scholarly journals Features of Pathogens, Epidemiology, and Diagnosis of COVID-19 and Reliable Suggestion: Aiming to Solve the Confusion in Clinical Practice

2020 ◽  
Vol 5 (5) ◽  
Keyword(s):  
Clinical Practice ◽  
Pediatric Patients ◽  
False Negative ◽  
Early Period ◽  
Respiratory Viruses ◽  
Rt Pcr ◽  
Virus Particles ◽  
Oral Transmission ◽  
Acid Test ◽  
Diagnosis Criterion

In past several months, the worldwide outbreak of COVID-19 infection is unstoppable, which results in millions of people infected and thousands of people dead. However, there are still something controversial in the virus mechanism, the epidemiological feature and the diagnose criterion of COVID-19, while we also have some consensus. The structure of SARS-CoV-2, the pathogen of COVID-19, is roughly similar with other coronavirus such as SARS-CoV and bat-CoV, but by sequencing the amino acid, recombination of virus particles, and observation in Electron microscope, it is obvious to find the some slight difference between the protein of SARS-CoV-2 and others’. The spike protein of SARSCoV-2 has a stronger ability to binding ACE2 than SARS-CoV. The carrier of SARS-CoV-2 is just as other respiratory viruses, like droplet, aerosol and surface, and the fecal-oral transmission is proved to be an efficient pathway. In clinical practice, the elder and the patients with comorbidity are more susceptible to infection and have poorer prognosis, while pediatric patients is the very opposite of it. Nucleic acid test represented by RT-PCR is a helpful method for diagnose, yet it has weaknesses of false negative in suspicious patient and resurgence in discharge patient. Serological and immunological test, reported not suitable for diagnose alone in early period, can be another reliable method that benefit the accuracy of diagnosis criterion when combined with RT-PCR.

scholarly journals Features of Pathogens, Epidemiology, and Diagnosis of COVID-19 and Reliable Suggestion: Aiming to Solve the Confusion in Clinical Practice

2020 ◽  
Vol 5 (5) ◽  
Keyword(s):  
Clinical Practice ◽  
Pediatric Patients ◽  
False Negative ◽  
Early Period ◽  
Respiratory Viruses ◽  
Rt Pcr ◽  
Virus Particles ◽  
Oral Transmission ◽  
Acid Test ◽  
Diagnosis Criterion

In past several months, the worldwide outbreak of COVID-19 infection is unstoppable, which results in millions of people infected and thousands of people dead. However, there are still something controversial in the virus mechanism, the epidemiological feature and the diagnose criterion of COVID-19, while we also have some consensus. The structure of SARS-CoV-2, the pathogen of COVID-19, is roughly similar with other coronavirus such as SARS-CoV and bat-CoV, but by sequencing the amino acid, recombination of virus particles, and observation in Electron microscope, it is obvious to find the some slight difference between the protein of SARS-CoV-2 and others’. The spike protein of SARSCoV-2 has a stronger ability to binding ACE2 than SARS-CoV. The carrier of SARS-CoV-2 is just as other respiratory viruses, like droplet, aerosol and surface, and the fecal-oral transmission is proved to be an efficient pathway. In clinical practice, the elder and the patients with comorbidity are more susceptible to infection and have poorer prognosis, while pediatric patients is the very opposite of it. Nucleic acid test represented by RT-PCR is a helpful method for diagnose, yet it has weaknesses of false negative in suspicious patient and resurgence in discharge patient. Serological and immunological test, reported not suitable for diagnose alone in early period, can be another reliable method that benefit the accuracy of diagnosis criterion when combined with RT-PCR.

scholarly journals Diagnostic Performance of SARS-CoV-2 Rapid Antigen Test in a Large, German Cohort

Children ◽  
2021 ◽  
Vol 8 (8) ◽  
pp. 682
Author(s):  
Olivier Mboma ◽  
Elmar Rieke ◽  
Parviz Ahmad-Nejad ◽  
Stefan Wirth ◽  
Malik Aydin
Keyword(s):  
Clinical Practice ◽  
Diagnostic Performance ◽  
False Negative ◽  
University Hospital ◽  
True Positive ◽  
Antigen Test ◽  
Rt Pcr ◽  
Everyday Clinical Practice ◽  
Ct Value ◽  
The Right

We assessed the performance of a rapid antigen test (RAT) in everyday clinical practice. Between 1 November 2020 until 1 April 2021 all in-patients at the Helios University Hospital Wuppertal, Germany, as well as the accompanying relatives at the Children’s Hospital received a SARS-CoV-2 RAT and a SARS-CoV-2 RT-PCR prior to admission. Out of 3686 patients, 22 (0.6%) subjects were tested positive by RT-PCR and RAT, and 3591 (97.4%) were negative by both methods, showing discordant results: RT-PCR+/RAT− in 58 (1.6%) and RT-PCR−/RAT+ in 15 patients (0.4%). Overall sensitivity and specificity of RAT was 27.5% (95%CI 18.1–38.6%) and 99.6% (95%CI 99.3–99.8%), respectively. The sensitivity was slightly higher in adults (30.4%, 95%CI 18.8–90.9%) than in pediatric subjects (20.8%, 95%CI 7.1–42.2%). False negative RAT had a statistically higher Ct-value (p < 0.001) compared to true positive values, and overall sensitivity increased to 80% [59.3–93.2%] with Ct value < 30. While the sensitivity of the RAT was poor compared with the RT-PCR, the specificity was excellent. However, the sensitivity increased with lower Ct value, and with the right anamnesis the RAT can be a quick and easy approach to distinguish people who are infectious with SARS-CoV-2 from noninfectious people, enabling appropriate triage in clinical practice while waiting for the RT-PCR result.

Scoring System for the Diagnosis of COVID-19

2020 ◽  
Vol 13 (1) ◽  
pp. 413-414 ◽  
Author(s):  
Mohamed Farouk Allam
Keyword(s):  
Scoring System ◽  
Clinical Symptoms ◽  
False Negative ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Negative Results ◽  
False Negative Results ◽  
Symptoms And Signs

Due to the international spread of COVID-19, the difficulty of collecting nasopharyngeal swab specimen from all suspected patients, the costs of RT-PCR and CT, and the false negative results of RT-PCR assay in 41% of COVID-19 patients, a scoring system is needed to classify the suspected patients in order to determine the need for follow-up, home isolation, quarantine or the conduction of further investigations. A scoring system is proposed as a diagnostic tool for suspected patients. It includes Epidemiological Evidence of Exposure, Clinical Symptoms and Signs, and Investigations (if available). This scoring system is simple, could be calculated in a few minutes, and incorporates the main possible data/findings of any patient.

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

Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1091
Author(s):  
Ali A. Rabaan ◽  
Raghavendra Tirupathi ◽  
Anupam A Sule ◽  
Jehad Aldali ◽  
Abbas Al Mutair ◽  
...  
Keyword(s):  
Viral Load ◽  
Real Time ◽  
Disease Severity ◽  
False Negative ◽  
Influential Factors ◽  
Confirmatory Test ◽  
Acid Extraction ◽  
Rt Pcr ◽  
Viral Kinetics ◽  
Ct Value

Real-time RT-PCR is considered the gold standard confirmatory test for coronavirus disease 2019 (COVID-19). However, many scientists disagree, and it is essential to understand that several factors and variables can cause a false-negative test. In this context, cycle threshold (Ct) values are being utilized to diagnose or predict SARS-CoV-2 infection. This practice has a significant clinical utility as Ct values can be correlated with the viral load. In addition, Ct values have a strong correlation with multiple haematological and biochemical markers. However, it is essential to consider that Ct values might be affected by pre-analytic, analytic, and post-analytical variables such as collection technique, specimen type, sampling time, viral kinetics, transport and storage conditions, nucleic acid extraction, viral RNA load, primer designing, real-time PCR efficiency, and Ct value determination method. Therefore, understanding the interpretation of Ct values and other influential factors could play a crucial role in interpreting viral load and disease severity. In several clinical studies consisting of small or large sample sizes, several discrepancies exist regarding a significant positive correlation between the Ct value and disease severity in COVID-19. In this context, a revised review of the literature has been conducted to fill the knowledge gaps regarding the correlations between Ct values and severity/fatality rates of patients with COVID-19. Various databases such as PubMed, Science Direct, Medline, Scopus, and Google Scholar were searched up to April 2021 by using keywords including “RT-PCR or viral load”, “SARS-CoV-2 and RT-PCR”, “Ct value and viral load”, “Ct value or COVID-19”. Research articles were extracted and selected independently by the authors and included in the present review based on their relevance to the study. The current narrative review explores the correlation of Ct values with mortality, disease progression, severity, and infectivity. We also discuss the factors that can affect these values, such as collection technique, type of swab, sampling method, etc.

scholarly journals Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal–oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication. Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1).

scholarly journals Evaluation of SARS-CoV-2 antigen-based rapid diagnostic kits in Pakistan: formulation of COVID-19 national testing strategy

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Umar Saeed ◽  
Sara Rizwan Uppal ◽  
Zahra Zahid Piracha ◽  
Azhar Rasheed ◽  
Zubair Aftab ◽  
...  
Keyword(s):  
Gold Standard ◽  
Injection Drug Users ◽  
Drug Users ◽  
Diagnostic Testing ◽  
False Negative ◽  
Cross Sectional Study ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Cross Sectional ◽  
Negative Results

AbstractRapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33,000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.

scholarly journals Superiority of MALDI-TOF Mass Spectrometry over Real-Time PCR for SARS-CoV-2 RNA Detection

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 730
Author(s):  
Magda Rybicka ◽  
Ewa Miłosz ◽  
Krzysztof Piotr Bielawski
Keyword(s):  
Mass Spectrometry ◽  
Gold Standard ◽  
Viral Genome ◽  
False Negative ◽  
Rt Pcr ◽  
Rna Detection ◽  
Maldi Tof ◽  
Negative Results ◽  
False Negative Results ◽  
Pcr Test

At present, the RT-PCR test remains the gold standard for early diagnosis of SARS-CoV-2. Nevertheless, there is growing evidence demonstrating that this technique may generate false-negative results. Here, we aimed to compare the new mass spectrometry-based assay MassARRAY® SARS-CoV-2 Panel with the RT-PCR diagnostic test approved for clinical use. The study group consisted of 168 suspected patients with symptoms of a respiratory infection. After simultaneous analysis by RT-PCR and mass spectrometry methods, we obtained discordant results for 17 samples (10.12%). Within fifteen samples officially reported as presumptive positive, 13 were positive according to the MS-based assay. Moreover, four samples reported by the officially approved RT-PCR as negative were positive in at least one MS assay. We have successfully demonstrated superior sensitivity of the MS-based assay in SARS-CoV-2 detection, showing that MALDI-TOF MS seems to be ideal for the detection as well as discrimination of mutations within the viral genome.

scholarly journals SAT0532 POSITIVE DISEASE-SPECIFIC AUTOANTIBODIES LOWER DIAGNOSTIC SENSITIVITY BUT HAVE LITTLE CLINICAL SIGNIFICANCE IN DIAGNOSING IgG4-RELATED DISEASE USING THE 2019 ACR/EULAR CLASSIFICATION CRITERIA IN DAILY CLINICAL PRACTICE

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1224.1-1224
Author(s):  
I. Mizushima ◽  
T. Yamano ◽  
H. Kawahara ◽  
S. Hibino ◽  
R. Nishioka ◽  
...  
Keyword(s):  
Clinical Practice ◽  
False Negative ◽  
Classification Criteria ◽  
Daily Clinical Practice ◽  
Exclusion Criterion ◽  
Inclusion Criteria ◽  
Related Disease ◽  
Igg4 Related Disease ◽  
Serum Igg4 ◽  
Disease Specific

Background:Recently, the 2019 ACR/EULAR classification criteria for IgG4-related disease (IgG4-RD) were published mainly to identify more homogeneous subjects for inclusion in clinical trials and observational studies [1]. However, although their high specificity is presumed to be useful to differentiate IgG4-RD from various mimickers, their value in daily clinical practice needs to be evaluated.Objectives:This study aimed to clarify the usefulness of the 2019 ACR/EULAR classification criteria for IgG4-RD and characteristics of false-negative patients in daily clinical practice.Methods:We retrospectively reviewed the medical records of 162 patients with IgG4-RD and 130 consecutive non-IgG4-RD patients (mimickers) diagnosed by experts whose serum IgG4 levels were measured at a single center in Japan. Using the collected data, we calculated sensitivity, specificity, and fulfillment rates for the entry criteria, exclusion criteria, and threshold of inclusion criteria points. In addition, to clarify the characteristics of false-negative cases in IgG4-RD, we performed an intergroup comparison of their clinical features including disease-specific autoantibodies.Results:Both the patients with IgG4-RD and mimickers were relatively old (66 and 65 years) with male predominance (67% and 60%). The final diagnoses of mimickers mainly consisted of cancer, lymphoma, vasculitis, sarcoidosis, multicentric Castleman’s disease, and atherosclerotic or infectious aortic aneurysm. The classification criteria had a sensitivity of 72.8% and a specificity of 100%. Of the 44 false-negative cases, one did not fulfill the entry criteria, 20 fulfilled one exclusion criterion, and 27 did not achieve sufficient inclusion criteria points. Compared with the true-positive cases, the false-negative cases had significantly fewer affected organs, lower serum IgG4 levels, higher serum CH50 levels, and lower prevalence of salivary/lacrimal gland and renal parenchymal lesions. They were also less likely to have had biopsies (61% vs 97%). Of note, positivity of disease-specific autoantibodies including SSA/Ro antibody, ANCA, ds-DNA antibody, and ACPA was the most common exclusion criterion fulfilled in 18 patients, only 2 of whom were diagnosed with a specific autoimmune disease (rheumatoid arthritis) complicated by IgG4-RD. The remaining 16 patients had no specific clinical symptoms related to such autoantibodies. In addition, compared with IgG4-RD patients without disease-specific autoantibodies, the 18 patients with them had almost equal serum IgG4 and complement levels, number of affected organs, and histopathology and immunostaining scores despite higher serum IgG and CRP levels.Conclusion:The present study suggests that the 2019 ACR/EULAR classification criteria for IgG4-RD has excellent diagnostic specificity and moderate sensitivity in daily clinical practice. Positive disease-specific autoantibodies alone, which lowered the sensitivity in this study, may have little clinical significance concerning the diagnosis of IgG4-RD.References:[1]Wallace ZS et al. The 2019 American College of Rheumatology/European League Against Rheumatism classification criteria for IgG4-related disease. Ann Rheum Dis. 2020 Jan;79(1):77-87.Disclosure of Interests:None declared

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