Should RT-PCR be considered a gold standard in the diagnosis of COVID-19?

Utility of Routine Laboratory Biomarkers to Detect COVID-19: A Systematic Review and Meta-Analysis

No routine laboratory biomarkers perform well enough in diagnosing COVID-19 in isolation for them to be used as a standalone diagnostic test or to help clinicians prioritize patients for treatment. Instead, other diagnostic tests are needed. The aim of this work was to statistically summarise routine laboratory biomarker measurements in COVID-19-positive and -negative patients to inform future work. A systematic literature review and meta-analysis were performed. The search included names of commonly used, routine laboratory tests in the UK NHS, and focused on research papers reporting laboratory results of patients diagnosed with COVID-19. A random effects meta-analysis of the standardized mean difference between COVID-19-positive and -negative groups was conducted for each biomarker. When comparing reported laboratory biomarker results, we identified decreased white blood cell, neutrophil, lymphocyte, eosinophil, and platelet counts; while lactate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase were elevated in COVID-19-positive compared to COVID-19-negative patients. Differences were identified across a number of routine laboratory biomarkers between COVID-19-positive and -negative patients. Further research is required to identify whether routine laboratory biomarkers can be used in the development of a clinical scoring system to aid with triage of patients.

Survival analysis of time to SARS-CoV-2 PCR negativisation to optimise PCR prescription in health workers: the Henares COVID-19 healthcare workers cohort study

Objectives

Reverse transcriptase PCR (RT-PCR) is considered the gold standard in diagnosing COVID-19. Infected healthcare workers do not go back to work until RT-PCR has demonstrated that the virus is no longer present in the upper respiratory tract. The aim of this study is to determine the most efficient time to perform RT-PCR prior to healthcare workers’ reincorporation.

Materials and methods

This is a cohort study of healthcare workers with RT-PCR-confirmed COVID-19. Data were collected using the medical charts of healthcare workers and completed with a telephone interview. Kaplan-Meier curves were used to determine the influence of several variables on the time to RT-PCR negativisation. The impact of the variables on survival was assessed using the Breslow test. A Cox regression model was developed including the associated variables.

Results

159 subjects with a positive RT-PCR out of 374 workers with suspected COVID-19 were included. The median time to negativisation was 25 days from symptom onset (IQR 20–35 days). Presence of IgG, dyspnoea, cough and throat pain were associated with significant longer time to negativisation. Cox logistic regression was used to adjust for confounding variables. Only dyspnoea and cough remained in the model as significant determinants of prolonged negativisation time. Adjusted HRs were 0.68 (0.48–096) for dyspnoea and 0.61 (0.42–0.88) for dry cough.

Conclusions

RT-PCR during the first 3 weeks leads to a high percentage of positive results. In the presence of respiratory symptoms, negativisation took nearly 1 week more. Those who developed antibodies needed longer time to negativisate.

Analysis of SARS-CoV-2 mutations in Mexico, Belize, and isolated regions of Guatemala and its implication in the diagnosis

The genomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide are publicly available and are derived from studies due to the increase in the number of cases. The importance of study of mutations is related to the possible virulence and diagnosis of SARS-CoV-2. To identify circulating mutations present in SARS-CoV-2 genomic sequences in Mexico, Belize, and Guatemala to find out if the same strain spread to the south, and analyze the specificity of the primers used for diagnosis in these samples. Twenty three complete SARS-CoV-2 genomic sequences, available in the GISAID database from May 8 to September 11, 2020 were analyzed and aligned versus the genomic sequence reported in Wuhan, China (NC_045512.2), using Clustal Omega. Open reading frames were translated using the ExPASy Translate Tool and UCSF Chimera (v.1.12) for amino acid substitutions analysis. Finally, the sequences were aligned versus primers used in the diagnosis of COVID-19. One hundred and eighty seven distinct variants were identified, of which 102 are missense, 66 synonymous and 19 noncoding. P4715L and P5828L substitutions in replicase polyprotein were found, as well as D614G in spike protein and L84S in ORF8 in Mexico, Belize, and Guatemala. The primers design by CDC of United States showed a positive E value. The genomic sequences of SARS-CoV-2 in Mexico, Belize, and Guatemala present similar mutations related to a virulent strain of greater infectivity, which could mean a greater capacity for inclusion in the host genome and be related to an increased spread of the virus in these countries, furthermore, its diagnosis would be affected.

Fatality and risk features for prognosis in COVID-19 according to the care approach - a retrospective cohort study

Introduction

This study analyzed the impact of a categorized approach, based on patients’ prognosis, on major outcomes and explanators in patients hospitalized for COVID-19 pneumonia in an academic center in Spain.

Methods

Retrospective cohort study (March 3 to May 2, 2020). Patients were categorized according to the followed clinical management, as maximum care or limited therapeutic effort (LTE). Main outcomes were all-cause mortality and need for invasive mechanical ventilation (IMV). Baseline factors associated with outcomes were analyzed by multiple logistic regression, estimating odds ratios (OR; 95%CI).

Results

Thirty-hundred and six patients were hospitalized, median age 65.0 years, 57.8% males, 53.3% Charlson index ≥3. The overall all-cause fatality rate was 15.0% (n = 46). Maximum care was provided in 238 (77.8%), IMV was used in 38 patients (16.0%), and 5.5% died. LTE was decided in 68 patients (22.2%), none received IMV and fatality was 48.5%. Independent risk factors of mortality under maximum care were lymphocytes <790/mm³, troponin T >15ng/L and hypotension. Advanced age, lymphocytes <790/mm³ and BNP >240pg/mL independently associated with IMV requirement.

Conclusion

Overall fatality in the cohort was 15% but markedly varied regarding the decided approach (maximum care versus LTE), translating into nine-fold higher mortality and different risk factors.

Mutations in Animal SARS-CoV-2 Induce Mismatches with the Diagnostic PCR Assays

Recently, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was detected in several animal species. After transmission to animals, the virus accumulates mutations in its genome as adaptation to the new animal host progresses. Therefore, we investigated whether these mutations result in mismatches with the diagnostic PCR assays and suggested proper modifications to the oligo sequences accordingly. A comprehensive bioinformatic analysis was conducted using 28 diagnostic PCR assays and 793 publicly available SARS-CoV-2 genomes isolated from animals. Sixteen out of the investigated 28 PCR assays displayed at least one mismatch with their targets at the 0.5% threshold. Mismatches were detected in seven, two, two, and six assays targeting the ORF1ab, spike, envelope, and nucleocapsid genes, respectively. Several of these mismatches, such as the deletions and mismatches at the 3' end of the primer or probe, are expected to negatively affect the diagnostic PCR assays resulting in false-negative results. The modifications to the oligo sequences should result in stronger template binding by the oligos, better sensitivity of the assays, and higher confidence in the result. It is necessary to monitor the targets of diagnostic PCR assays for any future mutations that may occur as the virus continues to evolve in animals.

A novel comprehensive metric to assess effectiveness of COVID-19 testing: Inter-country comparison and association with geography, government, and policy response

Testing and case identification are key strategies in controlling the COVID-19 pandemic. Contact tracing and isolation are only possible if cases have been identified. The effectiveness of testing should be assessed, but a single comprehensive metric is not available to assess testing effectiveness, and no timely estimates of case detection rate are available globally, making inter-country comparisons difficult. The purpose of this paper was to propose a single, comprehensive metric, called the COVID-19 Testing Index (CovTI) scaled from 0 to 100, derived from epidemiological indicators of testing, and to identify factors associated with this outcome. The index was based on case-fatality rate, test positivity rate, active cases, and an estimate of the detection rate. It used parsimonious modeling to estimate the true total number of COVID-19 cases based on deaths, testing, health system capacity, and government transparency. Publicly reported data from 165 countries and territories that had reported at least 100 confirmed cases by June 3, 2020 were included in the index. Estimates of detection rates aligned satisfactorily with previous estimates in literature (R2 = 0.44). As of June 3, 2020, the states with the highest CovTI included Hong Kong (93.7), Australia (93.5), Iceland (91.8), Cambodia (91.3), New Zealand (90.6), Vietnam (90.2), and Taiwan (89.9). Bivariate analyses showed the mean CovTI in countries with open public testing policies (66.9, 95% CI 61.0-72.8) was significantly higher than in countries with no testing policy (29.7, 95% CI 17.6-41.9) (p<0.0001). A multiple linear regression model assessed the association of independent grouping variables with CovTI. Open public testing and extensive contact tracing were shown to significantly increase CovTI, after adjusting for extrinsic factors, including geographic isolation and centralized forms of government. The correlation of testing and contact tracing policies with improved outcomes demonstrates the validity of this model to assess testing effectiveness and also suggests these policies were effective at improving health outcomes. This tool can be combined with other databases to identify other factors or may be useful as a standalone tool to help inform policymakers.

Characteristics of Three Different Chemiluminescence Assays for Testing for SARS-CoV-2 Antibodies

Several tests based on chemiluminescence immunoassay techniques have become available to test for SARS-CoV-2 antibodies. There is currently insufficient data on serology assay performance beyond 35 days after symptoms onset. We aimed to evaluate SARS-CoV-2 antibody tests on three widely used platforms. A chemiluminescent microparticle immunoassay (CMIA; Abbott Diagnostics, USA), a luminescence immunoassay (LIA; Diasorin, Italy), and an electrochemiluminescence immunoassay (ECLIA; Roche Diagnostics, Switzerland) were investigated. In a multigroup study, sensitivity was assessed in a group of participants with confirmed SARS-CoV-2 (n = 145), whereas specificity was determined in two groups of participants without evidence of COVID-19 (i.e., healthy blood donors, n = 191, and healthcare workers, n = 1002). Receiver operating characteristic (ROC) curves, multilevel likelihood ratios (LR), and positive (PPV) and negative (NPV) predictive values were characterized. Finally, analytical specificity was characterized in samples with evidence of the Epstein–Barr virus (EBV) (n = 9), cytomegalovirus (CMV) (n = 7), and endemic common-cold coronavirus infections (n = 12) taken prior to the current SARS-CoV-2 pandemic. The diagnostic accuracy was comparable in all three assays (AUC 0.98). Using the manufacturers' cut-offs, the sensitivities were 90%, 95% confidence interval [84,94] (LIA), 93% [88,96] (CMIA), and 96% [91,98] (ECLIA). The specificities were 99.5% [98.9,99.8] (CMIA), 99.7% [99.3,99.9] (LIA), and 99.9% [99.5,99.98] (ECLIA). The LR at half of the manufacturers' cut-offs were 60 (CMIA), 82 (LIA), and 575 (ECLIA) for positive and 0.043 (CMIA) and 0.035 (LIA, ECLIA) for negative results. ECLIA had higher PPV at low pretest probabilities than CMIA and LIA. No interference with EBV or CMV infection was observed, whereas endemic coronavirus in some cases provided signals in LIA and/or CMIA. Although the diagnostic accuracy of the three investigated assays is comparable, their performance in low-prevalence settings is different. Introducing gray zones at half of the manufacturers' cut-offs is suggested, especially for orthogonal testing approaches that use a second assay for confirmation.

Artificial intelligence and radiology: Combating the COVID-19 conundrum

The COVID-19 pandemic has necessitated rapid testing and diagnosis to manage its spread. While reverse transcriptase polymerase chain reaction (RT-PCR) is being used as the gold standard method to diagnose COVID-19, many scientists and doctors have pointed out some challenges related to the variability, accuracy, and affordability of this technique. At the same time, radiological methods, which were being used to diagnose COVID-19 in the early phase of the pandemic in China, were sidelined by many primarily due to their low specificity and the difficulty in conducting a differential diagnosis. However, the utility of radiological methods cannot be neglected. Indeed, over the past few months, healthcare consultants and radiologists in India have been using or advising the use of high-resolution computed tomography (HRCT) of the chest for early diagnosis and tracking of COVID-19, particularly in preoperative and asymptomatic patients. At the same time, scientists have been trying to improve upon the radiological method of COVID-19 diagnosis and monitoring by using artificial intelligence (AI)-based interpretation models. This review is an effort to compile and compare such efforts. To this end, the latest scientific literature on the use of radiology and AI-assisted radiology for the diagnosis and monitoring of COVID-19 has been reviewed and presented, highlighting the strengths and limitations of such techniques.

Loop-mediated isothermal amplification for the detection of SARS-CoV-2 in saliva

In the fight against the recent COVID-19 pandemics, testing is crucial. Nasopharyngeal swabs and real-time RT-PCR are used for the detection of the viral RNA. The collection of saliva is non-invasive, pain-free and does not require trained personnel. An alternative to RT-PCR is loop-mediated isothermal amplification coupled with reverse transcription (RT-LAMP) that is easy to perform, quick and does not require a thermal cycler. The aim of this study was to test whether SARS-CoV-2 RNA can be detected directly in saliva using RT-LAMP. We have tested 16 primer mixes from the available literature in three rounds of sensitivity assays. The selected RT-LAMP primer mix has a limit of detection of 6 copies of viral RNA per reaction in comparison with RT-PCR with 1 copy per reaction. Whole saliva, as well as saliva collected using Salivette collection tubes, interfered with the RT-LAMP analysis. Neither Chelex-100 nor protease treatment of saliva prevented the inhibitory effect of saliva. With the addition of the ribonuclease inhibitor, the sensitivity of the RT-LAMP assay was 12 copies per reaction of RNA in Salivette® saliva samples and 6 copies per reaction of RNA in whole saliva samples. This study shows that it is possible to combine the use of saliva and RT-LAMP for SARS-CoV-2 RNA detection without RNA extraction which was confirmed on a small set of correctly diagnosed clinical samples. Further studies should prove whether this protocol is suitable for point of care testing in the clinical setting.

Characteristics and Outcomes of Patients Undergoing Endoscopy During the COVID-19 Pandemic: A Multicenter Study from New York City

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic has significantly impacted the practice of endoscopy, but characteristics of COVID patients undergoing endoscopy have not been adequately described.

AIMS

To compare findings, clinical outcomes, and patient characteristics of endoscopies performed during the pandemic in patients with and without COVID-19.

METHODS

This was a retrospective multicenter study of adult endoscopies at six academic hospitals in New York between March 16 and April 30, 2020. Patient and procedure characteristics including age, sex, indication, findings, interventions, and outcomes were compared in patients testing positive, negative, or untested for COVID-19.

RESULTS

Six hundred and five endoscopies were performed on 545 patients during the study period. There were 84 (13.9%), 255 (42.2%), and 266 (44.0%) procedures on COVID-positive, negative, and untested patients, respectively. COVID patients were more likely to undergo endoscopy for gastrointestinal bleeding or gastrostomy tube placement, and COVID patients with gastrointestinal bleeding more often required hemostatic interventions on multivariable logistic regression. COVID patients had increased length of stay, intensive care unit admission, and intubation rate. Twenty-seven of 521 patients (5.2%) with no or negative COVID testing prior to endoscopy later tested positive, a median of 13.5 days post-procedure.

CONCLUSIONS

Endoscopies in COVID patients were more likely to require interventions, due either to more severe illness or a higher threshold to perform endoscopy. A significant number of patients endoscoped without testing were subsequently found to be COVID-positive. Gastroenterologists in areas affected by the pandemic must adapt to changing patterns of endoscopy practice and ensure pre-endoscopy COVID testing.

The Main Molecular and Serological Methods for Diagnosing COVID-19: An Overview Based on the Literature

Diagnostic tests have been considered as the main alternative for the control of coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a correct diagnosis allows for decision making when facing the disease, particularly as there is a lack of effective therapeutic protocols and vaccines. Thus, in this review, we summarized the main diagnostic approaches currently available for the diagnosis of SARS-CoV-2 infection in humans based on studies available in article databases. The tests can be organized into two main categories: nucleic acid-based tests, recommended for the initial detection of the virus, and serological tests, recommended for assessing the disease progression. The studies have shown that the performance of diagnostic methods depends on different factors, such as the type of samples and the characteristics of each assay. It was identified that the positivity of the tests is mainly related to the onset of symptoms. We also observed that point-of-care diagnoses are considered as one of the main trends in this area, due to the low-cost and simplicity of the assay; however, the analytical performance must be critically analyzed. Thus, the COVID-19 pandemic has highlighted the critical role of diagnostic technologies in the control of infectious diseases.

Evaluation of seven commercial RT-PCR kits for COVID-19 testing in pooled clinical specimens

There are more than 350 real‐time polymerase chain reaction (RT‐PCR) coronavirus disease‐2019 (COVID‐19) testing kits commercially available but these kits have not been evaluated for pooled sample testing. Thus, this study was planned to compare and evaluate seven commercially available kits for pooled samples testing. Diagnostic accuracy of (1) TRUPCR SARS‐CoV‐2 Kit (Black Bio), (2) TaqPath RT‐PCR COVID‐19 Kit (Thermo Fisher Scientific), (3) Allplex 2019‐nCOV Assay (Seegene), (4) Patho detect COVID‐19 PCR kit (My Lab), (5) LabGun COVID‐19 RT‐PCR Kit (Lab Genomics, Korea), (6) Fosun COVID‐19 RT‐PCR detection kit (Fosun Ltd.), (7) Real‐time Fluorescent RT‐PCR kit for SARS CoV‐2 (BGI) was evaluated on precharacterised 40 positive and 10 negative COVID‐19 sample pools. All seven kits detected all sample pools with low C_t values (<30); while testing weak positive pooled samples with high C_t value (>30); the TRUPCR Kit, TaqPath Kit, Allplex Assay, and BGI RT‐PCR kit showed 100% sensitivity, specificity, and accuracy. However, the Fosun kit, LabGun Kit, and Patho detect kit could detect only 90%, 85%, and 75% of weakly positive samples, respectively. We conclude that all seven commercially available RT‐PCR kits included in this study can be used for routine molecular diagnosis of COVID‐19. However, regarding performing pooled sample testing, it might be advisable to use those kits that performed best regarding positive identification in samples' pool, that is TRUPCR SARS‐CoV‐2 Kit, TaqPath RT‐PCR COVID‐19 Kit, Allplex 2019‐nCOV Assay, and BGI Real‐time RT‐PCR kit for detecting SARS CoV‐2.

Algorithms for testing COVID-19 focused on use of RT-PCR and high-affinity serological testing: A consensus statement from a panel of Latin American experts

The COVID-19 pandemic has caused an unprecedented public health, social, and economic crisis. Improving understanding on available tests for detecting COVID-19 is critical for effective management of the pandemic. We proposed that a multidisciplinary expert panel can establish recommendations on ideal use of diagnostic tools, with a focus on RT-PCR and serological high-affinity antibodies (both IgM and IgG) tests for the Latin America region.

Study design

A collaborative multidisciplinary panel of 5 recognized experts in Latin America (an infectious disease specialist, three pathologists, and an immunologist) was convened and supported by Roche Diagnostics to develop standard guidelines and an evidence-based document of best practices on the use of diagnostic tools for COVID-19.

Results

The authors reached consensus on the applicability of diagnostic tools to provide testing algorithms for the use of RT-PCR and serological high-affinity antibodies (both IgM and IgG) tests in three settings: 1) For asymptomatic subjects exposed to a SARS-CoV-2 infected person; 2) For epidemiological purposes and; 3) For symptomatic subjects.

Conclusion

The serological high-affinity SARS-CoV-2 antibodies (both IgM and IgG) tests play a key role in COVID-19 diagnosis. These tests can be applied for suspected false-negative RT-PCR results and for individual determination of response. The use of these tests can also contribute greatly to public health strategies, such as population screening and supporting vaccination planning. Serological status for high-affinity antibodies (both IgM and IgG) should be performed ideally 21 days after potential infectious contact, given that the majority of exposed individuals will have seroconverted.

Microfluidic Nano-Scale qPCR Enables Ultra-Sensitive and Quantitative Detection of SARS-CoV-2

A major challenge in controlling the COVID-19 pandemic is the high false-negative rate of the commonly used RT-PCR methods for SARS-CoV-2 detection in clinical samples. Accurate detection is particularly challenging in samples with low viral loads that are below the limit of detection (LoD) of standard one- or two-step RT-PCR methods. In this study, we implemented a three-step approach for SARS-CoV-2 detection and quantification that employs reverse transcription, targeted cDNA preamplification, and nano-scale qPCR based on a commercially available microfluidic chip. Using SARS-CoV-2 synthetic RNA and plasmid controls, we demonstrate that the addition of a preamplification step enhances the LoD of this microfluidic RT-qPCR by 1000-fold, enabling detection below 1 copy/µL. We applied this method to analyze 182 clinical NP swab samples previously diagnosed using a standard RT-qPCR protocol (91 positive, 91 negative) and demonstrate reproducible and quantitative detection of SARS-CoV-2 over five orders of magnitude (<1 to 106 viral copies/µL). Crucially, we detect SARS-CoV-2 with relatively low viral load estimates (<1 to 40 viral copies/µL) in 17 samples with negative clinical diagnosis, indicating a potential false-negative rate of 18.7% by clinical diagnostic procedures. In summary, this three-step nano-scale RT-qPCR method can robustly detect SARS-CoV-2 in samples with relatively low viral loads (<1 viral copy/µL) and has the potential to reduce the false-negative rate of standard RT-PCR-based diagnostic tests for SARS-CoV-2 and other viral infections.

Outcomes in COVID-19 Positive Neonates and Possibility of Viral Vertical Transmission: A Narrative Review

OBJECTIVE

Novel coronavirus disease 2019 (COVID-19) seems to affect adults and pediatric patients differently. While neonates are a special population, little is known about the neonatal outcomes. This study aimed to investigate the outcomes in COVID-19 positive neonates and incidence of vertical transmission of the virus by reviewing available literature.

STUDY DESIGN

This study is a narrative review of available literature on "COVID-19 in neonates," for which PubMed and Google Scholar were used to search the published articles.

RESULTS

We summarized the data from 39 published studies that are comprised of 326 COVID-19 positive peripartum mothers with respective neonatal outcomes. Twenty-three neonates have been reported to be COVID-19 positive. Male neonates were affected significantly more (79%) than female neonates. Approximately 3% neonates acquired infection through suspected vertical transmission. Strict infection prevention measures during the perinatal time can significantly reduce the chance of horizontal transmission of the virus. Overall, neonates were asymptomatic or mildly symptomatic regardless of gestational age at birth and required only supportive measures. There was 0% mortality in COVID-19 positive neonates.

CONCLUSION

From available published data to date, we can conclude that the prognosis of COVID-19 positive neonates is good with no mortality. There appears to be minimal vertical transmission of the infection.

KEY POINTS

· Majority of COVID-19 positive neonates showed mild clinical signs and symptoms with no mortality.. · Most COVID-19 positive neonates require only supportive measures.. · Possibility of viral vertical transmission is very low..

Chest x-ray in the COVID-19 pandemic: Radiologists' real-world reader performance

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Chest x-ray had a 89 % sensitivity detecting COVID-19 pneumonia during pandemic peak.

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Experienced radiologists had higher specificity than less-experienced ones.

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Overall and per-group sensitivity in detecting COVID-19 pneumonia increased over time.

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Overall and per-group accuracy in detecting COVID-19 pneumonia increased over time.

Purpose

To report real-world diagnostic performance of chest x-ray (CXR) readings during the COVID-19 pandemic.

Methods

In this retrospective observational study we enrolled all patients presenting to the emergency department of a Milan-based university hospital from February 24th to April 8th 2020 who underwent nasopharyngeal swab for reverse transcriptase-polymerase chain reaction (RT-PCR) and anteroposterior bedside CXR within 12 h. A composite reference standard combining RT-PCR results with phone-call-based anamnesis was obtained. Radiologists were grouped by CXR reading experience (Group-1, >10 years; Group-2, <10 years), diagnostic performance indexes were calculated for each radiologist and for the two groups.

Results

Group-1 read 435 CXRs (77.0 % disease prevalence): sensitivity was 89.0 %, specificity 66.0 %, accuracy 83.7 %. Group-2 read 100 CXRs (73.0 % prevalence): sensitivity was 89.0 %, specificity 40.7 %, accuracy 76.0 %. During the first half of the outbreak (195 CXRs, 66.7 % disease prevalence), overall sensitivity was 80.8 %, specificity 67.7 %, accuracy 76.4 %, Group-1 sensitivity being similar to Group-2 (80.6 % versus 81.5 %, respectively) but higher specificity (74.0 % versus 46.7 %) and accuracy (78.4 % versus 69.0 %). During the second half (340 CXRs, 81.8 % prevalence), overall sensitivity increased to 92.8 %, specificity dropped to 53.2 %, accuracy increased to 85.6 %, this pattern mirrored in both groups, with decreased specificity (Group-1, 58.0 %; Group-2, 33.3 %) but increased sensitivity (92.7 % and 93.5 %) and accuracy (86.5 % and 81.0 %, respectively).

Conclusions

Real-world CXR diagnostic performance during the COVID-19 pandemic showed overall high sensitivity with higher specificity for more experienced radiologists. The increase in accuracy over time strengthens CXR role as a first line examination in suspected COVID-19 patients.

Frequency of serological non-responders and false-negative RT-PCR results in SARS-CoV-2 testing: a population-based study

Objectives The sensitivity of molecular and serological methods for COVID-19 testing in an epidemiological setting is not well described. The aim of the study was to determine the frequency of negative RT-PCR results at first clinical presentation as well as negative serological results after a follow-up of at least 3 weeks. Methods Among all patients seen for suspected COVID-19 in Liechtenstein (n=1921), we included initially RT-PCR positive index patients (n=85) as well as initially RT-PCR negative (n=66) for follow-up with SARS-CoV-2 antibody testing. Antibodies were detected with seven different commercially available immunoassays. Frequencies of negative RT-PCR and serology results in individuals with COVID-19 were determined and compared to those observed in a validation cohort of Swiss patients (n=211). Results Among COVID-19 patients in Liechtenstein, false-negative RT-PCR at initial presentation was seen in 18% (12/66), whereas negative serology in COVID-19 patients was 4% (3/85). The validation cohort showed similar frequencies: 2/66 (3%) for negative serology, and 16/155 (10%) for false negative RT-PCR. COVID-19 patients with negative follow-up serology tended to have a longer disease duration (p=0.05) and more clinical symptoms than other patients with COVID-19 (p<0.05). The antibody titer from quantitative immunoassays was positively associated with the number of disease symptoms and disease duration (p<0.001). Conclusions RT-PCR at initial presentation in patients with suspected COVID-19 can miss infected patients. Antibody titers of SARS-CoV-2 assays are linked to the number of disease symptoms and the duration of disease. One in 25 patients with RT-PCR-positive COVID-19 does not develop antibodies detectable with frequently employed and commercially available immunoassays.

Diagnostic and Prognostic Value of Chest Radiographs for COVID-19 at Presentation

INTRODUCTION

Pulmonary opacities in COVID-19 increase throughout the illness and peak after ten days. The radiological literature mainly focuses on CT findings. The purpose of this study was to assess the diagnostic and prognostic value of chest radiographs (CXR) for coronavirus disease 2019 (COVID-19) at presentation.

METHODS

We retrospectively identified consecutive reverse transcription polymerase reaction-confirmed COVID-19 patients (n = 104, 75% men) and patients (n = 75, 51% men) with repeated negative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tests. Two radiologists blindly and independently reviewed the CXRs, documented findings, assigned radiographic assessment of lung edema (RALE) scores, and predicted the patients' COVID-19 status. We calculated interobserver reliability. The score use for diagnosis and prognosis of COVID-19 was evaluated with the area under the receiver operating characteristic curve.

RESULTS

The overall RALE score failed to identify COVID-19 patients at presentation. However, the score was inversely correlated with a COVID-19 diagnosis within ≤2 days, and a positive correlation was found six days after symptom onset.Interobserver agreement with regard to separating normal from abnormal CXRs was moderate (k = 0.408) with low specificity (25% and 27%). Definite pleural effusion had almost perfect agreement (k = 0.833) and substantially reduced the odds of a COVID-19 diagnosis. Disease distribution and experts' opinion on COVID-19 status had only fair interobserver agreement. The RALE score interobserver reliability was moderate to good (intraclass correlation coefficient = 0.745). A high RALE score predicted a poor outcome (intensive care unit hospitalization, intubation, or death) in COVID-19 patients; a score of ≥5 substantially increased the odds of having a poor outcome.

CONCLUSION

Chest radiography was found not to be a valid diagnostic tool for COVID-19, as normal or near-normal CXRs are more likely early in the disease course. Pleural effusions at presentation suggest a diagnosis other than COVID-19. More extensive lung opacities at presentation are associated with poor outcome in COVID-19 patients. Thus, patients with more than minimal opacities should be monitored closely for clinical deterioration. This clinical application of CXR is its greatest strength in COVID-19 as it impacts patient care.

EDTA-Anticoagulated Whole Blood for SARS-CoV-2 Antibody Testing by Electrochemiluminescence Immunoassay (ECLIA) and Enzyme-Linked Immunosorbent Assay (ELISA)

While lateral flow test formats can be utilized with whole blood and low sample volumes, their diagnostic characteristics are inferior to immunoassays based on chemiluminescence immunoassay (CLIA) or enzyme-linked immunosorbent assay (ELISA) technology. CLIAs and ELISAs can be automated to a high degree but commonly require larger serum or plasma volumes for sample processing. We addressed the suitability of EDTA-anticoagulated whole blood as an alternative sample material for antibody testing against SARS-CoV-2 by electro-CLIA (ECLIA; Roche, Rotkreuz, Switzerland) and ELISA (IgG and IgA; Euroimmun, Germany). Simultaneously drawn venous serum and EDTA-anticoagulated whole blood samples from 223 individuals were included. Correction of the whole blood results for hematocrit led to a good agreement with the serum results for weakly to moderately positive antibody signals. In receiver-operating characteristic curve analysis, all three assays displayed comparable diagnostic accuracy (area under the curve (AUC)) using corrected whole blood and serum (AUCs: 0.97 for ECLIA and IgG ELISA; 0.84 for IgA ELISA). In conclusion, our results suggest that the investigated assays can reliably detect antibodies against SARS-CoV-2 in hemolyzed whole blood anticoagulated with EDTA. Correction of these results for hematocrit is suggested. This study demonstrates that the automated processing of whole blood for identification of SARS-CoV-2 antibodies with common ECLIA and ELISA methods is accurate and feasible.

Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study

Background: Coronavirus Disease 2019 (COVID-19) has rapidly spread worldwide, becoming an unprecedented public health emergency. Rapid detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) suspected cases is crucial to control the spread of infection. We aimed to evaluate the time length of negativization from the onset of symptoms in healthcare workers (HCWs) with COVID-19, and to evaluate significant variations in cycle threshold (CT) values and gene positivity (E, RdRP, and N genes) among positive individuals who returned to work. Methods: We retrospectively analyzed a consecutive cohort of 182 SARS-CoV-2-positive HCWs in Milan, from 16 March to 30 April 2020. Nasopharyngeal swabs were tested by RT-PCR. Results: Asymptomatic HCWs were 17.6% (32/182), and 58 healed at 30 April 2020. The median time length of negativization was 4 weeks (35% of symptomatic versus 40% of asymptomatic HCWs). Four HCWs, healed at 30 April, turned positive within three weeks during controls set up in the work unit. Three-gene positivity had the greatest variability, and increasing CT values from single- to three-gene positivity among all age groups were observed. Conclusions: Self-isolation longer than two weeks and prolonged follow-up periods for the staff returning to work after COVID-19 could be the most suitable choices to counter the SARS-CoV-2 spread. Further studies are needed to investigate infectiousness profiles among positive individuals.

Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is responsible for the recent COVID-19 pandemic and polymerase chain reaction (PCR) is the current standard method for its diagnosis from patient samples. This study conducted a reassessment of published diagnostic PCR assays, including those recommended by the World Health Organization (WHO), through the evaluation of mismatches with publicly available viral sequences. An exhaustive evaluation of the sequence variability within the primer/probe target regions of the viral genome was performed using more than 17 000 viral sequences from around the world. The analysis showed the presence of mutations/mismatches in primer/probe binding regions of 7 assays out of 27 assays studied. A comprehensive bioinformatics approach for in silico inclusivity evaluation of PCR diagnostic assays of SARS-CoV-2 was validated using freely available software programs that can be applied to any diagnostic assay of choice. These findings provide potentially important information for clinicians, laboratory professionals and policy-makers.