and infection control. This study evaluated the performance of self-collected saliva samples compared to nasopharyngeal swabs using three commercial kits for the qualitative detection of severe acute respiratory [...] Read more.
Background: Self-collected saliva samples can increase the diagnostic efficiency and benefit healthcare workers, patient care, and infection control. This study evaluated the performance of self-collected saliva samples compared to nasopharyngeal swabs using three commercial kits for the qualitative detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods: Matched nasopharyngeal and saliva samples were collected from 103 patients with either asymptomatic or symptomatic COVID-19. Both samples were evaluated using three commercial kits (TaqCheck, Allplex, and TaqPath). To evaluate sample stability, viral RNA extraction was performed in the presence or absence of an RNA-stabilizing solution. Storage conditions, including the duration, temperature, and stability after freezing and thawing of the samples, were also evaluated. Results: All the saliva samples showed 100% concordance with the nasopharyngeal swab results using TaqCheck and Allplex kits, and 93% using TaqPath kit. No difference was observed in the samples that used the RNA-stabilizing solution compared to the group without the solution. The Ct values of the freeze–thawed samples after 30 days were higher than those on day 0; however, the results were consistent the fresh samples. Conclusion: The high concordance of SARS-CoV-2 detection via reverse transcription–polymerase chain reaction (RT-PCR) in matched saliva and nasopharyngeal samples using different commercial assays reinforces the concept that self-collected saliva samples are non-invasive, rapid, and reliable for diagnosing SARS-CoV-2 infection. Full article
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16 pages, 3000 KiB  
Article
Soluble ST2 as a Useful Biomarker for Predicting Clinical Outcomes in Hospitalized COVID-19 Patients
by Mikyoung Park, Mina Hur, Hanah Kim, Chae Hoon Lee, Jong Ho Lee, Hyung Woo Kim, Minjeong Nam and Seungho Lee
Diagnostics 2023, 13(2), 259; https://doi.org/10.3390/diagnostics13020259 - 10 Jan 2023
Cited by 3 | Viewed by 1446
Abstract
Soluble suppression of tumorigenesis-2 (sST2) is an emerging biomarker for sepsis as well as for heart failure. We investigated the prognostic utility of sST2 for predicting clinical outcomes in hospitalized coronavirus disease 2019 (COVID-19) patients. In a total of 52 hospitalized COVID-19 patients, [...] Read more.
Soluble suppression of tumorigenesis-2 (sST2) is an emerging biomarker for sepsis as well as for heart failure. We investigated the prognostic utility of sST2 for predicting clinical outcomes in hospitalized coronavirus disease 2019 (COVID-19) patients. In a total of 52 hospitalized COVID-19 patients, sST2 levels were measured using the ichroma ST2 assay (Boditech Med Inc., Chuncheon-si, Gang-won-do, Republic of Korea). Clinical outcomes included intensive care unit (ICU) admission, ventilator use, extracorporeal membrane oxygenation (ECMO) use, and 30-day mortality. sST2 was analyzed according to clinical outcomes. sST2, sequential organ failure assessment (SOFA) score, critical disease, and 4C mortality score were compared using the receiver operating characteristic (ROC) curve and Kaplan–Meier methods for clinical outcomes. The sST2 level differed significantly according to ICU admission, ventilator use, ECMO use, and 30-day mortality (all p < 0.05). On ROC curve analysis, sST2 predicted ICU admission, ventilator use, ECMO use, and 30-day mortality comparable to SOFA score but significantly better than critical disease. sST2 predicted ICU admission, ventilator use, and ECMO use significantly better than the 4C mortality score. On Kaplan–Meier survival analysis, hazard ratios (95% confidence interval) were 8.4 (2.7–26.8) for sST2, 14.8 (3.0–71.7) for SOFA score, 1.8 (0.5–6.5) for critical disease, and 11.7 (3.4–40.1) for 4C mortality score. This study demonstrated that sST2 could be a useful biomarker to predict ICU admission, ventilator use, ECMO use, and 30-day mortality in hospitalized COVID-19 patients. sST2 may be implemented as a prognostic COVID-19 biomarker in clinical practice. Full article
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25 pages, 1198 KiB  
Article
Has COVID-19 Modified the Weight of Known Systemic Inflammation Indexes and the New Ones (MCVL and IIC) in the Assessment as Predictive Factors of Complications and Mortality in Acute Pancreatitis?
by Patricia Mihaela Radulescu, Dragos Virgil Davitoiu, Vlad Dumitru Baleanu, Vlad Padureanu, Dumitru Sandu Ramboiu, Marin Valeriu Surlin, Tudor Constantin Bratiloveanu, Eugen Florin Georgescu, Costin Teodor Streba, Razvan Mercut, Elena Irina Caluianu, Emil Tiberius Trasca and Dumitru Radulescu
Diagnostics 2022, 12(12), 3118; https://doi.org/10.3390/diagnostics12123118 - 10 Dec 2022
Cited by 6 | Viewed by 2194
Abstract
We aimed at evaluating the prognostic capacity of the inflammatory indices derived from routine complete blood cell counts in two groups of patients with acute pancreatitis from two different time periods, before and during the COVID-19 pandemic, when a high incidence of complications [...] Read more.
We aimed at evaluating the prognostic capacity of the inflammatory indices derived from routine complete blood cell counts in two groups of patients with acute pancreatitis from two different time periods, before and during the COVID-19 pandemic, when a high incidence of complications with surgical risk and mortality was found. Two new markers were introduced: the mean corpuscular volume to lymphocyte ratio (MCVL) and the cumulative inflammatory index (IIC), which were calculated at a baseline in the two groups of patients. Of the already established markers, none of them managed to effectively predict the complications with surgical risk and mortality, with a decrease of less than 50% in specificity in the peri-COVID group. The MCVL had the best prediction of complications with surgical risk in both the pre-COVID and peri-COVID groups, validated it as an independent factor by multivariate analysis. The IIC had the best prediction of mortality in both periods and was proven to be an independent factor by multivariate analysis. As the IIC predicted death best, we tested the occurrence of death and found that patients with PA who had an IIC > 12.12 presented a risk of death 4.08 times higher in the pre-COVID group and 3.33 times higher in the peri-COVID group. The new MCVL and IIC independent markers had a superior sensitivity and specificity in predicting surgical risk complications and, respectively, mortality in the group of patients with acute pancreatitis during the COVID-19 pandemic, which makes them widely applicable in populations with modified immune and inflammatory status. Conclusions: In patients with acute pancreatitis, MCVL has a significant predictive value regarding complications with surgical risk (abscess, necrosis, and pseudocyst), and the IIC has a significant predictive value for mortality. Full article
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14 pages, 2920 KiB  
Article
How the COVID-19 Pandemic Affected Attendance at a Tertiary Orthopedic Center Emergency Department: A Comparison between the First and Second Waves
by Eleonora Carlicchi, Maria Eugenia Di Sabato, Antonino Cincotta, Riccardo Accetta, Alberto Aliprandi, Domenico Albano, Luca Maria Sconfienza and Carmelo Messina
Diagnostics 2022, 12(11), 2855; https://doi.org/10.3390/diagnostics12112855 - 18 Nov 2022
Viewed by 1004
Abstract
Italy was the first European country to face the SARS-CoV-2 virus (COVID-19) pandemic in 2020. The country quickly implemented strategies to contain contagions and re-organize medical resources. We evaluated the COVID-19 effects on the activity of a tertiary-level orthopedic emergency department (ED) during [...] Read more.
Italy was the first European country to face the SARS-CoV-2 virus (COVID-19) pandemic in 2020. The country quickly implemented strategies to contain contagions and re-organize medical resources. We evaluated the COVID-19 effects on the activity of a tertiary-level orthopedic emergency department (ED) during the first and second pandemic waves. We retrospectively collected and compared clinical radiological data of ED admissions during four periods: period A, first pandemic wave; period B, second pandemic wave; period C, three months before the COVID-19 outbreak; period D, same timeframe of the first wave but in 2019. During period A, we found a reduction in ED admissions (−68.2% and −59.9% compared with periods D and C) and a decrease in white codes (non-urgent) (−7.5%) compared with pre-pandemic periods, with a slight increase for all other codes: +6.3% green (urgent, not critical), +0.8% yellow (moderately critical) and +0.3% red (highly urgent, risk of death). We observed an increased rate of fracture diagnosis in period A: +14.9% and +13.3% compared with periods D and C. Our study shows that the COVID-19 pandemic caused a drastic change in the ED patient flow and clinical radiological activity, with a marked reduction in admissions and an increased rate of more severe triage codes and diagnosed fractures. Full article
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16 pages, 1675 KiB  
Article
Prognostic Nutritional Index, Controlling Nutritional Status (CONUT) Score, and Inflammatory Biomarkers as Predictors of Deep Vein Thrombosis, Acute Pulmonary Embolism, and Mortality in COVID-19 Patients
by Adrian Vasile Mureșan, Ioana Hălmaciu, Emil Marian Arbănași, Réka Kaller, Eliza Mihaela Arbănași, Ovidiu Aurelian Budișcă, Răzvan Marian Melinte, Vlad Vunvulea, Rareș Cristian Filep, Lucian Mărginean, Bogdan Andrei Suciu, Klara Brinzaniuc, Raluca Niculescu and Eliza Russu
Diagnostics 2022, 12(11), 2757; https://doi.org/10.3390/diagnostics12112757 - 11 Nov 2022
Cited by 29 | Viewed by 2520
Abstract
Background: Numerous tools, including nutritional and inflammatory markers, have been evaluated as the predictors of poor outcomes in COVID-19 patients. This study aims to verify the predictive role of the prognostic nutritional index (PNI), CONUT Score, and inflammatory markers (monocyte to lymphocyte ratio [...] Read more.
Background: Numerous tools, including nutritional and inflammatory markers, have been evaluated as the predictors of poor outcomes in COVID-19 patients. This study aims to verify the predictive role of the prognostic nutritional index (PNI), CONUT Score, and inflammatory markers (monocyte to lymphocyte ratio (MLR), neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR), systemic inflammatory index (SII), Systemic Inflammation Response Index (SIRI), and Aggregate Index of Systemic Inflammation (AISI)) in cases of deep vein thrombosis (DVT) and acute pulmonary embolism (APE) risk, as well as mortality, in COVID-19 patients. Methods: The present study was designed as an observational, analytical, retrospective cohort study, and included 899 patients over the age of 18 who had a COVID-19 infection, confirmed through real time-polymerase chain reaction (RT-PCR), and were admitted to the County Emergency Clinical Hospital and Modular Intensive Care Unit of UMFST “George Emil Palade” of Targu Mures, Romania between January 2020 and March 20212. Results: Non-Surviving patients were associated with a higher incidence of chronic kidney disease (p = 0.01), cardiovascular disease (atrial fibrillation (AF) p = 0.01; myocardial infarction (MI) p = 0.02; peripheral arterial disease (PAD) p = 0.0003), malignancy (p = 0.0001), tobacco (p = 0.0001), obesity (p = 0.01), dyslipidemia (p = 0.004), and malnutrition (p < 0.0001). Multivariate analysis showed that both nutritional and inflammatory markers had a high baseline value and were all independent predictors of adverse outcomes for all enrolled patients (for all p < 0.0001). The presence of PAD, malignancy, and tobacco, were also independent predictors of all outcomes. Conclusions: According to our findings, higher MLR, NLR, PLR, SII, SIRI, AISI, CONUT Score, and lower PNI values at admission strongly predict DVT risk, APE risk, and mortality in COVID-19 patients. Moreover, PAD, malignancy, and tobacco, all predicted all outcomes, while CKD predicts APE risk and mortality, but not the DVT risk. Full article
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11 pages, 1881 KiB  
Article
Performance Analysis of Self-Collected Nasal and Oral Swabs for Detection of SARS-CoV-2
by Ho-Jae Lim, Young-Hyun Baek, Min-Young Park, Jae-Hyun Yang, Min-Jin Kim, Nackmoon Sung, Yong-Hak Sohn, Sun-Hwa Lee, Jung-Eun Park and Yong-Jin Yang
Diagnostics 2022, 12(10), 2279; https://doi.org/10.3390/diagnostics12102279 - 21 Sep 2022
Cited by 5 | Viewed by 1995
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third highly pathogenic human coronavirus and is rapidly transmitted by infected individuals regardless of their symptoms. During the COVID-19 pandemic, owing to the dearth of skilled healthcare workers (HCWs) to collect samples for early [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third highly pathogenic human coronavirus and is rapidly transmitted by infected individuals regardless of their symptoms. During the COVID-19 pandemic, owing to the dearth of skilled healthcare workers (HCWs) to collect samples for early diagnosis, self-collection emerged as a viable alternative. To evaluate the reliability of self-collection, we compared the virus detection rate using 3990 self-collected swabs and HCW-collected swabs, procured from the same individuals and collected immediately after the self-collection. The results of multiplex reverse-transcription quantitative polymerase chain reaction revealed that the viral load in the HCW-collected swabs was marginally (18.4–28.8 times) higher than that in self-collected swabs. Self-collection showed no significant difference in sensitivity and specificity from HCW-collection (κ = 0.87, McNemar’s test; p = 0.19), indicating a comparable performance. These findings suggest that self-collected swabs are acceptable substitutes for HCW-collected swabs, and that their use improved the specimen screening efficiency and reduced the risk of SARS-CoV-2 infection among HCWs during and after the COVID-19 pandemic. Full article
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11 pages, 1346 KiB  
Article
A Novel Rolling Circle Amplification-Based Detection of SARS-CoV-2 with Multi-Region Padlock Hybridization
by Rajesh Kumari, Ji Won Lim, Matthew Ryan Sullivan, Rachel Malampy, Connor Baush, Irina Smolina, Howard Robin, Vadim V. Demidov, Giovanni Stefano Ugolini, Jared R. Auclair and Tania Konry
Diagnostics 2022, 12(9), 2252; https://doi.org/10.3390/diagnostics12092252 - 18 Sep 2022
Cited by 4 | Viewed by 2094
Abstract
SARS-CoV-2 has remained a global health burden, primarily due to the continuous evolution of different mutant strains. These mutations present challenges to the detection of the virus, as the target genes of qPCR, the standard diagnostic method, may possess sequence alterations. In this [...] Read more.
SARS-CoV-2 has remained a global health burden, primarily due to the continuous evolution of different mutant strains. These mutations present challenges to the detection of the virus, as the target genes of qPCR, the standard diagnostic method, may possess sequence alterations. In this study, we develop an isothermal one-step detection method using rolling circle amplification (RCA) for SARS-CoV-2. This novel strategy utilizes a multi-padlock (MP-RCA) approach to detect viral-RNA via a simplified procedure with the reliable detection of mutated strains over other procedures. We designed 40 padlock-based probes to target different sequences across the SARS-CoV-2 genome. We established an optimal one-step isothermal reaction protocol utilizing a fluorescent output detected via a plate reader to test a variety of padlock combinations. This method was tested on RNA samples collected from nasal swabs and validated via PCR. S-gene target failure (SGTF)-mutated strains of SARS-CoV-2 were included. We demonstrated that the sensitivity of our assay was linearly proportional to the number of padlock probes used. With the 40-padlock combination the MP-RCA assay was able to correctly detect 45 out 55 positive samples (81.8% efficiency). This included 10 samples with SGTF mutations which we were able to detect as positive with 100% efficiency. We found that the MP-RCA approach improves the sensitivity of the MP-RCA assay, and critically, allows for the detection of SARS-CoV-2 variants with SGTF. Our method offers the simplicity of the reaction and requires basic equipment compared to standard qPCR. This method provides an alternative approach to overcome the challenges of detecting SARS-CoV-2 and other rapidly mutating viruses. Full article
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10 pages, 834 KiB  
Article
Usefulness and Limitations of Anti-S IgG Assay in Detecting Previous SARS-CoV-2 Breakthrough Infection in Fully Vaccinated Healthcare Workers
by Gianluca Spiteri, Maria Grazia Lourdes Monaco, Gulser Caliskan, Angela Carta, Maria Diletta Pezzani, Giuseppe Lippi, Davide Gibellini, Giuseppe Verlato and Stefano Porru
Diagnostics 2022, 12(9), 2152; https://doi.org/10.3390/diagnostics12092152 - 04 Sep 2022
Viewed by 1449
Abstract
Introduction: The anti-spike (S) IgG assay is the most widely used method to assess the immunological response to COVID-19 vaccination. Several studies showed that subjects with perivaccination infection have higher anti-S IgG titers. However, a cut-off has not yet been identified so far [...] Read more.
Introduction: The anti-spike (S) IgG assay is the most widely used method to assess the immunological response to COVID-19 vaccination. Several studies showed that subjects with perivaccination infection have higher anti-S IgG titers. However, a cut-off has not yet been identified so far for distinguishing infected subjects after vaccination. This study thus evaluates the performance of the anti-S IgG assay in identifying subjects with breakthrough infections (BIs) and its potential usefulness for screening healthcare workers (HCWs). Methods: Out of 6400 HCWs of the University Hospital of Verona vaccinated with two doses of BNT162b2, 4462 never infected before subjects who had completed primary vaccination were tested for IgG anti-S 6 to 9 months after the second dose. Of these, 59 (1.3%) had a BI. The discriminant power of IgG anti-S in detecting previous breakthrough infection was tested by constructing receiver operating characteristic (ROC) curves. Results: The discriminant power for BI was rather good (area under the curve (AUC), 0.78) and increased with decreasing time elapsed between antibody titer assessment and previous SARS-CoV-2 infection. Accuracy (AUC) sensitivity increased from 0.78 (95% CI 0.70–0.85) for BI in the previous six months to 0.83 (95% CI 0.67–0.99) for those in the previous two months, and from 0.68 to 0.80, respectively. The specificity (0.86) and optimal cut-off (935 BAU/mL) remained unchanged. However, BI were rather rare (1.3%), so the positive predictive value (PPV) was low. Only 40 of the 664 HCWs with antibody titer > 935 BAU/mL had previously confirmed BI, yielding a PPV of only 6.0%. When adopting as cut-off the 90th percentile (1180 BAU/mL), PPV increased to 7.9% (35/441). Conclusions: The anti-S IgG assay displayed good sensitivity and specificity in discriminating subjects with BI, especially in recent periods. However, BIs were rare among HCWs, so that the anti-S IgG assay may have low PPV in this setting, thus limiting the usefulness of this test as a screening tool for HCWs. Further studies are needed to identify more effective markers of a previous infection in vaccinated subjects. Full article
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8 pages, 405 KiB  
Article
How Significant Are Xpert Xpress SARS-CoV-2 Test Findings When Only an N2 Gene Is Detected?
by Min-Kyung So, Hae-Sun Chung, Duk Hee Lee and Miae Lee
Diagnostics 2022, 12(9), 2133; https://doi.org/10.3390/diagnostics12092133 - 02 Sep 2022
Cited by 5 | Viewed by 1498
Abstract
The rapid identification of patients infected with COVID-19 during the SARS-CoV-2 pandemic is critical to operating emergency rooms effectively. Xpert Xpress SARS-CoV-2 (Xpert) assays are increasingly being used in the rapid screening of COVID-19. We evaluated the clinical performance of Xpert by comparing [...] Read more.
The rapid identification of patients infected with COVID-19 during the SARS-CoV-2 pandemic is critical to operating emergency rooms effectively. Xpert Xpress SARS-CoV-2 (Xpert) assays are increasingly being used in the rapid screening of COVID-19. We evaluated the clinical performance of Xpert by comparing findings with those of qRT-PCR evaluations and included the clinical features of patients visiting the emergency department. Positive results with Xpert testing (n = 370) were compared with qRT-PCR findings, demonstrating a 91.9% intertest agreement. We reviewed the subsequent COVID-19 test results and SARS-CoV-2 infection histories for individuals showing discrepancies in Xpert and qRT-PCR testing and determined whether the findings were true-positive or false-positive. The true-positive rate for Xpert testing was 95.4% (353/370); the remaining 17 samples (4.6%) were false-positive. All false-positive data for Xpert testing showed N2 signals amplified to Ct values of ≥40 with no E gene signals. Rapid Xpert testing is highly sensitive and shows a good performance overall in challenging situations, such as an emergency room. However, we considered the possibility of false-positive Xpert results given an N2 gene signal only, especially given high Ct values. We recommend interpreting test data with caution and considering retesting over time. Full article
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15 pages, 1881 KiB  
Article
Chest CT Severity Score and Systemic Inflammatory Biomarkers as Predictors of the Need for Invasive Mechanical Ventilation and of COVID-19 Patients’ Mortality
by Ioana Halmaciu, Emil Marian Arbănași, Réka Kaller, Adrian Vasile Mureșan, Eliza Mihaela Arbănași, Nicolae Bacalbasa, Bogdan Andrei Suciu, Ioana Iulia Cojocaru, Andreea Ioana Runcan, Florin Grosu, Vlad Vunvulea and Eliza Russu
Diagnostics 2022, 12(9), 2089; https://doi.org/10.3390/diagnostics12092089 - 29 Aug 2022
Cited by 26 | Viewed by 2414
Abstract
Background: Numerous tools, including inflammatory biomarkers and lung injury severity scores, have been evaluated as predictors of disease progression and the requirement for intensive therapy in COVID-19 patients. This study aims to verify the predictive role of inflammatory biomarkers [monocyte to lymphocyte ratio [...] Read more.
Background: Numerous tools, including inflammatory biomarkers and lung injury severity scores, have been evaluated as predictors of disease progression and the requirement for intensive therapy in COVID-19 patients. This study aims to verify the predictive role of inflammatory biomarkers [monocyte to lymphocyte ratio (MLR), neutrophil to lymphocyte ratio (NLR), systemic inflammatory index (SII), Systemic Inflammation Response Index (SIRI), Aggregate Index of Systemic Inflammation (AISI), and interleukin-6 (IL-6)] and the total system score (TSS) in the need for invasive mechanical ventilation (IMV) and mortality in COVID-19 patients. Methods: The present study was designed as an observational, analytical, retrospective cohort study and included all patients over 18 years of age with a diagnosis of COVID-19 pneumonia, confirmed through real time-polymerase chain reaction (RT-PCR) and radiological chest CT findings admitted to County Emergency Clinical Hospital of Targu-Mureș, Romania, and Modular Intensive Care Unit of UMFST “George Emil Palade” of Targu Mures, Romania between January 2021 and December 2021. Results: Non-Survivors patients were associated with higher age (p = 0.01), higher incidence of cardiac disease [atrial fibrillation (AF) p = 0.0008; chronic heart failure (CHF) p = 0.01], chronic kidney disease (CKD; p = 0.02), unvaccinated status (p = 0.001), and higher pulmonary parenchyma involvement (p < 0.0001). Multivariate analysis showed a high baseline value for MLR, NLR, SII, SIRI, AISI, IL-6, and TSS independent predictor of adverse outcomes for all recruited patients. Moreover, the presence of AF, CHF, CKD, and dyslipidemia were independent predictors of mortality. Furthermore, AF and dyslipidemia were independent predictors of IMV need. Conclusions: According to our findings, higher MLR, NLR, SII, SIRI, AISI, IL-6, and TSS values at admission strongly predict IMV requirement and mortality. Moreover, patients above 70 with AF, dyslipidemia, and unvaccinated status highly predicted IMV need and fatality. Likewise, CHF and CKD were independent predictors of increased mortality. Full article
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8 pages, 1134 KiB  
Communication
Strong Correlations between the Binding Antibodies against Wild-Type and Neutralizing Antibodies against Omicron BA.1 and BA.2 Variants of SARS-CoV-2 in Individuals Following Booster (Third-Dose) Vaccination
by Nungruthai Suntronwong, Suvichada Assawakosri, Sitthichai Kanokudom, Ritthideach Yorsaeng, Chompoonut Auphimai, Thanunrat Thongmee, Preeyaporn Vichaiwattana, Thaneeya Duangchinda, Warangkana Chantima, Pattarakul Pakchotanon, Jira Chansaenroj, Pornjarim Nilyanimit, Donchida Srimuan, Thaksaporn Thatsanatorn, Natthinee Sudhinaraset, Nasamon Wanlapakorn, Juthathip Mongkolsapaya and Yong Poovorawan
Diagnostics 2022, 12(8), 1781; https://doi.org/10.3390/diagnostics12081781 - 22 Jul 2022
Cited by 14 | Viewed by 1462
Abstract
This study examined the neutralizing activity and receptor-binding domain (RBD) antibody levels against wild-type and omicron BA.1 and BA.2 variants in individuals who received three doses of COVID-19 vaccination. The relationship between the anti-RBD IgG against wild-type and live virus neutralizing antibody titers [...] Read more.
This study examined the neutralizing activity and receptor-binding domain (RBD) antibody levels against wild-type and omicron BA.1 and BA.2 variants in individuals who received three doses of COVID-19 vaccination. The relationship between the anti-RBD IgG against wild-type and live virus neutralizing antibody titers against omicron BA.1 and BA.2 variants was examined. In total, 310 sera samples from individuals after booster vaccination (third-dose) were tested for specific IgG wild-type SARS-CoV-2 RBD and the omicron BA.1 surrogate virus neutralization test (sVNT). The live virus neutralization assay against omicron BA.1 and BA.2 was performed using the foci-reduction neutralization test (FRNT50). The anti-RBD IgG strongly correlated with FRNT50 titers against BA.1 and BA.2. Non-linear regression showed that anti-RBD IgG at the cut-off value ≥148 BAU/mL and ≥138 BAU/mL were related to the threshold for FRNT50 titers ≥20 against BA.1 and BA.2, respectively. A moderate correlation was observed between the sVNT and FRNT50 titers. At FRNT50 titers ≥20, the predicted sVNT for BA.1 and BA.2 was ≥10.57% and ≥11.52%, respectively. The study identified anti-RBD IgG and sVNT levels that predict detectable neutralizing antibodies against omicron variants. Assessment and monitoring of protective immunity support vaccine policies and will help identify optimal timing for booster vaccination. Full article
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9 pages, 1480 KiB  
Article
Comparison of Two RNA Extraction Methods for the Molecular Detection of SARS-CoV-2 from Nasopharyngeal Swab Samples
by Anna Scarabotto, Simona Balestro, Stella Gagliardi and Rosa Trotti
Diagnostics 2022, 12(7), 1561; https://doi.org/10.3390/diagnostics12071561 - 27 Jun 2022
Cited by 3 | Viewed by 1909
Abstract
Background: Rapid diagnosis of COVID-19 is essential in order to restrict the spread of the pandemic, and different approaches for SARS-CoV-2 testing have been proposed as cost-effective and less time-consuming alternatives. For virus detection, the real-time reverse transcriptase–polymerase chain reaction (RT-PCR) technique is [...] Read more.
Background: Rapid diagnosis of COVID-19 is essential in order to restrict the spread of the pandemic, and different approaches for SARS-CoV-2 testing have been proposed as cost-effective and less time-consuming alternatives. For virus detection, the real-time reverse transcriptase–polymerase chain reaction (RT-PCR) technique is still the “gold standard” for accuracy and reliability, but its performance is affected by the efficiency of nucleic acid extraction methods. Objective: In order to improve the SARS-CoV-2 diagnostic workflow, we compared a “standard” commercially available kit, based on viral RNA extraction from human swab samples by magnetic beads, with its technological evolution. The two methods differ mainly in their time consumption (9 vs. 35 min). Methods: We adopted the MAGABIO PLUS VIRUS DNA/RNA PURIFICATION KIT II (BIOER), defined as “standard”, with the automatic extractor BIOER (GenePure Pro fully automatic nucleic acid purification system) to isolate RNA from nasopharyngeal swabs for the detection of SARS-CoV-2 by RT-PCR. We tested this kit with a new faster version of the first one, defined as “rapid” (MAGABIO PLUS VIRUS RNA PURIFICATION KIT II). Results and Conclusion: The two evaluated procedures provided similar analytical results, but the faster method proved to be a more suitable tool for the detection of SARS-CoV-2 from nasopharyngeal swabs, due to a more rapid availability of results, which may contribute to improving both clinical decision making and patient safety. Full article
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14 pages, 1545 KiB  
Article
COVID-19 Underreporting in Brazil among Patients with Severe Acute Respiratory Syndrome during the Pandemic: An Ecological Study
by Tainá Momesso Lima, Camila Vantini Capasso Palamim, Vitória Franchini Melani, Matheus Ferreira Mendes, Letícia Rojina Pereira and Fernando Augusto Lima Marson
Diagnostics 2022, 12(6), 1505; https://doi.org/10.3390/diagnostics12061505 - 20 Jun 2022
Cited by 6 | Viewed by 1512
Abstract
Underreporting of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is a global problem and might hamper Coronavirus Disease (COVID-19) epidemiological control. Taking this into consideration, we estimated possible SARS-CoV-2 infection underreporting in Brazil among patients with severe acute respiratory syndrome (SARS). An [...] Read more.
Underreporting of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is a global problem and might hamper Coronavirus Disease (COVID-19) epidemiological control. Taking this into consideration, we estimated possible SARS-CoV-2 infection underreporting in Brazil among patients with severe acute respiratory syndrome (SARS). An ecological study using a descriptive analysis of the SARS report was carried out based on data supplied by the Influenza Epidemiological Surveillance Information (SIVEP)-Flu (in Brazilian Portuguese, Sistema de Vigilância Epidemiológica da Gripe) in the period between January 2015 and March 2021. The number of SARS cases and related deaths after infection by SARS-CoV-2 or Influenzae was described. The estimation of underreporting was evaluated considering the relative increase in the number of cases with undefined etiological agent comparing 2020 to 2015–2019; and descriptive analysis was carried out including data from January–March/2021. In our data, SARS-CoV-2 infection and the presence of SARS with undefined etiological agent were associated with the higher number of cases and deaths from SARS in 2020/2021. SARS upsurge was six times over that expected in 2020, according to SARS seasonality in previous years (2015–2019). The lowest possible underdiagnosis rate was observed in the age group < 2 y.o. and individuals over 30 y.o., with ~50%; while in the age groups 10–19 and 20–29 y.o., the rates were 200–250% and 100%, respectively. For the remaining age groups (2–5 and 5–9 y.o.) underreporting was over 550%, except for female individuals in the age group 2–5 y.o., in which a ~500% rate was found. Our study described that the SARS-CoV-2 infection underreporting rate in Brazil in SARS patients is alarming and presents different indices, mainly associated with the patients’ age groups. Our results, mainly the underreporting index according to sex and age, should be evaluated with caution. Full article
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10 pages, 5829 KiB  
Article
Predictors for COVID-19 Complete Remission with HRCT Pattern Evolution: A Monocentric, Prospective Study
by Diana Manolescu, Bogdan Timar, Felix Bratosin, Ovidiu Rosca, Cosmin Citu and Cristian Oancea
Diagnostics 2022, 12(6), 1397; https://doi.org/10.3390/diagnostics12061397 - 05 Jun 2022
Cited by 14 | Viewed by 2021
Abstract
There are growing concerns that some COVID-19 survivors may acquire fibrosis and other irreversible lung abnormalities. The purpose of this prospective study was to assess the rate and predictors of complete resolution of COVID-19 pneumonia by pursuing a hypothetical relation between time and [...] Read more.
There are growing concerns that some COVID-19 survivors may acquire fibrosis and other irreversible lung abnormalities. The purpose of this prospective study was to assess the rate and predictors of complete resolution of COVID-19 pneumonia by pursuing a hypothetical relation between time and imaging pattern evolution using HRCT findings. A monocentric prospective cohort study with a consecutive-case enrolment design was implemented during a five-month period, having a total of 683 post-COVID patients eligible for inclusion and 635 evaluations with complete follow-up for chest HRCT. The target for post-COVID evaluations consisted of performing HRCT 90 days after a confirmed SARS-CoV-2 infection. The studied patients had an average age of 54 years, ranging between 18 and 85 years old, and an average duration from the first symptoms until HRCT was performed of 74 days. At the post-COVID follow-up, 25.8% had a complete imagistic remission. The most common appearance with HRCT was “ground glass” in 86.6% in patients with persistent COVID-19, followed by reticulations, present in 78.8%, and respectively pleural thickening in 41.2% of cases. The mean total HRCT scores were statistically significantly higher in patients older than 65 years (10.6 ± 6.0) compared to the 40–65 group (6.1 ± 6.1) and the 18–40 age group (2.7 ± 4.8) (p < 0.001). Chest HRCT is a “time window” in documenting temporal persistent radiologic features of lung injury 90 days after SARS-CoV-2 infection, determining the pathologic basis of so-called “long COVID”. The complete remission was associated with a significantly higher average follow-up period and a significantly lower average patient age. Persistent HRCT features of ground glass, reticulation, and pleural thickening are associated with a higher total CT score and older age. Full article
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12 pages, 837 KiB  
Article
Variations in Biochemical Values under Stress in Children with SARS-CoV-2 Infection
by Alina Belu, Laura Mihaela Trandafir, Elena Țarcă, Elena Cojocaru, Otilia Frăsinariu, Magdalena Stârcea, Mihaela Moscalu, Razvan Calin Tiutiuca, Alina Costina Luca and Anca Galaction
Diagnostics 2022, 12(5), 1213; https://doi.org/10.3390/diagnostics12051213 - 12 May 2022
Cited by 1 | Viewed by 1406
Abstract
In the case of SARS-CoV-2 infection, children seem to be less affected than adults, but data regarding epidemiologic characteristics and biochemical values are poor and essentially based on limited case series. The aim of our study is to highlight the predictive value of [...] Read more.
In the case of SARS-CoV-2 infection, children seem to be less affected than adults, but data regarding epidemiologic characteristics and biochemical values are poor and essentially based on limited case series. The aim of our study is to highlight the predictive value of some biochemical markers at hospitalization, for the correct classification of the patient in the form of disease. Methods: We performed an analytical retrospective study on 82 pediatric patients diagnosed with COVID-19 in the emergency department, with moderate or severe form of disease, and treated in our tertiary hospital. We analyzed the epidemiologic characteristics, symptomatology and biochemical values and compare the data according to the form of disease. Results: The mean age at admission was 4.5 years (median 1 year) and the masculine/feminine ratio was 1.5. Comparing the data between the two groups of patients (42 severe/40 moderate), we observed that the severe form presented with a lower pH at admission (p = 0.02), hyperglycemia (p = 0.01), increased values of transaminases (p = 0.01 and 0.02) and hypoproteinemia (p = 0.01). Also, the severe form was statistically significantly associated with comorbidities, acute respiratory distress, rising of the inflammatory markers during hospitalization. Hyperlactatemia (Lactate > 1.5 mmol/L) was significantly associated with the age under one year (p < 0.001). Mortality rate was 9.75% and the median age at death was 3 months. Univariate logistic regression model shows that the presence of anemia increased the probability of death 88 times, comorbidities 23.3 times and ketoacidosis 16.4 times. Conclusions: Metabolic acidosis, hyperlactatemia, hyperglycemia, modified hepatic values and hypoproteinemia are biochemical markers associated with the severe form of disease in SARS-CoV-2 infection in children. Presence of anemia, comorbidities and ketoacidosis are important risk factors for death of pediatric patients with SARS-CoV-2 infection. Full article
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14 pages, 850 KiB  
Article
External Validation of the Modified 4C Deterioration Model and 4C Mortality Score for COVID-19 Patients in a Swiss Tertiary Hospital
by Adriana Wirth, Andrea Goetschi, Ulrike Held, Ataman Sendoel, Melina Stuessi-Helbling and Lars Christian Huber
Diagnostics 2022, 12(5), 1129; https://doi.org/10.3390/diagnostics12051129 - 03 May 2022
Cited by 5 | Viewed by 1434
Abstract
Prognostic models to predict the deterioration and mortality risk in COVID-19 patients are utterly needed to assist in informed decision making. Most of these models, however, are at high risk of bias, model overfitting, and unclear reporting. Here, we aimed to externally validate [...] Read more.
Prognostic models to predict the deterioration and mortality risk in COVID-19 patients are utterly needed to assist in informed decision making. Most of these models, however, are at high risk of bias, model overfitting, and unclear reporting. Here, we aimed to externally validate the modified (urea was omitted) 4C Deterioration Model and 4C Mortality Score in a cohort of Swiss COVID-19 patients and, second, to evaluate whether the inclusion of the neutrophil-to-lymphocyte ratio (NLR) improves the predictive performance of the models. We conducted a retrospective single-centre study with adult patients hospitalized with COVID-19. Both prediction models were updated by including the NLR. Model performance was assessed via the models’ discriminatory performance (area under the curve, AUC), calibration (intercept and slope), and their performance overall (Brier score). For the validation of the 4C Deterioration Model and Mortality Score, 546 and 527 patients were included, respectively. In total, 133 (24.4%) patients met the definition of in-hospital deterioration. Discrimination of the 4C Deterioration Model was AUC = 0.78 (95% CI 0.73–0.82). A total of 55 (10.44%) patients died in hospital. Discrimination of the 4C Mortality Score was AUC = 0.85 (95% CI 0.79–0.89). There was no evidence for an incremental value of the NLR. Our data confirm the role of the modified 4C Deterioration Model and Mortality Score as reliable prediction tools for the risk of deterioration and mortality. There was no evidence that the inclusion of NLR improved model performance. Full article
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10 pages, 696 KiB  
Article
The Clinical Manifestation of SARS-CoV-2 in Critically Ill Patients with Klebsiella pneumoniae NDM Hospitalized in the ICU of a Modular Hospital during the Third Wave of the Pandemic in Poland—An Observational Cohort Study
by Aneta Guzek, Zbigniew Rybicki, Agnieszka Woźniak-Kosek and Dariusz Tomaszewski
Diagnostics 2022, 12(5), 1118; https://doi.org/10.3390/diagnostics12051118 - 29 Apr 2022
Cited by 1 | Viewed by 1675
Abstract
There is limited information on the clinical characteristics of critically ill patients infected with SARS-CoV-2 and Klebsiella pneumoniae NDM. The objective of this study was to describe such a group of patients hospitalised in the intensive care unit of a large academic hospital [...] Read more.
There is limited information on the clinical characteristics of critically ill patients infected with SARS-CoV-2 and Klebsiella pneumoniae NDM. The objective of this study was to describe such a group of patients hospitalised in the intensive care unit of a large academic hospital during the third wave of the COVID-19 pandemic in Poland. Between 1 March and 30 June 2021, 103 patients were hospitalised, of whom 23 (22.3%) were positive for K. pneumoniae NDM; 14 (61%) of those patients died. Their hospitalisation time varied between 9 and 47 days. Five of the 23 patients (21.7%) were otherwise healthy. In contrast, the others suffered from cardiovascular problems (11, 47.8%), obesity (6, 26.1%), diabetes (5, 21.7%), neurological problems (4, 17.4%), or kidney disease (1, 4.3%); 4 (17.4%) were heavy smokers, and 1 (4.3%) had a history of alcohol abuse. K. pneumoniae NDM was isolated from urine samples of all patients. In 17 patients (73.9%), it was also isolated from other sources: from the respiratory tract in 10 (43.8%), from the blood in 2 (8.7%), and the central venous catheter was contaminated in 1 case (4.3%). Fourteen of the patients (60.9%) were colonised K. pneumoniae NDM. In four patients (17.4%), bacterial and fungal coinfection occurred. In one case (4.4%), two fungal species, Candida albicans and Candida glabrata, were isolated simultaneously. The most frequently administered antimicrobial agent was colistin (60.9%), followed by meropenem (47.8%), vancomycin (47.8%), ceftriaxone (34.8%), linezolid (30.4%), piperacillin/tazobactam (30.4%), and trimethoprim/sulfamethoxazole (30.4%). Other less-frequently administered agents included amikacin, amoxicillin/clavulanate, tigecycline, ciprofloxacin, fosfomycin, clindamycin, and cloxacillin. Fluconazole was administered in 14 patients (60.7%) and micafungin was administered in 2 (8.7%). Full article
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11 pages, 1495 KiB  
Article
Neutrophile-to-Lymphocyte Ratio (NLR) Identifies Patients with Coronavirus Infectious Disease 2019 (COVID-19) at High Risk for Deterioration and Mortality—A Retrospective, Monocentric Cohort Study
by Jutta Rose, Flurina Suter, Eva Furrer, Ataman Sendoel, Melina Stüssi-Helbling and Lars C. Huber
Diagnostics 2022, 12(5), 1109; https://doi.org/10.3390/diagnostics12051109 - 28 Apr 2022
Cited by 5 | Viewed by 1538
Abstract
Among people infected with SARS-CoV-2, the determination of clinical features associated with poor outcome is essential to identify those at high risk of deterioration. Here, we aimed to investigate clinical phenotypes of patients hospitalized due to COVID-19 and to examine the predictive value [...] Read more.
Among people infected with SARS-CoV-2, the determination of clinical features associated with poor outcome is essential to identify those at high risk of deterioration. Here, we aimed to investigate clinical phenotypes of patients hospitalized due to COVID-19 and to examine the predictive value of the neutrophil-to-lymphocyte ratio (NLR) in a representative patient collective of the Swiss population. We conducted a retrospective monocentriccohort study with patients hospitalized due to COVID-19 between 27 February and 31 December 2020. Data were analyzed descriptively, using the binary logistic regression model, proportional odds logistic regression model, competing risk analysis, and summary measure analysis. A total of 454 patients were included in our study. Dyspnea, elevated respiratory rate, low oxygen saturation at baseline, age, and presence of multiple comorbidities were associated with a more severe course of the disease. A high NLR at baseline was significantly associated with disease severity, unfavorable outcome, and mortality. In non-survivors, NLR further increased during hospital stay, whereas in survivors, NLR decreased. In conclusion, our data emphasize the importance of accurate history taking and clinical examination upon admission and confirm the role of baseline NLR as a surrogate marker for increased disease severity, unfavorable outcome, and mortality in patients hospitalized due to infection with SARS-CoV-2. Full article
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7 pages, 211 KiB  
Communication
Performance Evaluation of a Rapid Antigen Test (RAT) during Omicron Pandemic Wave in Greece, Conducted by Different Personnel, and Comparison with Performance in Previous Wave (Alpha Variant) Period
by Maria A. Kyritsi, Matthaios Speletas, Varvara Mouchtouri, Evangelia Vachtsioli, Dimitrios Babalis, Olympia Kouliou, Anastasia Tsispara, Maria Tseroni and Christos Hadjichristodoulou
Diagnostics 2022, 12(5), 1048; https://doi.org/10.3390/diagnostics12051048 - 21 Apr 2022
Cited by 7 | Viewed by 1544
Abstract
Due to the prevailing ambiguity regarding the performance of rapid antigen tests (RATs) for B.1.1.529 (Omicron) variant diagnosis, a commercial RAT was evaluated in the emergency ward of a general hospital in Larissa, Central Greece. The sampling and the evaluation were repeated twice [...] Read more.
Due to the prevailing ambiguity regarding the performance of rapid antigen tests (RATs) for B.1.1.529 (Omicron) variant diagnosis, a commercial RAT was evaluated in the emergency ward of a general hospital in Larissa, Central Greece. The sampling and the evaluation were repeated twice by different personnel. Discordance between the two samplings was observed regarding the sensitivity (47.5%, 95% CI: 39.0–56.1 vs. 78.6%, 95% CI: 69.1–86.2) and specificity (93.8%, 95% CI: 86.0–97.9 vs. 100.0%, 95% CI: 93.3–100.0) of the RAT. Furthermore, the test displayed slightly lower sensitivity (78.6% vs. 85.5%, 95% CI: 79.1–90.5) compared to its initial evaluation that was conducted by our team when the B.1.1.7 (Alpha) variant was dominant. Full article
6 pages, 393 KiB  
Communication
SARS-CoV-2 Antigen Testing Intervals: Twice or Thrice a Week?
by Chin Shern Lau and Tar-Choon Aw
Diagnostics 2022, 12(5), 1039; https://doi.org/10.3390/diagnostics12051039 - 21 Apr 2022
Cited by 1 | Viewed by 1235
Abstract
Antigen testing for SARS-CoV-2 has become an increasingly prominent screening tool in the ongoing COVID-19 pandemic and can be performed multiple times a week. However, the optimal weekly frequency of antigen testing is unclear; the Centers for Disease Control and Prevention recommends 1–3 [...] Read more.
Antigen testing for SARS-CoV-2 has become an increasingly prominent screening tool in the ongoing COVID-19 pandemic and can be performed multiple times a week. However, the optimal weekly frequency of antigen testing is unclear; the Centers for Disease Control and Prevention recommends 1–3 times a week, while some experts support testing 2–3 times a week. In our own laboratory, all staff (n = 161) underwent twice- and thrice-weekly antigen tests during different periods from August 2021 to the present as part of routine COVID-19 surveillance of healthcare workers. No cases of COVID-19 were detected with either regimen. While more frequent SARS-CoV-2 antigen testing may allow antigen testing to be an important surrogate for RT-PCR testing, performing SARS-CoV-2 antigen tests twice or thrice a week shows no inferiority to each other in screening for COVID-19. Full article
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8 pages, 251 KiB  
Article
COVID-19 Disease and Associated Thrombocytopenia: Pathogenesis and a Clue to the Etiology
by Adil Abozaid Eissa
Diagnostics 2022, 12(5), 1038; https://doi.org/10.3390/diagnostics12051038 - 20 Apr 2022
Cited by 1 | Viewed by 1432
Abstract
(1) Background: Hospital mortality in patients suffering from SARS-CoV-2 infection has been associated with thrombocytopenia. The present study was conducted to establish the correlation of thrombocytopenia and the severity of infection. The impact of IL-1Ra gene polymorphism on the incidence and severity of [...] Read more.
(1) Background: Hospital mortality in patients suffering from SARS-CoV-2 infection has been associated with thrombocytopenia. The present study was conducted to establish the correlation of thrombocytopenia and the severity of infection. The impact of IL-1Ra gene polymorphism on the incidence and severity of thrombocytopenia was also studied. (2) Methods: Various biochemical parameters measured in all the 1200 enrolled patients included full blood counts, renal and liver function tests, iron study, inflammatory markers, and coagulation assays. A further 70 patients each were selected from the severe thrombocytopenic and non-thrombocytopenic patient groups to study the IL-1Ra gene polymorphism by RCR. (3) Results: Out of 1200 patients, 436 (36.3%) had thrombocytopenia. Among these patients, 118 (27.1%), 75 (17.2%), and 42 (9.6%) had mild, moderate, severe, and very severe thrombocytopenia, respectively. Severe cases mostly resulted from peripheral consumption (73.5%), hemo-phagocytosis (15.4%), and bone marrow suppression (11.11%). A statistically significant correlation was found between the occurrence and severity of thrombocytopenia with perturbated levels of inflammatory markers and the presence of comorbidities. The IL-1Ra∗3 variant was found to be significantly associated with thrombocytopenia. The IL-1Ra∗2 variant was significantly seen among controls. (4) Conclusions: The present study revealed a significant correlation between thrombocytopenia and the severity of COVID-19 disease. Moreover, the IL-1Ra∗3 variant of IL-1Ra gene was associated with thrombocytopenia. Full article
11 pages, 1262 KiB  
Article
Rapid and Reliable Detection of SARS-CoV-2 Using Direct RT-LAMP
by Sherif A. El-Kafrawy, Mai M. El-Daly, Ahmed M. Hassan, Steve M. Harakeh, Thamir A. Alandijany and Esam I. Azhar
Diagnostics 2022, 12(4), 828; https://doi.org/10.3390/diagnostics12040828 - 28 Mar 2022
Cited by 12 | Viewed by 2172
Abstract
Background: The global pandemic coronavirus SARS-CoV-2 has a healthcare, social and economic burden. To limit the spread of the virus, the World Health Organization (WHO) urgently called for extensive screening of suspected individuals; thus, a quick, simple, and sensitive diagnostic assay is always [...] Read more.
Background: The global pandemic coronavirus SARS-CoV-2 has a healthcare, social and economic burden. To limit the spread of the virus, the World Health Organization (WHO) urgently called for extensive screening of suspected individuals; thus, a quick, simple, and sensitive diagnostic assay is always in need. Methods: We applied reverse transcription-loop-mediated isothermal amplification (RT-LAMP) for the detection of SARS-CoV-2. The RT-LAMP method was optimized by evaluating two fluorescence amplification mixes and several reaction times, and results were compared to the standard real-time RT-PCR (rtRT-PCR). The assay was validated using 200 nasopharyngeal swabs collected in viral transport media (62 positive for SARS-CoV-2, and 138 negative for SARS-CoV-2 detected by the rtRT-PCR method). The samples were diluted 1:4 in diethylpyrocarbonate (DEPC)-treated water, utilized for RT-LAMP using different singleplex and multiplex sets of LAMP primers (N gene, S gene, and orf1ab gene), and incubated at 65 °C using real-time PCR 7500. Results: Our direct detection with the RT-LAMP protocol showed 100% concordance (sensitivity and specificity) with the standard protocol used for the detection of SARS-CoV-2 nucleic acid. Conclusions: In this study, we set up a rapid, simple, and sensitive RT-LAMP assay for the detection of SARS-CoV-2 in clinical samples. The assay is suitable for point of care detection in public hospitals, medical centers in rural areas, and in transportation hubs. Full article
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13 pages, 1074 KiB  
Article
The Utility of Laboratory Parameters for Cardiac Inflammation in Heart Failure Patients Hospitalized with SARS-CoV-2 Infection
by Ciprian Nicolae Pilut, Cosmin Citu, Florin Gorun, Felix Bratosin, Oana Maria Gorun, Bogdan Burlea, Ioana Mihaela Citu, Mirela Loredana Grigoras, Diana Manolescu and Adrian Gluhovschi
Diagnostics 2022, 12(4), 824; https://doi.org/10.3390/diagnostics12040824 - 27 Mar 2022
Cited by 16 | Viewed by 2213
Abstract
COVID-19 has been associated with cardiovascular consequences, including myocardial infarction, thromboembolic events, arrhythmia, and heart failure. Numerous overlapping mechanisms, such as the IL-6 dependent cytokine storm and unopposed angiotensin II stimulation, could be responsible for these consequences. Cardiac damage is hypothesized to be [...] Read more.
COVID-19 has been associated with cardiovascular consequences, including myocardial infarction, thromboembolic events, arrhythmia, and heart failure. Numerous overlapping mechanisms, such as the IL-6 dependent cytokine storm and unopposed angiotensin II stimulation, could be responsible for these consequences. Cardiac damage is hypothesized to be a consequence of the direct viral infection of cardiomyocytes, resulting in increased metabolic demand, immunological activation, and microvascular dysfunction. Patients with pre-existing chronic heart failure are therefore at increased risk of decompensation, further heart damage, and significant health deterioration. Based on the aforementioned assumptions, we developed a study aiming to provide a detailed description of changes in biological parameters and cardiac injury markers of patients with heart failure and SARS-CoV-2 infection by correlating them with the clinical presentation and COVID-19 vaccination status, to predict the probability of ICU admission based on their initial hospital presentation. A two-year retrospective study was performed on heart failure patients with a history of SARS-CoV-2 infection and detailed records of biological biomarkers; a total of 124 eligible patients with COVID-19 and 236 without COVID-19 were recruited. Patients with heart failure and SARS-CoV-2 infection had significantly elevated baseline biological parameters and cardiac markers compared to those without COVID-19. Several cardiac injury markers were identified as significant independent risk factors for ICU admission: CK-MB (HR = 4.1, CI [2.2–6.9]), myoglobin (HR = 5.0, CI [2.3–7.8]), troponin-I (HR = 7.1 [4.4–9.6]), troponin-T (HR = 4.9, CI [1.7–7.4]). The elevation of a basic panel of acute inflammation markers (CRP, IL-6, fibrinogen), D-dimers, and BNP was also a significant risk factor. The follow-up of survivors at four weeks after viral clearance determined a worsened clinical picture by NYHA classification, worsened cardiac ultrasound findings, and a mild improvement in cardiac and inflammatory markers. Increased levels of myocardial damage parameters in association with cardiac ultrasound findings and basic inflammatory markers may enable early risk assessment and triage in hospitalized heart failure patients infected with SARS-CoV-2. Full article
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7 pages, 580 KiB  
Communication
The Effect of Varying Interval Definitions on the Prevalence of SARS-CoV-2 Reinfections: A Retrospective Cross-Sectional Cohort Study
by Sjoerd M. Euser, Tieme Weenink, Jan M. Prins, Milly Haverkort, Irene Manders, Steven van Lelyveld, Bjorn L. Herpers, Jan Sinnige, Jayant Kalpoe, Dominic Snijders, James Cohen Stuart, Fred Slijkerman Megelink, Erik Kapteijns, Jeroen den Boer, Alex Wagemakers and Dennis Souverein
Diagnostics 2022, 12(3), 719; https://doi.org/10.3390/diagnostics12030719 - 15 Mar 2022
Cited by 1 | Viewed by 1528
Abstract
Background: We assessed the SARS-CoV-2 reinfection rate in a large patient cohort, and evaluated the effect of varying time intervals between two positive tests on assumed reinfection rates using viral load data. Methods: All positive SARS-CoV-2 samples collected between 1 March 2020 and [...] Read more.
Background: We assessed the SARS-CoV-2 reinfection rate in a large patient cohort, and evaluated the effect of varying time intervals between two positive tests on assumed reinfection rates using viral load data. Methods: All positive SARS-CoV-2 samples collected between 1 March 2020 and 1 August 2021 from a laboratory in the region Kennemerland, the Netherlands, were included. The reinfection rate was analyzed using different time intervals between two positive tests varying between 2 and 16 weeks. SARS-CoV-2 PCR crossing point (Cp) values were used to estimate viral loads. Results: In total, 679,513 samples were analyzed, of which 53,366 tests (7.9%) were SARS-CoV-2 positive. The number of reinfections varied between 260 (0.52%) for an interval of 2 weeks, 89 (0.19%) for 4 weeks, 52 (0.11%) for 8 weeks, and 37 (0.09%) for a minimum interval of 16 weeks between positive tests. The median Cp-value (IQR) in the second positive samples decreased when a longer interval was chosen, but stabilized from week 8 onwards. Conclusions: Although the calculated reinfection prevalence was relatively low (0.11% for the 8-week time interval), choosing a different minimum interval between two positive tests resulted in major differences in reinfection rates. As reinfection Cp-values stabilized after 8 weeks, we hypothesize this interval to best reflect novel infection rather than persistent shedding. Full article
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10 pages, 2141 KiB  
Article
Evaluation and Comparison of the Predictive Value of 4C Mortality Score, NEWS, and CURB-65 in Poor Outcomes in COVID-19 Patients: A Retrospective Study from a Single Center in Romania
by Cosmin Citu, Florin Gorun, Andrei Motoc, Adrian Ratiu, Oana Maria Gorun, Bogdan Burlea, Octavian Neagoe, Ioana Mihaela Citu, Ovidiu Rosca, Felix Bratosin, Mirela Loredana Grigoras, Raul Patrascu and Daniel Malita
Diagnostics 2022, 12(3), 703; https://doi.org/10.3390/diagnostics12030703 - 13 Mar 2022
Cited by 20 | Viewed by 2262
Abstract
To date, the COVID-19 pandemic has caused millions of deaths across the world. Prognostic scores can improve the clinical management of COVID-19 diagnosis and treatment. The objective of this study was to assess the predictive role of 4C Mortality, CURB-65, and NEWS in [...] Read more.
To date, the COVID-19 pandemic has caused millions of deaths across the world. Prognostic scores can improve the clinical management of COVID-19 diagnosis and treatment. The objective of this study was to assess the predictive role of 4C Mortality, CURB-65, and NEWS in COVID-19 mortality among the Romanian population. A single-center, retrospective, observational study was conducted on patients with reverse transcriptase-polymerase chain reaction (RT-PCR)-proven COVID-19 admitted to the Municipal Emergency Clinical Hospital of Timisoara, Romania, between 1 October 2020 and 15 March 2021. Receiver operating characteristic (ROC) and area under the curve (AUC) analyses were performed to determine the discrimination accuracy of the three scores. The mean values of the risk scores were higher in the non-survivors group (survivors group vs. non-survivors group: 8 vs. 15 (4C Mortality Score); 3 vs. 8.5 (NEWS); 1 vs. 3 (CURB-65)). In terms of mortality risk prediction, the NEWS performed best, with an AUC of 0.86, and the CURB-65 score performed poorly, with an AUC of 0.80. CURB-65, NEWS, and 4C Mortality scores were significant mortality predictors in the analysis, with acceptable calibration. Among the scores assessed in our study, NEWS had the highest performance in predicting in-hospital mortality in COVID-19 patients. Thus, the findings from this study suggest that the use of NEWS may be beneficial to the early identification of high-risk COVID-19 patients and the provision of more aggressive care to reduce mortality associated with COVID-19. Full article
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11 pages, 719 KiB  
Article
The AIFELL Score as a Predictor of Coronavirus Disease 2019 (COVID-19) Severity and Progression in Hospitalized Patients
by Ian Levenfus, Enrico Ullmann, Katja Petrowski, Jutta Rose, Lars C. Huber, Melina Stüssi-Helbling and Macé M. Schuurmans
Diagnostics 2022, 12(3), 604; https://doi.org/10.3390/diagnostics12030604 - 27 Feb 2022
Cited by 3 | Viewed by 3090
Abstract
Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has caused a global burden for health care systems due to high morbidity and mortality rates, leading to caseloads that episodically surpass hospital resources. Due to different disease manifestations, the triage of patients at high [...] Read more.
Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has caused a global burden for health care systems due to high morbidity and mortality rates, leading to caseloads that episodically surpass hospital resources. Due to different disease manifestations, the triage of patients at high risk for a poor outcome continues to be a major challenge for clinicians. The AIFELL score was developed as a simple decision instrument for emergency rooms to distinguish COVID-19 patients in severe disease stages from less severe COVID-19 and non-COVID-19 cases. In the present study, we aimed to evaluate the AIFELL score as a prediction tool for clinical deterioration and disease severity in hospitalized COVID-19 patients. During the second wave of the COVID-19 pandemic in Switzerland, we analyzed consecutively hospitalized patients at the Triemli Hospital Zurich from the end of November 2020 until mid-February 2021. Statistical analyses were performed for group comparisons and to evaluate significance. AIFELL scores of patients developing severe COVID-19 stages IIb and III during hospitalization were significantly higher upon admission compared to those patients not surpassing stages I and IIa. Group comparisons indicated significantly different AIFELL scores between each stage. In conclusion, the AIFELL score at admission was useful to predict the disease severity and progression in hospitalized COVID-19 patients. Full article
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9 pages, 4063 KiB  
Article
An In Vivo Observational Histological Study of Peripheral Arterial Damage in Patients with Acute Limb Ischemia in SARS-CoV-2 Infection
by Sorin Barac, Roxana Ramona Onofrei, Codruta Lazureanu, Robert Barna, Adrian Tutelca and Andreea Luciana Rata
Diagnostics 2022, 12(2), 488; https://doi.org/10.3390/diagnostics12020488 - 14 Feb 2022
Cited by 2 | Viewed by 1488
Abstract
Thromboembolic events, such as acute limb ischemia, were reported worldwide in patients with COVID-19, suggesting that SARS-CoV-2 infection acts like a redoubtable prothrombotic factor in these patients. The aim of the study was to summarize the histopathological changes found in the arterial wall, [...] Read more.
Thromboembolic events, such as acute limb ischemia, were reported worldwide in patients with COVID-19, suggesting that SARS-CoV-2 infection acts like a redoubtable prothrombotic factor in these patients. The aim of the study was to summarize the histopathological changes found in the arterial wall, intraarterial thrombus, and adjacent skeletal muscles. Considering the lack of evidence from in vivo studies, we performed observational histological research of peripheral arterial damage in patients with acute limb ischemia and SARS-CoV-2 infection. We investigated 22 patients with acute limb ischemia and SARS and harvested histopathological samples from those who agreed to this procedure. We performed histologic tissue harvesting during the revascularization procedure from the thrombosed area of the common femoral artery. Morphologic analysis was made on the hematoxylin-eosin (HE) stain. Special stains were also used—Elastica van Gieson (EvG) and Alcian Blue—Periodic Acid—Schiff (AB-PAS) and primary antibodies—CD45 and CD61. Our patients had significant risk factors for thrombus formation, since all of them had arterial hypertension, 81% had dyslipidemia, 73% were obese, 63% suffered from diabetes mellitus, and 45% were active smokers. The histological findings using immunohistochemistry (CD45 and CD68 reactions) or special and usual stains underlined the mechanism for ischemia production in SARS-CoV-2 patients. The main histological findings in our study were endothelial destruction and inflammation that were found in all analyzed structures. Full article
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6 pages, 831 KiB  
Communication
Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading
by Valerio Caputo, Giulia Calvino, Claudia Strafella, Andrea Termine, Carlo Fabrizio, Giulia Trastulli, Arcangela Ingrascì, Cristina Peconi, Silvia Bardini, Angelo Rossini, Antonino Salvia, Giovanna Borsellino, Luca Battistini, Carlo Caltagirone, Raffaella Cascella and Emiliano Giardina
Diagnostics 2022, 12(2), 467; https://doi.org/10.3390/diagnostics12020467 - 11 Feb 2022
Cited by 11 | Viewed by 2207
Abstract
The emergence of the Omicron SARS-CoV-2 variant caused public health concerns worldwide, raising the need for the improvement of rapid monitoring strategies. The present manuscript aimed at providing evidence of the utility of a diagnostic kit for the routine testing of SARS-CoV-2 infection [...] Read more.
The emergence of the Omicron SARS-CoV-2 variant caused public health concerns worldwide, raising the need for the improvement of rapid monitoring strategies. The present manuscript aimed at providing evidence of the utility of a diagnostic kit for the routine testing of SARS-CoV-2 infection as a cost-effective method for tracking the Omicron variant in Italy. The study was conducted on patients’ naso-oropharyngeal-swab-derived RNA samples. These samples were subjected to RT-PCR using the TaqPath COVID-19 RT PCR CE IVD kit. Nonparametric testing and polynomial models fitting were used to compare the spreading of Alpha, Delta and Omicron variants. The samples of interest were correctly amplified and displayed the presence of S gene-target failure, suggesting that these patients carry the Omicron variant. The trend of diffusion was found to be significantly different and more rapid compared with that of the Alpha and Delta variants in our cohorts. Overall, these results highlight that the S gene target failure was a very useful tool for the immediate and inexpensive tracking of Omicron variant in the three weeks from the first detection. Thus, our approach could be used as a first-line screening to reduce the time and costs of monitoring strategies, facilitating the management of preventive and counteracting measures against COVID-19. Full article
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9 pages, 748 KiB  
Article
Evaluation and Modelling of the Performance of an Automated SARS-CoV-2 Antigen Assay According to Sample Type, Target Population and Epidemic Trends
by Nicolas Yin, Cyril Debuysschere, Valery Daubie, Marc Hildebrand, Charlotte Martin, Sonja Curac, Fanny Ponthieux, Marie-Christine Payen, Olivier Vandenberg and Marie Hallin
Diagnostics 2022, 12(2), 447; https://doi.org/10.3390/diagnostics12020447 - 09 Feb 2022
Cited by 2 | Viewed by 1394
Abstract
The Lumipulse® G SARS-CoV-2 Ag assay performance was evaluated on prospectively collected saliva and nasopharyngeal swabs (NPS) of recently ill in- and outpatients and according to the estimated viral load. Performances were calculated using RT-PCR positive NPS from patients with symptoms [...] Read more.
The Lumipulse® G SARS-CoV-2 Ag assay performance was evaluated on prospectively collected saliva and nasopharyngeal swabs (NPS) of recently ill in- and outpatients and according to the estimated viral load. Performances were calculated using RT-PCR positive NPS from patients with symptoms ≤ 7 days and RT-PCR negative NPS as gold standard. In addition, non-selected positive NPS were analyzed to assess the performances on various viral loads. This assay yielded a sensitivity of 93.1% on NPS and 71.4% on saliva for recently ill patients. For NPS with a viral load > 103 RNA copies/mL, sensitivity was 96.4%. A model established on our daily routine showed fluctuations of the performances depending on the epidemic trends but an overall good negative predictive value. Lumipulse® G SARS-CoV-2 assay yielded good performance for an automated antigen detection assay on NPS. Using it for the detection of recently ill patients or to screen high-risk patients could be an interesting alternative to the more expensive RT-PCR. Full article
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21 pages, 2484 KiB  
Article
Fast and Accurate Surrogate Virus Neutralization Test Based on Antibody-Mediated Blocking of the Interaction of ACE2 and SARS-CoV-2 Spike Protein RBD
by Denis E. Kolesov, Maria V. Sinegubova, Lutsia K. Dayanova, Inna V. Dolzhikova, Ivan I. Vorobiev and Nadezhda A. Orlova
Diagnostics 2022, 12(2), 393; https://doi.org/10.3390/diagnostics12020393 - 03 Feb 2022
Cited by 5 | Viewed by 2577
Abstract
The humoral response to the SARS-CoV-2 S protein determines the development of protective immunity against this infection. The standard neutralizing antibodies detection method is a live virus neutralization test. It can be replaced with an ELISA-based surrogate virus neutralization test (sVNT), measuring the [...] Read more.
The humoral response to the SARS-CoV-2 S protein determines the development of protective immunity against this infection. The standard neutralizing antibodies detection method is a live virus neutralization test. It can be replaced with an ELISA-based surrogate virus neutralization test (sVNT), measuring the ability of serum antibodies to inhibit complex formation between the receptor-binding domain (RBD) of the S protein and the cellular ACE2 receptor. There are conflicting research data on the sVNT methodology and the reliability of its results. We show that the performance of sVNT dramatically improves when the intact RBD from the Wuhan-Hu-1 virus variant is used as the plate coating reagent, and the HRP-conjugated soluble ACE2 is used as the detection reagent. This design omits the pre-incubation step in separate tubes or separate microplate and allows the simple quantification of the results using the linear regression, utilizing only 3–4 test sample dilutions. When this sVNT was performed for 73 convalescent plasma samples, its results showed a very strong correlation with VNT (Spearman’s Rho 0.83). For the RBD, bearing three amino acid substitutions and corresponding to the SARS-CoV-2 beta variant, the inhibitory strength was diminished for 18 out of 20 randomly chosen serum samples, and the magnitude of this decrease was not similar to the change in overall anti-RBD IgG level. The sVNT assay design with the ACE2-HRP is preferable over the assay with the RBD-HRP reagent and is suitable for mass screening of neutralizing antibodies titers. Full article
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11 pages, 15154 KiB  
Article
Development, Analytical, and Clinical Evaluation of Rapid Immunochromatographic Antigen Test for SARS-CoV-2 Variants Detection
by Jidapa Szekely, Jenureeyah Mongkolprasert, Nitikorn Jeayodae, Chadarat Senorit, Panuttha Chaimuti, Piyawut Swangphon, Natthaphon Nanakorn, Teerapat Nualnoi, Paweena Wongwitwichot and Theerakamol Pengsakul
Diagnostics 2022, 12(2), 381; https://doi.org/10.3390/diagnostics12020381 - 02 Feb 2022
Cited by 7 | Viewed by 5834
Abstract
The antigen rapid diagnostic test (Ag-RDT) is a useful diagnostic tool for the detection and management of COVID-19 spread. Global SARS-CoV-2 variant outbreaks have highlighted the need for a test capable of detecting SARS-CoV-2 variants with high sensitivity and a low limit of [...] Read more.
The antigen rapid diagnostic test (Ag-RDT) is a useful diagnostic tool for the detection and management of COVID-19 spread. Global SARS-CoV-2 variant outbreaks have highlighted the need for a test capable of detecting SARS-CoV-2 variants with high sensitivity and a low limit of detection. This study aimed to develop and evaluate, both analytically and clinically, an antigen rapid diagnostic test (the KestrelTM COVID-19 Ag Rapid Test) for professional use. A lateral flow immunoassay-based diagnostic test kit was developed, and various aspects of its analytical performance were evaluated. This test kit was clinically evaluated by two independent laboratories and showed closely related results of 96.49% and 98.33% of sensitivity, 100% and 100% of specificity, and 99.01% and 99.44% of accuracy, respectively. A limit of detection was observed at values as low as 0.156 ng/mL for recombinant SARS-CoV-2 nucleocapsid protein. Moreover, the test kit successfully detected the recombinant SARS-CoV-2 nucleocapsid protein (NP) of wild-type, Alpha-, Beta-, Gamma-, Delta-, Epsilon-, Kappa-, and Omicron-variants as positive results. Therefore, the KestrelTM COVID-19 Ag Rapid Test may have potential use for effective COVID-19 screening, surveillance, and infection control in a variety of global SARS-CoV-2 variant outbreaks. Full article
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4 pages, 514 KiB  
Communication
Undetected Omicron Transmission in Romania—Report of the First Detected Case of Locally Acquired Omicron Infection and Complete Epidemiological Investigation
by Anca Streinu-Cercel, Oana Săndulescu, Victor Daniel Miron, Simona Paraschiv, Corina Casangiu, Robert Hohan, Leontina Bănică, Marius Surleac and Adrian Streinu-Cercel
Diagnostics 2022, 12(2), 348; https://doi.org/10.3390/diagnostics12020348 - 29 Jan 2022
Cited by 7 | Viewed by 2173
Abstract
The occurrence of the omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has importantly impacted surveillance and diagnosis, and has changed the therapeutic landscape of coronavirus disease 2019 (COVID-19). We present the first documented case of locally acquired SARS-CoV-2 omicron variant [...] Read more.
The occurrence of the omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has importantly impacted surveillance and diagnosis, and has changed the therapeutic landscape of coronavirus disease 2019 (COVID-19). We present the first documented case of locally acquired SARS-CoV-2 omicron variant in Romania in a patient with no recent travel outside the country. We also present the full results of the epidemiological investigation that led to the identification of the index case in a co-worker who had developed mild symptoms shortly after returning from the UK and who had undergone multiple rapid antigen tests with negative results prior to being tested by RT-PCR. We highlight potential lessons learned and describe further directions for actionable research and development in the field of COVID-19. Full article
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13 pages, 877 KiB  
Article
SARS-CoV-2 Sero-Surveillance in Greece: Evolution over Time and Epidemiological Attributes during the Pre-Vaccination Pandemic Era
by Michalis Koureas, Zacharoula Bogogiannidou, Alexandros Vontas, Maria A. Kyritsi, Varvara A. Mouchtouri, Katerina Dadouli, Lemonia Anagnostopoulos, Paraskevi Mina, Alexia Matziri, Maria Ntouska, Maria Tsigaridaki, Vasiliki Gkiata, Konstantinos K. Tsilidis, Evangelia E. Ntzani, Panagiotis Prezerakos, Sotirios Tsiodras, Matthaios Speletas and Christos Hadjichristodoulou
Diagnostics 2022, 12(2), 295; https://doi.org/10.3390/diagnostics12020295 - 25 Jan 2022
Cited by 1 | Viewed by 2623
Abstract
Background: Nation-wide SARS-CoV-2 seroprevalence surveys provide valuable insights into the course of the pandemic, including information often not captured by routine surveillance of reported cases. Methods: A serosurvey of IgG antibodies against SARS-CoV-2 was conducted in Greece between March and December 2020. It [...] Read more.
Background: Nation-wide SARS-CoV-2 seroprevalence surveys provide valuable insights into the course of the pandemic, including information often not captured by routine surveillance of reported cases. Methods: A serosurvey of IgG antibodies against SARS-CoV-2 was conducted in Greece between March and December 2020. It was designed as a cross-sectional survey repeated at monthly intervals. The leftover sampling methodology was used and a geographically stratified sampling plan was applied. Results: Of 55,947 serum samples collected, 705 (1.26%) were found positive for anti-SARS-CoV-2 antibodies, with higher seroprevalence (9.09%) observed in December 2020. Highest seropositivity levels were observed in the “0–29” and “30–49” year age groups. Seroprevalence increased with age in the “0–29” age group. Highly populated metropolitan areas were characterized with elevated seroprevalence levels (11.92% in Attica, 12.76% in Thessaloniki) compared to the rest of the country (5.90%). The infection fatality rate (IFR) was estimated at 0.451% (95% CI: 0.382–0.549%) using aggregate data until December 2020, and the ratio of actual to reported cases was 9.59 (7.88–11.33). Conclusions: The evolution of seroprevalence estimates aligned with the course of the pandemic and varied widely by region and age group. Young and middle-aged adults appeared to be drivers of the pandemic during a severe epidemic wave under strict policy measures. Full article
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9 pages, 537 KiB  
Article
SARS-CoV-2 Saliva Mass Screening in Primary Schools: A 10-Week Sentinel Surveillance Study in Munich, Germany
by Sebastian Vogel, Ulrich von Both, Elisabeth Nowak, Janina Ludwig, Alexandra Köhler, Noah Lee, Elisabeth Dick, Anita Rack-Hoch, Bernd Wicklein, Jessica Neusser, Tobias Wagner, Alexandra Schubö, Maxim Ustinov, Werner Schimana, Stephan Busche, Laura Kolberg and Martin Hoch
Diagnostics 2022, 12(1), 162; https://doi.org/10.3390/diagnostics12010162 - 11 Jan 2022
Cited by 5 | Viewed by 1361
Abstract
Representative, actively collected surveillance data on asymptomatic SARS-CoV-2 infections in primary schoolchildren remain scarce. We evaluated the feasibility of a saliva mass screening concept and assessed infectious activity in primary schools. During a 10-week period from 3 March to 21 May 2021, schoolchildren [...] Read more.
Representative, actively collected surveillance data on asymptomatic SARS-CoV-2 infections in primary schoolchildren remain scarce. We evaluated the feasibility of a saliva mass screening concept and assessed infectious activity in primary schools. During a 10-week period from 3 March to 21 May 2021, schoolchildren and staff from 17 primary schools in Munich participated in the sentinel surveillance, cohort study. Participants were tested using the Salivette® system, testing was supervised by trained school staff, and samples were processed via reverse transcription quantitative polymerase chain reaction (RT-qPCR). We included 4433 participants: 3752 children (median age, 8 [range, 6–13] years; 1926 girls [51%]) and 681 staff members (median age, 41 [range, 14–71] years; 592 women [87%]). In total, 23,905 samples were processed (4640 from staff), with participants representing 8.3% of all primary schoolchildren in Munich. Only eight cases were detected: Five out of 3752 participating children (0.13%) and three out of 681 staff members (0.44%). There were no secondary cases. In conclusion, supervised Salivette® self-sampling was feasible, reliable, and safe and thus constituted an ideal method for SARS-CoV-2 mass screenings in primary schoolchildren. Our findings suggest that infectious activity among asymptomatic primary schoolchildren and staff was low. Primary schools appear to continue to play a minor role in the spread of SARS-CoV-2 despite high community incidence rates. Full article
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10 pages, 1469 KiB  
Article
The Predictive Role of NLR, d-NLR, MLR, and SIRI in COVID-19 Mortality
by Cosmin Citu, Florin Gorun, Andrei Motoc, Ioan Sas, Oana Maria Gorun, Bogdan Burlea, Ioana Tuta-Sas, Larisa Tomescu, Radu Neamtu, Daniel Malita and Ioana Mihaela Citu
Diagnostics 2022, 12(1), 122; https://doi.org/10.3390/diagnostics12010122 - 06 Jan 2022
Cited by 59 | Viewed by 3321
Abstract
(1) Background: Since its discovery, COVID-19 has caused more than 256 million cases, with a cumulative death toll of more than 5.1 million, worldwide. Early identification of patients at high risk of mortality is of great importance in saving the lives of COVID-19 [...] Read more.
(1) Background: Since its discovery, COVID-19 has caused more than 256 million cases, with a cumulative death toll of more than 5.1 million, worldwide. Early identification of patients at high risk of mortality is of great importance in saving the lives of COVID-19 patients. The study aims to assess the utility of various inflammatory markers in predicting mortality among hospitalized patients with COVID-19. (2) Methods: A retrospective observational study was conducted among 108 patients with laboratory-confirmed COVID-19 hospitalized between 1 May 2021 and 31 October 2021 at Municipal Emergency Clinical Hospital of Timisoara, Romania. Blood cell counts at admission were used to obtain NLR, dNLR, MLR, PLR, SII, and SIRI. The association of inflammatory index and mortality was assessed via Kaplan–Maier curves univariate Cox regression and binominal logistic regression. (3) Results: The median age was 63.31 ± 14.83, the rate of in-hospital death being 15.7%. The optimal cutoff for NLR, dNLR, MLR, and SIRI was 9.1, 9.6, 0.69, and 2.2. AUC for PLR and SII had no statistically significant discriminatory value. The binary logistic regression identified elevated NLR (aOR = 4.14), dNLR (aOR = 14.09), and MLR (aOR = 3.29), as independent factors for poor clinical outcome of COVID-19. (4) Conclusions: NLR, dNLR, MLR have significant predictive value in COVID-19 mortality. Full article
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11 pages, 847 KiB  
Article
Clinical Sensitivity, Specificity and Epidemiology of SARS-CoV-2 Serological Testing Using the Biozek COVID-19 Test
by Dennis Souverein, Theo G. Mank, Sjoerd M. Euser and Bjorn L. Herpers
Diagnostics 2022, 12(1), 60; https://doi.org/10.3390/diagnostics12010060 - 28 Dec 2021
Viewed by 1525
Abstract
Background: Clinical validation using the Biozek COVID-19 test including sensitivity and specificity and associated patient-reported symptoms with SARS-CoV-2 seropositivity. Methods: 316 sera were analyzed including 47 hospitalized cases, 50 mild cases and 219 negative controls. Results were read visually by two technicians and [...] Read more.
Background: Clinical validation using the Biozek COVID-19 test including sensitivity and specificity and associated patient-reported symptoms with SARS-CoV-2 seropositivity. Methods: 316 sera were analyzed including 47 hospitalized cases, 50 mild cases and 219 negative controls. Results were read visually by two technicians and in case of discrepancy by a third. Models were created between independent variables and IgG seropositivity using multivariable logistic regression analysis. Results: Sensitivity of both IgM and IgG together for hospitalized patients at all time periods was 68.1% (32/47) and 90.0% (27/30) after 10 days or more. From mild/asymptomatic cases the combined IgM and IgG sensitivity was 92.0% (46/50) and 91.8% (45/49) after 10 days or more. In the group of non-COVID-19 cases, the overall specificity was 99.1% (217/219). For IgG alone, the specificity was 99.5% (218/219). In the multivariable analysis loss of smell remained the strongest associated variable with an odds ratio (95%CI): 6.82 (5.61–8.31), p-value < 0.001. Our final prediction model yielded a ROC-AUC of 0.77 (0.74–0.81) showing acceptable discrimination. Conclusions: The Biozek COVID-19 test showed high specificity and good sensitivity 10 days after the first sickness day. Solely IgM positive tests must be interpreted with caution and preferably excluded. In order to capture most symptomatic COVID-19 cases, loss of smell should be included within symptomatic screening policies. Full article
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12 pages, 1540 KiB  
Article
Impact of the Nucleic Acid Extraction Method and the RT-qPCR Assay on SARS-CoV-2 Detection in Low-Viral Samples
by Magdalena Komiazyk, Jarosław Walory, Aleksandra Kozinska, Izabela Wasko and Anna Baraniak
Diagnostics 2021, 11(12), 2247; https://doi.org/10.3390/diagnostics11122247 - 30 Nov 2021
Cited by 9 | Viewed by 2536
Abstract
COVID-19 was initially reported in China at the end of 2019 and soon thereafter, in March 2020, the WHO declared it a pandemic. Until October 2021, over 240 million COVID-19 cases were recorded, with 4.9 mln deaths. In order to stop the spread [...] Read more.
COVID-19 was initially reported in China at the end of 2019 and soon thereafter, in March 2020, the WHO declared it a pandemic. Until October 2021, over 240 million COVID-19 cases were recorded, with 4.9 mln deaths. In order to stop the spread of this disease, it is crucial to monitor and detect any infected person. The etiologic agent of COVID-19 is a novel coronavirus called SARS-CoV-2. The gold standard for the detection of the virus is the RT-qPCR method. This study evaluated two RNA extraction methods and four commercial RT-qPCR assays routinely used in diagnostic laboratories for detecting SARS-CoV-2 in human specimens from the upper respiratory tract. We analyzed a panel of 70 clinical samples with varying RNA loads. Our study demonstrated the significant impact of the diagnostic methods selected by the laboratory on the SARS-CoV-2 detection in clinical specimens with low viral loads. Full article
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6 pages, 675 KiB  
Article
Correlation between Commercial Anti-RBD IgG Titer and Neutralization Titer against SARS-CoV-2 Beta Variant
by Rosana Wing-Shan Poon, Lu Lu, Carol Ho-Yan Fong, Tak-Chuen Ip, Lin-Lei Chen, Ricky Rui-Qi Zhang, Cyril Chik-Yan Yip, Vincent Chi-Chung Cheng, Kwok-Hung Chan, Kwok-Yung Yuen and Kelvin Kai-Wang To
Diagnostics 2021, 11(12), 2216; https://doi.org/10.3390/diagnostics11122216 - 27 Nov 2021
Cited by 4 | Viewed by 1881
Abstract
Objectives: The emergence of SARS-CoV-2 variants of concern (VOCs) have diminished the effectiveness of vaccines and are associated with a rebound in the number of COVID-19 cases globally. These variants contain mutations at the spike (S) protein receptor binding site (RBD), which affect [...] Read more.
Objectives: The emergence of SARS-CoV-2 variants of concern (VOCs) have diminished the effectiveness of vaccines and are associated with a rebound in the number of COVID-19 cases globally. These variants contain mutations at the spike (S) protein receptor binding site (RBD), which affect antibody binding. Current commercially available antibody assays were developed before the VOCs emerged. It is unclear whether the levels of these commercially available antibody assays can predict the neutralizing antibody titers against the VOCs. In this study, we sought to determine the correlation between the binding antibody concentration and microneutralization antibody titer against the beta variant. Methods: This study included 58 COVID-19 patients. The concentrations of IgG against the SARS-CoV-2 spike protein RBD and nucleocapsid (N) protein were measured using the Abbott SARS-CoV-2 IgG II Quant assay and the SARS-CoV-2 IgG assay, respectively. The neutralization antibody titer against the wild type lineage A SARS-CoV-2 and against the beta variant (B.1.351) was determined using a conventional live virus neutralization test. Results: The geometric mean MN titer (GMT) against the beta variant was significantly lower than that against the wild type lineage A virus (5.6 vs. 47.3, p < 0.0001). The anti-RBD IgG had a better correlation with the neutralizing antibody titer than that of the anti-N IgG assay against the wild type lineage A virus (Spearman rho, 0.5901 vs. 0.3827). However, the correlation between the anti-RBD or the anti-N IgG and the MN titer against the beta variant was poor. Conclusions: Currently available commercial antibody assays may not predict the level of neutralizing antibodies against the variants. A new generation of antibody tests specific for variants are required. Full article
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9 pages, 11193 KiB  
Article
SARS-CoV-2 Infection Prevalence in the Population of South-Eastern Poland
by Ewa Stępień, Marcin Koleśnik, Katarzyna Mitura, Maria Malm, Bartłomiej Drop, Marian Jędrych and Małgorzata Polz-Dacewicz
Diagnostics 2021, 11(11), 2115; https://doi.org/10.3390/diagnostics11112115 - 15 Nov 2021
Cited by 2 | Viewed by 1465
Abstract
COVID-19 outbreak began in Wuhan, China, and has spread to other continents, including Europe, placing pressure on healthcare systems. Poland is one of the European countries with the highest number of SARS-CoV-2 infections and COVID-19-related deaths. The aim of this study was to [...] Read more.
COVID-19 outbreak began in Wuhan, China, and has spread to other continents, including Europe, placing pressure on healthcare systems. Poland is one of the European countries with the highest number of SARS-CoV-2 infections and COVID-19-related deaths. The aim of this study was to analyze the presence of SARS-CoV-2 in the population of south-eastern Poland. The correlation between viral infection and demographic data (gender, age, place of residence) and cancer was also investigated. A total of 44,801 samples were tested, of which 4862 cases were diagnosed with SARS-CoV-2 infections. A total of 14,970 samples were tested in cancer patients. The RT-PCR method was used to detect viral nucleic acid. In this study, significantly, the highest rate of virus detection was among people living in Lublin and the lowest among people living in a small town (p < 0.0001). Moreover, there was no significant relationship between sex and the frequency of virus detection. The highest number of SARS-CoV-2 infections was observed in the age groups 10–19, 20–29, 30–39, and 90+ (p = 0.0001). In cancer patients, the percentage of positive cases was significantly lower than in the rest (p = 0.0001). Full article
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15 pages, 9152 KiB  
Article
A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue
by Rama Devudu Puligedda, Fetweh H. Al-Saleem, Cristoph Wirblich, Chandana Devi Kattala, Marko Jović, Laura Geiszler, Himani Devabhaktuni, Giora Z. Feuerstein, Matthias J. Schnell, Markus Sack, Lawrence L. Livornese, Jr. and Scott K. Dessain
Diagnostics 2021, 11(11), 2092; https://doi.org/10.3390/diagnostics11112092 - 12 Nov 2021
Cited by 7 | Viewed by 3464
Abstract
Efforts to control SARS-CoV-2 have been challenged by the emergence of variant strains that have important implications for clinical and epidemiological decision making. Four variants of concern (VOCs) have been designated by the Centers for Disease Control and Prevention (CDC), namely, B.1.617.2 (delta), [...] Read more.
Efforts to control SARS-CoV-2 have been challenged by the emergence of variant strains that have important implications for clinical and epidemiological decision making. Four variants of concern (VOCs) have been designated by the Centers for Disease Control and Prevention (CDC), namely, B.1.617.2 (delta), B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), although the last three have been downgraded to variants being monitored (VBMs). VOCs and VBMs have shown increased transmissibility and/or disease severity, resistance to convalescent SARS-CoV-2 immunity and antibody therapeutics, and the potential to evade diagnostic detection. Methods are needed for point-of-care (POC) testing to rapidly identify these variants, protect vulnerable populations, and improve surveillance. Antigen-detection rapid diagnostic tests (Ag-RDTs) are ideal for POC use, but Ag-RDTs that recognize specific variants have not yet been implemented. Here, we describe a mAb (2E8) that is specific for the SARS-CoV-2 spike protein N501 residue. The 2E8 mAb can distinguish the delta VOC from variants with the N501Y meta-signature, which is characterized by convergent mutations that contribute to increased virulence and evasion of host immunity. Among the N501Y-containing mutants formerly designated as VOCs (alpha, beta, and gamma), a previously described mAb, CB6, can distinguish beta from alpha and gamma. When used in a sandwich ELISA, these mAbs sort these important SARS-CoV-2 variants into three diagnostic categories, namely, (1) delta, (2) alpha or gamma, and (3) beta. As delta is currently the predominant variant globally, they will be useful for POC testing to identify N501Y meta-signature variants, protect individuals in high-risk settings, and help detect epidemiological shifts among SARS-CoV-2 variants. Full article
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10 pages, 2428 KiB  
Article
COVID-19 Diagnostics Outside and Inside the National Health Service: A Single Institutional Experience
by Lukasz Fulawka and Aleksandra Kuzan
Diagnostics 2021, 11(11), 2044; https://doi.org/10.3390/diagnostics11112044 - 04 Nov 2021
Cited by 4 | Viewed by 2217
Abstract
The COVID-19 epidemic has been going on continuously for more than 1.5 years. Fast and reliable diagnosis is a key component of an outbreak response strategy. Our goal is to present the statistics from one of the diagnostic points of a large city [...] Read more.
The COVID-19 epidemic has been going on continuously for more than 1.5 years. Fast and reliable diagnosis is a key component of an outbreak response strategy. Our goal is to present the statistics from one of the diagnostic points of a large city in Poland. Swabs of the throat or nasopharynx of people reporting for molecular diagnostics of SARS-CoV-2 presence were taken. CE-IVD-certified RNA isolation and RT-PCR assays were used. According to our data, the prevalence of SARS-CoV-2 infection in the examined population equaled 14.7%; however, large differences were observed depending on where the sampling point was located: as much as 50.3% of positive results for samples collected at a stationary point, 36.2% for samples from inpatients and hospital staff, and only 8.9% for samples from patients whose test was paid by their employer. The age structure of the infected population was fairly even, with a slightly higher number of people over 50 years of age. Men were examined more often, but it was among women that a higher percentage of infection was recorded. Every fifth test was performed for a foreigner, but compared to Poles, a much lower incidence of infection was found in these samples. We conclude that due to the high prevalence of infection in patients from social care centers and in those referred to hospitals, it is recommended that a special sanitary regime is followed in those settings. We will evaluate the effectiveness of vaccinations, expecting that the coming months bring positive changes in the statistics on prevalence. Full article
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10 pages, 1507 KiB  
Article
Valid and Reliable Assessment of Upper Respiratory Tract Specimen Collection Skills during the COVID-19 Pandemic
by Tobias Todsen, Anne Bohr, Lisette Hvid Hovgaard, Rebekka Consuelo Eið, Thomas Benfield, Morten B. S. Svendsen, Nikolai Kirkby, Lars Konge, Christian von Buchwald, Jacob Melchiors and Martin Tolsgaard
Diagnostics 2021, 11(11), 1987; https://doi.org/10.3390/diagnostics11111987 - 26 Oct 2021
Cited by 5 | Viewed by 2239
Abstract
Proper specimen collection is the most important step to ensure accurate testing for the coronavirus disease 2019 (COVID-19) and other infectious diseases. Assessment of healthcare workers’ upper respiratory tract specimen collection skills is needed to ensure samples of high-quality clinical specimens for COVID-19 [...] Read more.
Proper specimen collection is the most important step to ensure accurate testing for the coronavirus disease 2019 (COVID-19) and other infectious diseases. Assessment of healthcare workers’ upper respiratory tract specimen collection skills is needed to ensure samples of high-quality clinical specimens for COVID-19 testing. This study explored the validity evidence for a theoretical MCQ-test and checklists developed for nasopharyngeal (NPS) and oropharyngeal (OPS) specimen collection skills assessment. We found good inter-item reliability (Cronbach’s alpha = 0.76) for the items of the MCQ-test and high inter-rater reliability using the checklist for the assessment of OPS and NPS skills on 0.86 and 0.87, respectively. The MCQ scores were significantly different between experts (mean 98%) and novices (mean 66%), p < 0.001, and a pass/fail score of 91% was established. We found a significant discrimination between checklist scores of experts (mean 95% score for OPS and 89% for NPS) and novices (mean 50% score for OPS and 36% for NPS), p < 0.001, and a pass/fail score was established of 76% for OPS and 61% for NPS. Further, the results also demonstrated that a group of non-healthcare educated workers can perform upper respiratory tract specimen collection comparably to experts after a short and focused simulation-based training session. This study, therefore, provides validity evidence for the use of a theoretical and practical test for upper respiratory specimens’ collection skills that can be used for competency-based training of the workers in the COVID-19 test centers. Full article
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15 pages, 4586 KiB  
Article
Development of an Enzyme-Linked Immunosorbent Assay (ELISA) for Accurate and Prompt Coronavirus Disease 2019 (COVID-19) Diagnosis Using the Rational Selection of Serological Biomarkers
by Theano Lagousi, John Routsias and Vana Spoulou
Diagnostics 2021, 11(11), 1970; https://doi.org/10.3390/diagnostics11111970 - 23 Oct 2021
Cited by 8 | Viewed by 2831
Abstract
Prompt COVID-19 diagnosis is urgently required to support infection control measures. Currently available serological tests for measuring SARS-CoV-2 antibodies use different target antigens, although their sensitivity and specificity presents a challenge. We aimed to develop an “in-house” serological ELISA to measure antibodies against [...] Read more.
Prompt COVID-19 diagnosis is urgently required to support infection control measures. Currently available serological tests for measuring SARS-CoV-2 antibodies use different target antigens, although their sensitivity and specificity presents a challenge. We aimed to develop an “in-house” serological ELISA to measure antibodies against SARS-CoV-2 by combining different protein antigens. Sera (n = 44) from COVID-19-confirmed patients were evaluated against different SARS-CoV-2 protein antigens and all potential combinations using ELISA. Patients’ sera were also evaluated against commercially available ELISA diagnostic kits. The mixture containing RBD 2.5 μg/mL, S2 1 μg/mL and N 1.5 μg/mL was found to be the most potent. Plates were incubated with patients’ sera (1:100), and goat anti-human alkaline phosphatase-conjugated IgG, ΙgM and IgA antibody was added. The cut-off value for each assay was determined using the mean optical density plus two standard deviations of pre-pandemic controls. The “in-house” ELISA displayed 91% sensitivity and 97% specificity for IgG antibodies, whereas its sensitivity and specificity for IgM and IgA were 75% and 95% and 73% and 91%, respectively. The “in-house” ELISA developed here combined three SARS-CoV-2 antigens (RBD, S2 and N) as capture antigens and displayed comparable and even higher sensitivity and specificity than otherwise quite reliable commercially available ELISA diagnostic kits. Full article
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7 pages, 633 KiB  
Article
Variant Prediction by Analyzing RdRp/S Gene Double or Low Amplification Pattern in Allplex SARS-CoV-2 Assay
by Min-Kyung So, Sholhui Park, Kyunghoon Lee, Soo-Kyung Kim, Hae-Sun Chung and Miae Lee
Diagnostics 2021, 11(10), 1854; https://doi.org/10.3390/diagnostics11101854 - 08 Oct 2021
Cited by 10 | Viewed by 2249
Abstract
The spread of delta variants (B.1.671.2) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a severe global threat. Multiplex real-time PCR is a common method for confirming SARS-CoV-2 infection, however, additional tests, such as whole genomic sequencing, are required to reveal the [...] Read more.
The spread of delta variants (B.1.671.2) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a severe global threat. Multiplex real-time PCR is a common method for confirming SARS-CoV-2 infection, however, additional tests, such as whole genomic sequencing, are required to reveal the presence or type of viral mutation. Moreover, applying whole genomic sequencing to all SARS-CoV-2 positive samples is challenging due to time and cost constraints. Here, we report that the double or low amplification curve observed during RNA-dependent RNA polymerase (RdRp) gene/S gene amplification in the Allplex SARS-CoV-2 Assay is related to delta/alpha variants. We analyzed the RdRp/S gene amplification curve using 94 samples confirmed as SARS-CoV-2 infection by the Allplex SARS-CoV-2 Assay from January to August, 2021. These positive samples identified variant types using the Novaplex SARS-CoV-2 Variants I and IV Assays. Overall, 17 samples showing a double curve and 11 samples showing a low amplification pattern were associated with alpha-/delta-type strains with variants in the P681 region. The double or low curve shown in the RdRp gene amplification curve had 100% sensitivity and 100% specificity for diagnosing delta/alpha variants. During the SARS-CoV-2 virus diagnostic RT-PCR test using the Allplex SARS-CoV-2 Assay, we could consider the presence of delta/alpha variants in the samples with double or low amplification curve of the RdRp/S gene channel. This PCR amplification curve abnormality enables rapid and cost-effective variant type prediction during SARS-CoV-2 diagnostic testing in clinical laboratories. Full article
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10 pages, 1005 KiB  
Article
Reliable Diagnostics of SARS-CoV-2 Infections Using One- and Two-Gene Molecular Tests for a Viral RNA Detection—Results Questioning Previous Observations
by Tomasz Bogiel, Mateusz Rzepka and Dagmara Depka
Diagnostics 2021, 11(10), 1839; https://doi.org/10.3390/diagnostics11101839 - 05 Oct 2021
Cited by 4 | Viewed by 2098
Abstract
SARS-CoV-2 is a new virus from the Coronaviridae family and its rapid spread is now the most important medical problem worldwide. Currently used tests vary in the number and selection of SARS-CoV-2 target genes. Meanwhile, the choice of the appropriate target gene may [...] Read more.
SARS-CoV-2 is a new virus from the Coronaviridae family and its rapid spread is now the most important medical problem worldwide. Currently used tests vary in the number and selection of SARS-CoV-2 target genes. Meanwhile, the choice of the appropriate target gene may be important in terms of a reliable detection of a viral RNA. As some researchers questioned the sensitivity of the monogenic VIASURE SARS-CoV-2 S gene Real Time PCR Detection Kit (CerTest Biotec, Zaragoza, Spain) in mid-2020, the aim of the study was to evaluate the usefulness of this kit, used along with the BD MAX™ System (Becton Dickinson, East Rutherford, NJ, USA), and compare the results with two-gene Bosphore Novel Coronavirus (2019-nCoV) Detection Kit v1 (Anatolia Diagnostics and Biotechnology Products Inc., Istanbul, Turkey). Both tests were carried out on 306 nasopharyngeal/oropharyngeal swabs. The consistent results (72 positive and 225 negative results found simultaneously in both kits) were obtained for 297 (97.1%) samples altogether, while discrepancies between the results of the evaluated tests were observed for nine (2.9%) specimens. There were no statistically significant differences between the method used and the frequency of positive results. Both tests, targeted at detecting one and two genes, are effective in SARS-CoV-2 RNA detection. Full article
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11 pages, 1101 KiB  
Article
Feasibility and Diagnostic Accuracy of Saliva-Based SARS-CoV-2 Screening in Educational Settings and Children Aged <12 Years
by Martin Hoch, Sebastian Vogel, Ute Eberle, Laura Kolberg, Valerie Gruenthaler, Volker Fingerle, Nikolaus Ackermann, Andreas Sing, Bernhard Liebl, Johannes Huebner, Simone Kuttiadan, Anita Rack-Hoch, Melanie Meyer-Buehn, Tilmann Schober and Ulrich von Both
Diagnostics 2021, 11(10), 1797; https://doi.org/10.3390/diagnostics11101797 - 29 Sep 2021
Cited by 4 | Viewed by 2238
Abstract
Children have been disproportionately affected during the COVID-19 pandemic. We aimed to assess a saliva-based algorithm for SARS-CoV-2 testing to be used in schools and childcare institutions under pandemic conditions. A weekly SARS-CoV-2 sentinel study in primary schools, kindergartens, and childcare facilities was [...] Read more.
Children have been disproportionately affected during the COVID-19 pandemic. We aimed to assess a saliva-based algorithm for SARS-CoV-2 testing to be used in schools and childcare institutions under pandemic conditions. A weekly SARS-CoV-2 sentinel study in primary schools, kindergartens, and childcare facilities was conducted over a 12-week-period. In a sub-study covering 7 weeks, 1895 paired oropharyngeal and saliva samples were processed for SARS-CoV-2 rRT-PCR testing in both asymptomatic children (n = 1243) and staff (n = 652). Forty-nine additional concurrent swab and saliva samples were collected from SARS-CoV-2 infected patients (patient cohort). The Salivette® system was used for saliva collection and assessed for feasibility and diagnostic performance. For children, a mean of 1.18 mL saliva could be obtained. Based on results from both cohorts, the Salivette® testing algorithm demonstrated the specificity of 100% (95% CI 99.7–100) and sensitivity of 94.9% (95% CI 81.4–99.1) with oropharyngeal swabs as reference. Agreement between sampling systems was 100% for moderate to high viral load situations (defined as Ct-values <33 from oropharyngeal swabs). Comparative analysis of Ct-values derived from saliva vs. oropharyngeal swabs demonstrated a significant difference (mean 4.23; 95% CI 2.48–6.00). In conclusion, the Salivette® system proved to be an easy-to-use, safe and feasible saliva collection method and a more pleasant alternative to oropharyngeal swabs for SARS-CoV-2 testing in children aged 3 years and above. Full article
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12 pages, 1354 KiB  
Article
Fast SARS-CoV-2 Variant Detection Using Snapback Primer High-Resolution Melting
by Joseph C. Lownik, Jared S. Farrar, Grayson W. Way, Angela McKay, Pavitra Roychoudhury, Alexander L. Greninger and Rebecca K. Martin
Diagnostics 2021, 11(10), 1788; https://doi.org/10.3390/diagnostics11101788 - 28 Sep 2021
Cited by 8 | Viewed by 2229
Abstract
SARS-CoV-2, the virus responsible for COVID-19, emerged in late 2019 and has since spread throughout the world, infecting over 200 million people. The fast spread of SARS-CoV-2 showcased the need for rapid and sensitive testing methodologies to help track the disease. Over the [...] Read more.
SARS-CoV-2, the virus responsible for COVID-19, emerged in late 2019 and has since spread throughout the world, infecting over 200 million people. The fast spread of SARS-CoV-2 showcased the need for rapid and sensitive testing methodologies to help track the disease. Over the past 18 months, numerous SARS-CoV-2 variants have emerged. Many of these variants are suggested to be more transmissible as well as less responsive to neutralization by vaccine-induced antibodies. Viral whole-genome sequencing is the current standard for tracking these variants. However, whole-genome sequencing is costly and the technology and expertise are limited to larger reference laboratories. Here, we present the feasibility of a fast, inexpensive methodology using snapback primer-based high-resolution melting to test for >20 high-consequence SARS-CoV-2 spike mutations. This assay can distinguish between multiple variant lineages and be completed in roughly 2 h for less than $10 per sample. Full article
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6 pages, 668 KiB  
Article
Evaluation of the Advanta Dx SARS-CoV-2 RT-PCR Assay, a High-Throughput Extraction-Free Diagnostic Test for the Detection of SARS-CoV-2 in Saliva: A Diagnostic Accuracy Study
by Sofia Balaska, Dimitrios Pilalas, Anna Takardaki, Paraskevoula Koutra, Eleftheria Parasidou, Ioanna Gkeka, Areti Tychala, Georgios Meletis, Barbara Fyntanidou, Simeon Metallidis, Efthymia Protonotariou and Lemonia Skoura
Diagnostics 2021, 11(10), 1766; https://doi.org/10.3390/diagnostics11101766 - 26 Sep 2021
Cited by 7 | Viewed by 1869
Abstract
Nasopharyngeal swab specimen (NPS) molecular testing is considered the gold standard for SARS-CoV-2 detection. However, saliva is an attractive, noninvasive specimen alternative. The aim of the study was to evaluate the diagnostic accuracy of Advanta Dx SARS-CoV-2 RT-PCR saliva-based assay against paired NPS [...] Read more.
Nasopharyngeal swab specimen (NPS) molecular testing is considered the gold standard for SARS-CoV-2 detection. However, saliva is an attractive, noninvasive specimen alternative. The aim of the study was to evaluate the diagnostic accuracy of Advanta Dx SARS-CoV-2 RT-PCR saliva-based assay against paired NPS tested with either NeumoDxTM SARS-CoV-2 assay or Abbott Real Time SARS-CoV-2 assay as the reference method. We prospectively evaluated the method in two settings: a diagnostic outpatient and a healthcare worker screening convenience sample, collected in November–December 2020. SARS-CoV-2 was detected in 27.7% (61/220) of diagnostic samples and in 5% (10/200) of screening samples. Overall, saliva test in diagnostic samples had a sensitivity of 88.5% (77.8–95.3%) and specificity of 98.1% (94.6–99.6%); in screening samples, the sensitivity was 90% (55.5–99.7%) and specificity 100% (98.1–100%). Our data suggests that the Fluidigm Advanta Dx RT-PCR saliva-based assay may be a reliable diagnostic tool for COVID-19 diagnosis in symptomatic individuals and screening asymptomatic healthcare workers. Full article
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6 pages, 843 KiB  
Article
Performance of a Surrogate SARS-CoV-2-Neutralizing Antibody Assay in Natural Infection and Vaccination Samples
by Kwok-Hung Chan, Ka-Yi Leung, Ricky-Ruiqi Zhang, Danlei Liu, Yujing Fan, Honglin Chen, Kwok-Yung Yuen and Ivan Fan-Ngai Hung
Diagnostics 2021, 11(10), 1757; https://doi.org/10.3390/diagnostics11101757 - 24 Sep 2021
Cited by 24 | Viewed by 2231
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing antibody (NAb) production is a crucial humoral response that can reduce re-infection or breakthrough infection. The conventional test used to measure NAb production capacity levels is the live virus-neutralizing assay. However, this test must be conducted [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing antibody (NAb) production is a crucial humoral response that can reduce re-infection or breakthrough infection. The conventional test used to measure NAb production capacity levels is the live virus-neutralizing assay. However, this test must be conducted under biosafety level-3 containment. Pseudovirus or surrogate NAb tests, such as angiotensin-converting enzyme 2 inhibition tests, can be performed under level-2 containment. The aim of this study was to evaluate the performance of a surrogate SARS-CoV-2 NAb assay (sNAb) using samples from naturally infected individuals and vaccine recipients in comparison with the live virus microneutralization assay (vMN). Three hundred and eighty serum samples which were collected from 197 patients with COVID-19, 96 vaccine recipients and 84 normal individuals were analyzed. Overall, the sensitivity, specificity, positive predictive value, and negative predictive value of the sNAb (iFlash-2019-NAb assay, Shenzhen, China) were 97.9%, 94.9%, 98.2%, and 93.8%, respectively. Agreement for the assay relative to vMN for naturally infected individuals and vaccine recipients were 98.5% and 93.9%, respectively. A correlation analysis between sNAb and the vMN for both of these groups yielded an R2 value of 0.83. The iFlash RBD NAb assay is found to be sensitive and reliable for neutralizing antibody measurement in patients with the 2019 coronavirus disease and those who have been vaccinated against it. Full article
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12 pages, 1281 KiB  
Article
Performance of Seven SARS-CoV-2 Self-Tests Based on Saliva, Anterior Nasal and Nasopharyngeal Swabs Corrected for Infectiousness in Real-Life Conditions: A Cross-Sectional Test Accuracy Study
by Miroslav Homza, Hana Zelena, Jaroslav Janosek, Hana Tomaskova, Eduard Jezo, Alena Kloudova, Jakub Mrazek, Vera Murinova and Rastislav Madar
Diagnostics 2021, 11(9), 1567; https://doi.org/10.3390/diagnostics11091567 - 28 Aug 2021
Cited by 10 | Viewed by 4071
Abstract
Many studies reported good performance of nasopharyngeal swab-based antigen tests for detecting SARS-CoV-2-positive individuals; however, studies independently evaluating the quality of antigen tests utilizing anterior nasal swabs or saliva swabs are still rare, although such tests are widely used for mass testing. In [...] Read more.
Many studies reported good performance of nasopharyngeal swab-based antigen tests for detecting SARS-CoV-2-positive individuals; however, studies independently evaluating the quality of antigen tests utilizing anterior nasal swabs or saliva swabs are still rare, although such tests are widely used for mass testing. In our study, sensitivities, specificities and predictive values of seven antigen tests for detection of SARS-CoV-2 (one using nasopharyngeal swabs, two using anterior nasal swabs and four using saliva) were evaluated. In a setting of a high-capacity testing center, nasopharyngeal swabs for quantitative PCR (qPCR) were taken and, at the same time, antigen testing was performed in accordance with manufacturers’ instructions for the respective tests. In samples where qPCR and antigen tests yielded different results, virus culture was performed to evaluate the presence of the viable virus. Sensitivities and specificities of individual tests were calculated using both qPCR and qPCR corrected for viability as the reference. In addition, calculations were also performed for data categorized according to the cycle threshold and symptomatic status. The test using nasopharyngeal swabs yielded the best results (sensitivity of 80.6% relative to PCR and 91.2% when corrected for viability) while none of the remaining tests (anterior nasal swab or saliva-based tests) came even close to the WHO criteria for overall sensitivity. Hence, we advise caution when using antigen tests with alternative sampling methods without independent validation. Full article
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13 pages, 1406 KiB  
Article
A Diagnostic Model to Predict SARS-CoV-2 Positivity in Emergency Department Using Routine Admission Hematological Parameters
by Rossana Soloperto, Giovanna Guiotto, Giuseppe Tozzi, Maurizio Fumi and Angelo Tozzi
Diagnostics 2021, 11(9), 1566; https://doi.org/10.3390/diagnostics11091566 - 28 Aug 2021
Cited by 1 | Viewed by 3413
Abstract
Early detection of SARS-CoV-2 in the emergency department (ED) is a crucial necessity, especially in settings of overcrowding: establishing a pre-diagnostic test probability of infection would help to triage patients and reduce diagnostic errors, and it could be useful in resource-limited countries. Here, [...] Read more.
Early detection of SARS-CoV-2 in the emergency department (ED) is a crucial necessity, especially in settings of overcrowding: establishing a pre-diagnostic test probability of infection would help to triage patients and reduce diagnostic errors, and it could be useful in resource-limited countries. Here, we established and validated a clinical predictor of infection based on routine admission hematological parameters. The diagnostic model was developed by comparing 85 consecutive patients with symptomatic COVID-19 confirmed by RT-PCR with 85 symptomatic, SARS-CoV-2-negative controls. Abnormal hematological parameters significantly (p < 0.05) associated with SARS-CoV-2 infection were used to derive a “cumulative score” between 0 and 16. The model was validated in an independent cohort of 170 SARS-CoV-2-positive patients. Several routine hematology parameters were significantly (p < 0.05) associated with SARS-CoV-2 infection. A “cumulative score” score ≥7 discriminated COVID-19-postive patients from controls with a sensitivity of 94% and specificity of 100% (p < 0.001). The high sensitivity of the predictive model was confirmed in the prospective validation set, and the cumulative score (i) predicted SARS-CoV-2 positivity even when the first oro-nasopharyngeal swab RT-PCR result was reported as a false negative in both cohorts and (ii) resulted to be independent from disease severity. The cumulative score based on routine blood parameters can be used to predict an early and accurate diagnosis of SARS-CoV-2 infection in symptomatic patients, thereby facilitating triage and optimizing early management and isolation from the COVID-19 free population, particularly useful in overcrowding situations and in resource-poor settings. Full article
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10 pages, 657 KiB  
Article
Mouth Washing Impaired SARS-CoV-2 Detection in Saliva
by Monique Melo Costa, Nicolas Benoit, Hervé Tissot-Dupont, Matthieu Million, Bruno Pradines, Samuel Granjeaud and Lionel Almeras
Diagnostics 2021, 11(8), 1509; https://doi.org/10.3390/diagnostics11081509 - 22 Aug 2021
Cited by 4 | Viewed by 2230
Abstract
Background: A previous study demonstrated the performance of the Salivette® (SARSTEDT, Numbrecht, Germany) as a homogeneous saliva collection system to diagnose COVID-19 by RT-qPCR, notably for symptomatic and asymptomatic patients. However, for convalescent patients, the corroboration of molecular detection of SARS-CoV-2 in [...] Read more.
Background: A previous study demonstrated the performance of the Salivette® (SARSTEDT, Numbrecht, Germany) as a homogeneous saliva collection system to diagnose COVID-19 by RT-qPCR, notably for symptomatic and asymptomatic patients. However, for convalescent patients, the corroboration of molecular detection of SARS-CoV-2 in paired nasopharyngeal swabs (NPS) and saliva samples was unsatisfactory. Objectives: The aim of the present work was to assess the concordance level of SARS-CoV-2 detection between paired sampling of NPSs and saliva collected with Salivette® at two time points, with ten days of interval. Results: A total of 319 paired samples from 145 outpatients (OP) and 51 healthcare workers (HW) were collected. Unfortunately, at day ten, 73 individuals were lost to follow-up, explaining some kinetic missing data. Due to significant waiting rates at hospitals, most of the patients ate and/or drank while waiting for their turn. Consequently, mouth washing was systematically proposed prior to saliva collection. None of the HW were diagnosed as SARS-CoV-2 positive using NPS or saliva specimens at both time points (n = 95) by RT-qPCR. The virus was detected in 56.3% (n = 126/224) of the NPS samples from OP, but solely 26.8% (n = 60/224) of the paired saliva specimens. The detection of the internal cellular control, the human RNase P, in more than 98% of the saliva samples, underlined that the low sensitivity of saliva specimens (45.2%) for SARS-CoV-2 detection was not attributed to an improper saliva sample storing or RNA extraction. Conclusions: This work revealed that mouth washing decreased viral load of buccal cavity conducting to impairment of SARS-CoV-2 detection. Viral loads in saliva neo-produced appeared insufficient for molecular detection of SARS-CoV-2. At the time when saliva tests could be a rapid, simple and non-invasive strategy to assess large scale schoolchildren in France, the determination of the performance of saliva collection becomes imperative to standardize procedures. Full article
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Review

Jump to: Research, Other

11 pages, 272 KiB  
Review
Health Research and Education during and after the COVID-19 Pandemic: An Australian Clinician and Researcher Perspective
by Dennis J. Cordato, Kaneez Fatima Shad, Wissam Soubra and Roy G. Beran
Diagnostics 2023, 13(2), 289; https://doi.org/10.3390/diagnostics13020289 - 12 Jan 2023
Cited by 6 | Viewed by 1847
Abstract
Introduction: The COVID-19 pandemic had an unprecedented global effect on teaching and education. This review discusses research, education and diagnostics from the perspectives of four academic clinicians and researchers across different facilities in Australia. Materials and methods: The study adopted a literature review [...] Read more.
Introduction: The COVID-19 pandemic had an unprecedented global effect on teaching and education. This review discusses research, education and diagnostics from the perspectives of four academic clinicians and researchers across different facilities in Australia. Materials and methods: The study adopted a literature review and an Australian researcher’s perspective on the impact of the COVID-19 pandemic on health education, research and diagnostics. Results: At the start of the pandemic, medical facilities had to adhere urgently to major work restrictions, including social distancing, mask-wearing rules and/or the closure of facilities to protect staff, students and patients from the risk of COVID-19 infection. Telemedicine and telehealth services were rapidly implemented and adapted to meet the needs of medical education, the teaching of students, trainee doctors, nursing and allied health staff and became a widely accepted norm. The impact on clinical research and education saw the closure of clinical trials and the implementation of new methods in the conducting of trials, including electronic consents, remote patient assessments and the ability to commence fully virtual clinical trials. Academic teaching adapted augmented reality and competency-based teaching to become important new modes of education delivery. Diagnostic services also required new policies and procedures to ensure the safety of personnel. Conclusions: As a by-product of the COVID-19 pandemic, traditional, face-to-face learning and clinical research were converted into online formats. An hybrid environment of traditional methods and novel technological tools has emerged in readiness for future pandemics that allows for virtual learning with concurrent recognition of the need to provide for interpersonal interactions. Full article
23 pages, 1222 KiB  
Review
Outcome of Newborns with Confirmed or Possible SARS-CoV-2 Vertical Infection—A Scoping Review
by Andreea Moza, Florentina Duica, Panagiotis Antoniadis, Elena S. Bernad, Diana Lungeanu, Marius Craina, Brenda C. Bernad, Corina Paul, Cezara Muresan, Razvan Nitu, Raluca Dumache and Daniela Iacob
Diagnostics 2023, 13(2), 245; https://doi.org/10.3390/diagnostics13020245 - 09 Jan 2023
Cited by 9 | Viewed by 2013
Abstract
Severe acute respiratory syndrome virus 2 (SARS-CoV-2), the virus that causes 2019 coronavirus disease (COVID-19), has been isolated from various tissues and body fluids, including the placenta, amniotic fluid, and umbilical cord of newborns. In the last few years, much scientific effort has [...] Read more.
Severe acute respiratory syndrome virus 2 (SARS-CoV-2), the virus that causes 2019 coronavirus disease (COVID-19), has been isolated from various tissues and body fluids, including the placenta, amniotic fluid, and umbilical cord of newborns. In the last few years, much scientific effort has been directed toward studying SARS-CoV-2, focusing on the different features of the virus, such as its structure and mechanisms of action. Moreover, much focus has been on developing accurate diagnostic tools and various drugs or vaccines to treat COVID-19. However, the available evidence is still scarce and consistent criteria should be used for diagnosing vertical transmission. Applying the PRISMA ScR guidelines, we conducted a scoping review with the primary objective of identifying the types, and examining the range, of available evidence of vertical transmission of SARS-CoV-2 from mother to newborn. We also aimed to clarify the key concepts and criteria for diagnosis of SARS-CoV-2 vertical infection in neonates and summarize the existing evidence and advance the awareness of SARS-CoV-2 vertical infection in pregnancy. Most studies we identified were case reports or case series (about 30% of poor quality and inconsistent reporting of the findings). Summarizing the existing classification criteria, we propose an algorithm for consistent diagnosis. Registration: INPLASY2022120093. Full article
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40 pages, 2446 KiB  
Review
Tracking SARS-CoV-2: Novel Trends and Diagnostic Strategies
by Linda P. Guaman-Bautista, Erick Moreta-Urbano, Claudia G. Oña-Arias, Marbel Torres-Arias, Nikolaos C. Kyriakidis, Koray Malcı, Nestor Jonguitud-Borrego, Leonardo Rios-Solis, Espiridion Ramos-Martinez, Andrés López-Cortés and Carlos Barba-Ostria
Diagnostics 2021, 11(11), 1981; https://doi.org/10.3390/diagnostics11111981 - 26 Oct 2021
Cited by 12 | Viewed by 4696
Abstract
The COVID-19 pandemic has had an enormous impact on economies and health systems globally, therefore a top priority is the development of increasingly better diagnostic and surveillance alternatives to slow down the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In [...] Read more.
The COVID-19 pandemic has had an enormous impact on economies and health systems globally, therefore a top priority is the development of increasingly better diagnostic and surveillance alternatives to slow down the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In order to establish massive testing and contact tracing policies, it is crucial to have a clear view of the diagnostic options available and their principal advantages and drawbacks. Although classical molecular methods such as RT-qPCR are broadly used, diagnostic alternatives based on technologies such as LAMP, antigen, serological testing, or the application of novel technologies such as CRISPR-Cas for diagnostics, are also discussed. The present review also discusses the most important automation strategies employed to increase testing capability. Several serological-based diagnostic kits are presented, as well as novel nanotechnology-based diagnostic methods. In summary, this review provides a clear diagnostic landscape of the most relevant tools to track COVID-19. Full article
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Other

Jump to: Research, Review

7 pages, 11348 KiB  
Interesting Images
Cryptococcal Pneumonia: An Unusual Complication in a COVID-19 Patient
by Jan Štingl, Julie Hylmarová, Martina Lengerová, Jan Maláska and Jan Stašek
Diagnostics 2022, 12(8), 1944; https://doi.org/10.3390/diagnostics12081944 - 12 Aug 2022
Cited by 4 | Viewed by 1772
Abstract
Cryptococcal superinfection is a rare but potentially fatal complication, especially if its detection and subsequent treatment are delayed. Histopathological findings of pulmonary parenchyma from a deceased patient with these complications were acquired. Quite interestingly, only a minimal inflammatory reaction could be seen in [...] Read more.
Cryptococcal superinfection is a rare but potentially fatal complication, especially if its detection and subsequent treatment are delayed. Histopathological findings of pulmonary parenchyma from a deceased patient with these complications were acquired. Quite interestingly, only a minimal inflammatory reaction could be seen in an individual with no previously known immune suppression, indicating a disturbance of the immune system. This finding was well in concordance with the described changes in cellular immunity in COVID-19. We report the case of a 60 year old male with critical coronavirus disease 2019 (COVID-19) complicated by cryptococcal pneumonia and multiorgan failure. Both X-ray and CT scans revealed lung infiltrates corresponding with COVID-19 infection early after the onset of symptoms. Despite receiving standard treatment, the patient progressed into multiple organ failure, requiring mechanical ventilation, circulatory support, and haemodialysis. Cryptococcus neoformans was detected by subsequent BAL, and specific antifungal treatment was instituted. His clinical status deteriorated despite all treatment, and he died of refractory circulatory failure after 21 days from hospital admission. Histopathological findings confirmed severe diffuse alveolar damage (DAD) caused by COVID-19 and cryptococcal pneumonia. Timely diagnosis of cryptococcal superinfection may be challenging; therefore, PCR panels detecting even uncommon pathogens should be implemented while taking care of critical COVID-19 patients. Full article
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50 pages, 1520 KiB  
Systematic Review
Performance of Antigen Detection Tests for SARS-CoV-2: A Systematic Review and Meta-Analysis
by Anastasia Tapari, Georgia G. Braliou, Maria Papaefthimiou, Helen Mavriki, Panagiota I. Kontou, Georgios K. Nikolopoulos and Pantelis G. Bagos
Diagnostics 2022, 12(6), 1388; https://doi.org/10.3390/diagnostics12061388 - 04 Jun 2022
Cited by 20 | Viewed by 4551
Abstract
Coronavirus disease 2019 (COVID-19) initiated global health care challenges such as the necessity for new diagnostic tests. Diagnosis by real-time PCR remains the gold-standard method, yet economical and technical issues prohibit its use in points of care (POC) or for repetitive tests in [...] Read more.
Coronavirus disease 2019 (COVID-19) initiated global health care challenges such as the necessity for new diagnostic tests. Diagnosis by real-time PCR remains the gold-standard method, yet economical and technical issues prohibit its use in points of care (POC) or for repetitive tests in populations. A lot of effort has been exerted in developing, using, and validating antigen-based tests (ATs). Since individual studies focus on few methodological aspects of ATs, a comparison of different tests is needed. Herein, we perform a systematic review and meta-analysis of data from articles in PubMed, medRxiv and bioRxiv. The bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities was used. Most of the AT types for SARS-CoV-2 were lateral flow immunoassays (LFIA), fluorescence immunoassays (FIA), and chemiluminescence enzyme immunoassays (CLEIA). We identified 235 articles containing data from 220,049 individuals. All ATs using nasopharyngeal samples show better performance than those with throat saliva (72% compared to 40%). Moreover, the rapid methods LFIA and FIA show about 10% lower sensitivity compared to the laboratory-based CLEIA method (72% compared to 82%). In addition, rapid ATs show higher sensitivity in symptomatic patients compared to asymptomatic patients, suggesting that viral load is a crucial parameter for ATs performed in POCs. Finally, all methods perform with very high specificity, reaching around 99%. LFIA tests, though with moderate sensitivity, appear as the most attractive method for use in POCs and for performing seroprevalence studies. Full article
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9 pages, 457 KiB  
Systematic Review
LumiraDX SARS-CoV-2 Antigen Test for Diagnosing Acute SARS-CoV-2 Infection: Critical Literature Review and Meta-Analysis
by Giuseppe Lippi, Brandon M. Henry and Mario Plebani
Diagnostics 2022, 12(4), 947; https://doi.org/10.3390/diagnostics12040947 - 11 Apr 2022
Cited by 7 | Viewed by 2016
Abstract
We present here a critical literature review and meta-analysis on the accuracy of the LumiraDX SARS-CoV-2 Antigen Test for diagnosing acute SARS-CoV-2 infection. An electronic search was conducted in the Scopus and Medline databases using the keywords “LumiraDX” AND “COVID-19” OR “SARS-CoV-2”, without [...] Read more.
We present here a critical literature review and meta-analysis on the accuracy of the LumiraDX SARS-CoV-2 Antigen Test for diagnosing acute SARS-CoV-2 infection. An electronic search was conducted in the Scopus and Medline databases using the keywords “LumiraDX” AND “COVID-19” OR “SARS-CoV-2”, without date (i.e., up to 1 February 2022) or language restrictions, for detecting clinical studies where the diagnostic accuracy of the LumiraDX SARS-CoV-2 Antigen Test was compared with reference molecular diagnostic methods. All studies where the rates of true positive, true negative, false positive and false negative cases were available for constructing a 2 × 2 table and providing pooled estimates of diagnostic sensitivity, specificity and accuracy were included in a pooled analysis. The study was conducted in accordance with the PRISMA (preferred reporting items for systematic reviews and meta-analyses) reporting checklist. Eleven studies (n = 8527 samples) could be included in our pooled analysis, while five additional documents provided diagnostic accuracy data but could not be extracted for construction of a 2 × 2 table. The pooled diagnostic sensitivity and specificity were 0.86 (95%CI, 0.84–0.88) and 0.99 (95%CI, 0.98–0.99), respectively, while the area under the summary receiver operating characteristic curve was 0.974 (95%CI, 0.965–0.983) and the agreement was 96.8% (95%CI, 96.4–97.1%), with kappa statistics of 0.87 (95%CI, 0.85–0.88). In conclusion, the diagnostic performance of the LumiraDX SARS-CoV-2 Antigen Test would allow the conclusion that it may be seen as a reliable alternative to molecular testing for the rapid preliminary screening of acute SARS-CoV-2 infections. Full article
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13 pages, 4827 KiB  
Case Report
COVID-19 Infection Complicated by Disseminated Intravascular Coagulation during Pregnancy—Two Cases Report
by Małgorzata Skalska-Świstek, Hubert Huras, Andrzej Piotr Jaworowski, Rafał Świstek and Magdalena Kołak
Diagnostics 2022, 12(3), 655; https://doi.org/10.3390/diagnostics12030655 - 08 Mar 2022
Cited by 7 | Viewed by 2597
Abstract
Coagulopathies are one of the obstetric complications affecting the period of pregnancy, childbirth, and puerperium. One of the more severe and complex disorders of the haemostatic system is the disseminated intravascular coagulation syndrome (DIC), in which generalised activation of the coagulation system and [...] Read more.
Coagulopathies are one of the obstetric complications affecting the period of pregnancy, childbirth, and puerperium. One of the more severe and complex disorders of the haemostatic system is the disseminated intravascular coagulation syndrome (DIC), in which generalised activation of the coagulation system and activation of inflammatory cells occurs. DIC syndrome was observed in patients whose pregnancy was complicated by SARS-CoV-2 infection. Both the course of these cases and literature review indicate that particular notice should be paid to laboratory parameters of the coagulation system, closely monitoring the well-being of the foetus and, in the situation of acute DIC development, it is advised to deliver a baby and initiate intensive therapy. Full article
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5 pages, 495 KiB  
Case Report
SARS-CoV-2 Viral RNA Is Detected in the Bone Marrow in Post-Mortem Samples Using RT-LAMP
by Tomasz Jurek, Marta Rorat, Łukasz Szleszkowski, Miron Tokarski, Izabela Pielka and Małgorzata Małodobra-Mazur
Diagnostics 2022, 12(2), 515; https://doi.org/10.3390/diagnostics12020515 - 17 Feb 2022
Cited by 6 | Viewed by 4773
Abstract
Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, viral RNA has been detected in several different human tissues and organs. This study reports the detection of SARS-CoV-2 RNA in the bone marrow. Post-mortem samples were taken in [...] Read more.
Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, viral RNA has been detected in several different human tissues and organs. This study reports the detection of SARS-CoV-2 RNA in the bone marrow. Post-mortem samples were taken in a sterile manner during two forensic autopsies from the nasopharyngeal region, vitreous humor, cerebrospinal fluid, and bone marrow. SARS-CoV-2 was subsequently diagnosed via Genomtec® SARS-CoV-2 EvaGreen® RT-LAMP CE-IVD Duo Kit. In both postmortem patients, SARS-CoV-2 RNA was detected in bone marrow samples. However, both the vitreous humor and cerebrospinal fluid from the same patients gave negative results using the same test system. The evidence of viral RNA in the bone marrow, along with other reports supports the thesis that SARS-CoV-2 infections are systemic in nature, the consequences of which would profoundly influence both the testing and survival of patients. Full article
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7 pages, 943 KiB  
Case Report
First Case of COVID-19 Treated with Monoclonal Anti-Spike Antibodies in a Patient with Cystic Fibrosis in Romania
by Iustina Violeta Stan, Victor Daniel Miron, Ioana Alexandra Vangheli, Radu Marian Gheorghiu, Anca Streinu-Cercel, Oana Săndulescu and Mihai Craiu
Diagnostics 2022, 12(1), 137; https://doi.org/10.3390/diagnostics12010137 - 07 Jan 2022
Cited by 3 | Viewed by 1785
Abstract
Patients with chronic lung conditions, including cystic fibrosis, may be prone to severe COVID-19. Therefore, therapeutic intervention should be prompt and tailored to all associated comorbidities. We report the case of a 17-year-old male adolescent with cystic fibrosis and multiple chronic conditions (bronchiectasis, [...] Read more.
Patients with chronic lung conditions, including cystic fibrosis, may be prone to severe COVID-19. Therefore, therapeutic intervention should be prompt and tailored to all associated comorbidities. We report the case of a 17-year-old male adolescent with cystic fibrosis and multiple chronic conditions (bronchiectasis, exocrine pancreatic insufficiency, chronic multidrug resistant Pseudomonas aeruginosa colonization, nasal polyposis, chronic sinusitis, ventricular extrasystoles and multiple drug allergies), who presented with an acute episode of productive cough, and was confirmed with moderate COVID-19 based on positive RT-PCR for SARS-CoV-2 and lung imaging showing isolated foci of interstitial pneumonia. Intravenous treatment with the monoclonal antibody cocktail casirivimab and imdevimab was administered. The evolution was favorable, with rapid remission of the inflammatory syndrome and gradual decrease of cough, without progression to severe or critical COVID-19, but with complications such as repeated hemoptysis, which was due to the patient’s underlying conditions, and which required close monitoring for timely adjustment of the patient’s chronic treatment. Full article
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6 pages, 963 KiB  
Case Report
Case Report of COVID-19 after Full Vaccination: Viral Loads and Anti-SARS-CoV-2 Antibodies
by Magdalena Komiazyk, Jaroslaw Walory, Jan Gawor, Iza Ksiazek, Robert Gromadka and Anna Baraniak
Diagnostics 2021, 11(10), 1815; https://doi.org/10.3390/diagnostics11101815 - 30 Sep 2021
Cited by 8 | Viewed by 3228
Abstract
The introduction of effective vaccines against SARS-CoV-2 is expected to prevent COVID-19. However, sporadic cases of infection in vaccinated persons have been reported. We describe a case of a double-dose vaccinated woman with COVID-19. All stages of infection were observed, from no identification [...] Read more.
The introduction of effective vaccines against SARS-CoV-2 is expected to prevent COVID-19. However, sporadic cases of infection in vaccinated persons have been reported. We describe a case of a double-dose vaccinated woman with COVID-19. All stages of infection were observed, from no identification of virus, then the start of the infection, a high viral load, coming out of viraemia, and finally no detection of the virus. Despite the high viral load, the woman demonstrated mild COVID-19 symptoms, manifested only by a sore throat. The antibody results showed that she produced both post-infectious and post-vaccination immune responses. Phylogenetic analysis of the obtained viral genome sequence indicated that the virus belonged to the UK SARS-CoV-2 lineage B.1.1.7 (GR 501Y.V1; 20I/S:501Y.V1; Alpha variant). Full article
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7 pages, 650 KiB  
Case Report
COVID-19 in Patients with Active Tuberculosis
by Monika Kozińska and Ewa Augustynowicz-Kopeć
Diagnostics 2021, 11(10), 1768; https://doi.org/10.3390/diagnostics11101768 - 26 Sep 2021
Cited by 5 | Viewed by 1839
Abstract
Data on the coincidence of tuberculosis (TB) and COVID-19 are limited, and previous observations are based on the results of just a few studies, which has led to polarized views on the course of infection with SARS-CoV-2 in patients with active TB. We [...] Read more.
Data on the coincidence of tuberculosis (TB) and COVID-19 are limited, and previous observations are based on the results of just a few studies, which has led to polarized views on the course of infection with SARS-CoV-2 in patients with active TB. We present the first two cases of TB and COVID-19 coinfection in the population of patients in Poland, diagnosed shortly after the outbreak of the global pandemic. In the first patient, TB was very advanced at the time of infection with SARS-CoV-2. From the third day of hospitalisation, respiratory failure was increasing, with no improvement after the use of high-flow oxygen therapy and mechanical ventilation. On the seventh day of hospitalization, the patient died. In the second presented case, therapeutic success was achieved despite the coincidence of COVID-19, infection with HIV, and extrapulmonary and pulmonary TB. The patient had symptoms of renal failure and the SARS-CoV-2 infection was mild and asymptomatic. Because both patients were in the care of a homeless shelter, a molecular epidemiological investigation was carried out. Different DNA profiles of Mycobacterium tuberculosis complex isolates detected in clinical materials from patients ruled out the transmission of tuberculosis. Based on our analysis, it is impossible to clearly define the influence of active TB on the course of SARS-CoV-2 infection. We can only suggest that coinfection is particularly dangerous for socially disadvantaged people, the elderly, and people with other comorbidities. In the coming years, a negative impact of the current pandemic on control programmes will be observed for many infectious diseases, including TB. Full article
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