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1.
PLoS One ; 17(1): e0262174, 2022.
Article in English | MEDLINE | ID: covidwho-1622354

ABSTRACT

OBJECTIVES: The aim of this study was to evaluate the clinical performance of the Fluorecare SARS-CoV-2 Spike Protein Test Kit, a rapid immunochromatographic assay for SARS-CoV-2 detection. Moreover, we sought to point out the strategy adopted by a local company to lift the lockdown without leading to an increase in the number of COVID-19 cases, by performing a precise and timely health surveillance. METHODS: The rapid Fluorecare SARS-CoV-2 Spike Protein Test was performed immediately after sampling following the manufacturer's instructions. RT-PCRs were performed within 24 hours of specimen collection. A total amount of 253 nasopharyngeal samples from 121 individuals were collected between March 16 and April 2, 2021 and tested. RESULTS: Of 253 nasopharyngeal samples, 11 (9.1%) were positive and 242 (90.9%) were negative for SARS-CoV-2 RNA by RT-PCR assays. The rapid SARS-CoV-2 antigen detection test's mean sensitivity and specificity were 84,6% (95% CI, 54.6-98.1%) and 100% (95% CI, 98.6-100%), respectively. Two false negative test results were obtained from samples with high RT-PCR cycle threshold (Ct). CONCLUSION: Our study suggested that Fluorecare SARS-CoV-2 Spike Protein Test can be introduced into daily diagnostic practice, as its mean sensitivity and specificity follow the standards recommended by WHO and IFCC Task Force. In addition, we underlined how the strategy adopted by a local company to risk assessment and health surveillance was appropriate for infection containment. This real-life scenario gave us the possibility to experience potential approaches aimed to preserve public health and work activities.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/virology , Nasopharynx/virology , Spike Glycoprotein, Coronavirus/genetics , Antigens, Viral/immunology , Communicable Disease Control/methods , False Negative Reactions , False Positive Reactions , Humans , RNA, Viral/genetics , Retrospective Studies , SARS-CoV-2/genetics , Sensitivity and Specificity , Specimen Handling
2.
Philos Trans A Math Phys Eng Sci ; 380(2214): 20210121, 2022 Jan 10.
Article in English | MEDLINE | ID: covidwho-1603979

ABSTRACT

We develop a statistical model for the testing of disease prevalence in a population. The model assumes a binary test result, positive or negative, but allows for biases in sample selection and both type I (false positive) and type II (false negative) testing errors. Our model also incorporates multiple test types and is able to distinguish between retesting and exclusion after testing. Our quantitative framework allows us to directly interpret testing results as a function of errors and biases. By applying our testing model to COVID-19 testing data and actual case data from specific jurisdictions, we are able to estimate and provide uncertainty quantification of indices that are crucial in a pandemic, such as disease prevalence and fatality ratios. This article is part of the theme issue 'Data science approach to infectious disease surveillance'.


Subject(s)
COVID-19 Testing , COVID-19 , Bias , False Positive Reactions , Humans , Models, Statistical , SARS-CoV-2 , Selection Bias , Sensitivity and Specificity
3.
AIDS Rev ; 23(3): 153-163, 2021 06 03.
Article in English | MEDLINE | ID: covidwho-1579385

ABSTRACT

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly infectious RNA coronavirus responsible for the pandemic of the coronavirus disease 2019 (COVID-19). Recent advances in virology, epidemiology, diagnosis, and clinical management of COVID-19 have contributed to the control and prevention of this disease, but re-positivity of SARS-CoV-2 in recovered COVID-19 patients has brought a new challenge for this worldwide anti-viral battle. Reverse transcription polymerase chain reaction (RT-PCR) tests of the SARS-CoV-2 pathogen is widely used in clinical diagnosis, but a positive RT-PCR result may be multifactorial, including false positive, SARS-CoV-2 RNA fragment shedding, reinfection of SARS-CoV-2, or re-activation of COVID-19. Re-infection of SARS-CoV-2 or re-activation of COVID-19 is an indicator of live viral carriers and isolation/treatment is needed, but SARS-CoV-2 RNA fragment shedding is not. SARS-CoV-2 RNA is recently reported to integrate into the host genome, but the far-reaching outcome is currently unclear. Therefore, it is critical for appropriate manipulation and prevention of COVID-19 to distinguish these causal factors of SARS-CoV-2 re-positivity. In this review article, we updated the current knowledge of SARS-CoV-2 re-positivity in discharged COVID-19 patients with a focus on re-infection and re-activation. We proposed a hypothetical flowchart for handling of the SARS-CoV-2 re-positive cases.


Subject(s)
COVID-19/pathology , RNA, Viral/analysis , Reinfection/virology , SARS-CoV-2/genetics , Virus Activation/genetics , Adaptive Immunity/immunology , Adolescent , Adult , Aged , Aged, 80 and over , Antibodies, Viral/blood , COVID-19/diagnosis , Child , Child, Preschool , False Positive Reactions , Female , Humans , Infant , Male , Middle Aged , Reverse Transcriptase Polymerase Chain Reaction , Young Adult
4.
PLoS One ; 16(12): e0260487, 2021.
Article in English | MEDLINE | ID: covidwho-1581781

ABSTRACT

At the start of the COVID-19 pandemic, the Centers for Disease Control and Prevention (CDC) designed, manufactured, and distributed the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel for SARS-CoV-2 detection. The diagnostic panel targeted three viral nucleocapsid gene loci (N1, N2, and N3 primers and probes) to maximize sensitivity and to provide redundancy for virus detection if mutations occurred. After the first distribution of the diagnostic panel, state public health laboratories reported fluorescent signal in the absence of viral template (false-positive reactivity) for the N3 component and to a lesser extent for N1. This report describes the findings of an internal investigation conducted by the CDC to identify the cause(s) of the N1 and N3 false-positive reactivity. For N1, results demonstrate that contamination with a synthetic template, that occurred while the "bulk" manufactured materials were located in a research lab for quality assessment, was the cause of false reactivity in the first lot. Base pairing between the 3' end of the N3 probe and the 3' end of the N3 reverse primer led to amplification of duplex and larger molecules resulting in false reactivity in the N3 assay component. We conclude that flaws in both assay design and handling of the "bulk" material, caused the problems with the first lot of the 2019-nCoV Real-Time RT-PCR Diagnostic Panel. In addition, within this study, we found that the age of the examined diagnostic panel reagents increases the frequency of false positive results for N3. We discuss these findings in the context of improvements to quality control, quality assurance, and assay validation practices that have since been improved at the CDC.


Subject(s)
COVID-19 , DNA Primers , False Positive Reactions , Humans , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2
5.
Br J Radiol ; 95(1129): 20210759, 2022 Jan 01.
Article in English | MEDLINE | ID: covidwho-1566545

ABSTRACT

OBJECTIVE: To determine the diagnostic accuracy of a deep-learning (DL)-based algorithm using chest computed tomography (CT) scans for the rapid diagnosis of coronavirus disease 2019 (COVID-19), as compared to the reference standard reverse-transcription polymerase chain reaction (RT-PCR) test. METHODS: In this retrospective analysis, data of COVID-19 suspected patients who underwent RT-PCR and chest CT examination for the diagnosis of COVID-19 were assessed. By quantifying the affected area of the lung parenchyma, severity score was evaluated for each lobe of the lung with the DL-based algorithm. The diagnosis was based on the total lung severity score ranging from 0 to 25. The data were randomly split into a 40% training set and a 60% test set. Optimal cut-off value was determined using Youden-index method on the training cohort. RESULTS: A total of 1259 patients were enrolled in this study. The prevalence of RT-PCR positivity in the overall investigated period was 51.5%. As compared to RT-PCR, sensitivity, specificity, positive predictive value, negative predictive value and accuracy on the test cohort were 39.0%, 80.2%, 68.0%, 55.0% and 58.9%, respectively. Regarding the whole data set, when adding those with positive RT-PCR test at any time during hospital stay or "COVID-19 without virus detection", as final diagnosis to the true positive cases, specificity increased from 80.3% to 88.1% and the positive predictive value increased from 68.4% to 81.7%. CONCLUSION: DL-based CT severity score was found to have a good specificity and positive predictive value, as compared to RT-PCR. This standardized scoring system can aid rapid diagnosis and clinical decision making. ADVANCES IN KNOWLEDGE: DL-based CT severity score can detect COVID-19-related lung alterations even at early stages, when RT-PCR is not yet positive.


Subject(s)
COVID-19/diagnostic imaging , Deep Learning , Adult , Aged , COVID-19/diagnosis , COVID-19/pathology , False Negative Reactions , False Positive Reactions , Female , Humans , Image Processing, Computer-Assisted , Male , Radiography, Thoracic , Reproducibility of Results , Retrospective Studies , Sensitivity and Specificity , Severity of Illness Index , Tomography, X-Ray Computed
6.
J Clin Pathol ; 74(12): 804-807, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1526517

ABSTRACT

AIMS: This short study was performed to better understand the time frame associated with changes in SARS-CoV-2 nucleic acid testing and provide recommendations for repeat testing. Recommendations are useful as little guidance is available for repeat testing in patients being followed expectantly for changes in disease. METHODS: A review of laboratory data of tests for SARS-CoV-2 nucleic acid was performed selecting patients who had changing results. Time between changes in test results was determined to provide guidance for repeat testing. RESULTS: The Interquartile Range (IQR) of data for patients who had a negative to positive change in laboratory testing (progression) was 6-16 days (median=9 days). The IQR of data for patients who had a positive to negative change in test results (remission) was 9-21 days (median=14 days). CONCLUSION: Because sampling of the nares or nasopharynx can be variable, repeat testing should be performed swiftly when symptomatic patients are negative. The data in this short study vary widely, so authors recommend repeat testing during a period of time associated with the IQR or median (see results above).


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , Nasopharynx/virology , SARS-CoV-2/genetics , COVID-19/therapy , COVID-19/virology , Disease Progression , False Negative Reactions , False Positive Reactions , Humans , Predictive Value of Tests , Remission Induction , Reproducibility of Results , SARS-CoV-2/isolation & purification , Time Factors , Treatment Outcome
7.
Comput Math Methods Med ; 2021: 9269173, 2021.
Article in English | MEDLINE | ID: covidwho-1511543

ABSTRACT

Early diagnosis of the harmful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), along with clinical expertise, allows governments to break the transition chain and flatten the epidemic curve. Although reverse transcription-polymerase chain reaction (RT-PCR) offers quick results, chest X-ray (CXR) imaging is a more reliable method for disease classification and assessment. The rapid spread of the coronavirus disease 2019 (COVID-19) has triggered extensive research towards developing a COVID-19 detection toolkit. Recent studies have confirmed that the deep learning-based approach, such as convolutional neural networks (CNNs), provides an optimized solution for COVID-19 classification; however, they require substantial training data for learning features. Gathering this training data in a short period has been challenging during the pandemic. Therefore, this study proposes a new model of CNN and deep convolutional generative adversarial networks (DCGANs) that classify CXR images into normal, pneumonia, and COVID-19. The proposed model contains eight convolutional layers, four max-pooling layers, and two fully connected layers, which provide better results than the existing pretrained methods (AlexNet and GoogLeNet). DCGAN performs two tasks: (1) generating synthetic/fake images to overcome the challenges of an imbalanced dataset and (2) extracting deep features of all images in the dataset. In addition, it enlarges the dataset and represents the characteristics of diversity to provide a good generalization effect. In the experimental analysis, we used four distinct publicly accessible datasets of chest X-ray images (COVID-19 X-ray, COVID Chest X-ray, COVID-19 Radiography, and CoronaHack-Chest X-Ray) to train and test the proposed CNN and the existing pretrained methods. Thereafter, the proposed CNN method was trained with the four datasets based on the DCGAN synthetic images, resulting in higher accuracy (94.8%, 96.6%, 98.5%, and 98.6%) than the existing pretrained models. The overall results suggest that the proposed DCGAN-CNN approach is a promising solution for efficient COVID-19 diagnosis.


Subject(s)
Algorithms , COVID-19 Testing/methods , COVID-19/classification , COVID-19/diagnostic imaging , Deep Learning , SARS-CoV-2 , COVID-19 Testing/statistics & numerical data , Databases, Factual , Early Diagnosis , False Positive Reactions , Humans , Neural Networks, Computer , Pandemics , ROC Curve , Radiography, Thoracic/statistics & numerical data , Software Design , Tomography, X-Ray Computed/statistics & numerical data
8.
Sci Rep ; 11(1): 21460, 2021 11 02.
Article in English | MEDLINE | ID: covidwho-1500518

ABSTRACT

Population screening played a substantial role in safely reopening the economy and avoiding new outbreaks of COVID-19. PCR-based pooled screening makes it possible to test the population with limited resources by pooling multiple individual samples. Our study compared different population-wide screening methods as transmission-mitigating interventions, including pooled PCR, individual PCR, and antigen screening. Incorporating testing-isolation process and individual-level viral load trajectories into an epidemic model, we further studied the impacts of testing-isolation on test sensitivities. Results show that the testing-isolation process could maintain a stable test sensitivity during the outbreak by removing most infected individuals, especially during the epidemic decline. Moreover, we compared the efficiency, accuracy, and cost of different screening methods during the pandemic. Our results show that PCR-based pooled screening is cost-effective in reversing the pandemic at low prevalence. When the prevalence is high, PCR-based pooled screening may not stop the outbreak. In contrast, antigen screening with sufficient frequency could reverse the epidemic, despite the high cost and the large numbers of false positives in the screening process.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/genetics , Antigens, Viral/genetics , Antigens, Viral/metabolism , COVID-19/epidemiology , COVID-19/virology , COVID-19 Nucleic Acid Testing/economics , False Negative Reactions , False Positive Reactions , Humans , Pandemics , Polymerase Chain Reaction/economics , Reproducibility of Results , SARS-CoV-2/isolation & purification , Viral Load
9.
Sci Rep ; 11(1): 21126, 2021 10 26.
Article in English | MEDLINE | ID: covidwho-1493210

ABSTRACT

Rapid identification of SARS-CoV-2-infected individuals is a cornerstone for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swabs. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. We conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV) designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR, to saliva RT-PCR and to nasopharyngeal antigen testing. Overall, 117 of the 1718 participants (7%) tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% and 97%, respectively. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p = 0.028). Considering six alternate criteria for reference tests, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%. The detection of SARS-CoV-2 in crude saliva samples with an RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing.Registration number: NCT04578509.


Subject(s)
Ambulatory Care/methods , COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , COVID-19/metabolism , SARS-CoV-2 , Saliva/metabolism , Adult , Diagnostic Tests, Routine , False Negative Reactions , False Positive Reactions , Female , Humans , Male , Middle Aged , Molecular Diagnostic Techniques , Molecular Medicine , Nasopharynx/virology , Nucleic Acid Amplification Techniques , Point-of-Care Systems , Point-of-Care Testing , Prospective Studies , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Reproducibility of Results , Sensitivity and Specificity
10.
Nature ; 599(7884): 191, 2021 11.
Article in English | MEDLINE | ID: covidwho-1493056
11.
Microbiol Spectr ; 9(2): e0068321, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1476397

ABSTRACT

Antigen-based rapid diagnostics tests (Ag-RDTs) are useful tools for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. However, misleading demonstrations of the Abbott Panbio coronavirus disease 2019 (COVID-19) Ag-RDT on social media claimed that SARS-CoV-2 antigen could be detected in municipal water and food products. To offer a scientific rebuttal to pandemic misinformation and disinformation, this study explored the impact of using the Panbio SARS-CoV-2 assay with conditions falling outside manufacturer recommendations. Using Panbio, various water and food products, laboratory buffers, and SARS-CoV-2-negative clinical specimens were tested with and without manufacturer buffer. Additional experiments were conducted to assess the role of each Panbio buffer component (tricine, NaCl, pH, and Tween 20) as well as the impact of temperature (4°C, 20°C, and 45°C) and humidity (90%) on assay performance. Direct sample testing (without the kit buffer) resulted in false-positive signals resembling those obtained with SARS-CoV-2 positive controls tested under proper conditions. The likely explanation of these artifacts is nonspecific interactions between the SARS-CoV-2-specific conjugated and capture antibodies, as proteinase K treatment abrogated this phenomenon, and thermal shift assays showed pH-induced conformational changes under conditions promoting artifact formation. Omitting, altering, and reverse engineering the kit buffer all supported the importance of maintaining buffering capacity, ionic strength, and pH for accurate kit function. Interestingly, the Panbio assay could tolerate some extremes of temperature and humidity outside manufacturer claims. Our data support strict adherence to manufacturer instructions to avoid false-positive SARS-CoV-2 Ag-RDT reactions, otherwise resulting in anxiety, overuse of public health resources, and dissemination of misinformation. IMPORTANCE With the Panbio severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen test being deployed in over 120 countries worldwide, understanding conditions required for its ideal performance is critical. Recently on social media, this kit was shown to generate false positives when manufacturer recommendations were not followed. While erroneous results from improper use of a test may not be surprising to some health care professionals, understanding why false positives occur can help reduce the propagation of misinformation and provide a scientific rebuttal for these aberrant findings. This study demonstrated that the kit buffer's pH, ionic strength, and buffering capacity were critical components to ensure proper kit function and avoid generation of false-positive results. Typically, false positives arise from cross-reacting or interfering substances; however, this study demonstrated a mechanism where false positives were generated under conditions favoring nonspecific interactions between the two antibodies designed for SARS-CoV-2 antigen detection. Following the manufacturer instructions is critical for accurate test results.


Subject(s)
Antigens, Viral/analysis , COVID-19 Serological Testing/methods , Drinking Water/virology , Food/virology , SARS-CoV-2/isolation & purification , Buffers , COVID-19/diagnosis , Communication , False Positive Reactions , Humans , SARS-CoV-2/immunology
12.
Comput Math Methods Med ; 2021: 2203636, 2021.
Article in English | MEDLINE | ID: covidwho-1443668

ABSTRACT

Coronavirus disease 2019 (COVID-19) arising from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a global pandemic since its first report in December 2019. So far, SARS-CoV-2 nucleic acid detection has been deemed as the golden standard of COVID-19 diagnosis. However, this detection method often leads to false negatives, thus triggering missed COVID-19 diagnosis. Therefore, it is urgent to find new biomarkers to increase the accuracy of COVID-19 diagnosis. To explore new biomarkers of COVID-19 in this study, expression profiles were firstly accessed from the GEO database. On this basis, 500 feature genes were screened by the minimum-redundancy maximum-relevancy (mRMR) feature selection method. Afterwards, the incremental feature selection (IFS) method was used to choose a classifier with the best performance from different feature gene-based support vector machine (SVM) classifiers. The corresponding 66 feature genes were set as the optimal feature genes. Lastly, the optimal feature genes were subjected to GO functional enrichment analysis, principal component analysis (PCA), and protein-protein interaction (PPI) network analysis. All in all, it was posited that the 66 feature genes could effectively classify positive and negative COVID-19 and work as new biomarkers of the disease.


Subject(s)
Biomarkers/metabolism , COVID-19/genetics , COVID-19/metabolism , Algorithms , COVID-19 Testing , Computational Biology , False Negative Reactions , False Positive Reactions , Gene Expression Profiling , Humans , Machine Learning , Models, Statistical , Principal Component Analysis , Protein Interaction Mapping , Research Design , Sensitivity and Specificity
13.
PLoS Med ; 18(9): e1003777, 2021 09.
Article in English | MEDLINE | ID: covidwho-1440982

ABSTRACT

BACKGROUND: Rapid detection, isolation, and contact tracing of community COVID-19 cases are essential measures to limit the community spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to identify a parsimonious set of symptoms that jointly predict COVID-19 and investigated whether predictive symptoms differ between the B.1.1.7 (Alpha) lineage (predominating as of April 2021 in the US, UK, and elsewhere) and wild type. METHODS AND FINDINGS: We obtained throat and nose swabs with valid SARS-CoV-2 PCR test results from 1,147,370 volunteers aged 5 years and above (6,450 positive cases) in the REal-time Assessment of Community Transmission-1 (REACT-1) study. This study involved repeated community-based random surveys of prevalence in England (study rounds 2 to 8, June 2020 to January 2021, response rates 22%-27%). Participants were asked about symptoms occurring in the week prior to testing. Viral genome sequencing was carried out for PCR-positive samples with N-gene cycle threshold value < 34 (N = 1,079) in round 8 (January 2021). In univariate analysis, all 26 surveyed symptoms were associated with PCR positivity compared with non-symptomatic people. Stability selection (1,000 penalized logistic regression models with 50% subsampling) among people reporting at least 1 symptom identified 7 symptoms as jointly and positively predictive of PCR positivity in rounds 2-7 (June to December 2020): loss or change of sense of smell, loss or change of sense of taste, fever, new persistent cough, chills, appetite loss, and muscle aches. The resulting model (rounds 2-7) predicted PCR positivity in round 8 with area under the curve (AUC) of 0.77. The same 7 symptoms were selected as jointly predictive of B.1.1.7 infection in round 8, although when comparing B.1.1.7 with wild type, new persistent cough and sore throat were more predictive of B.1.1.7 infection while loss or change of sense of smell was more predictive of the wild type. The main limitations of our study are (i) potential participation bias despite random sampling of named individuals from the National Health Service register and weighting designed to achieve a representative sample of the population of England and (ii) the necessary reliance on self-reported symptoms, which may be prone to recall bias and may therefore lead to biased estimates of symptom prevalence in England. CONCLUSIONS: Where testing capacity is limited, it is important to use tests in the most efficient way possible. We identified a set of 7 symptoms that, when considered together, maximize detection of COVID-19 in the community, including infection with the B.1.1.7 lineage.


Subject(s)
COVID-19/complications , COVID-19/diagnosis , Models, Biological , Ageusia/diagnosis , Ageusia/etiology , Ageusia/virology , Anosmia/diagnosis , Anosmia/etiology , Anosmia/virology , Appetite , Area Under Curve , COVID-19/virology , Chills/diagnosis , Chills/etiology , Chills/virology , Communicable Disease Control , Cough/diagnosis , Cough/etiology , Cough/virology , England , False Positive Reactions , Female , Fever/diagnosis , Fever/etiology , Fever/virology , Humans , Male , Mass Screening , Myalgia/diagnosis , Myalgia/etiology , Myalgia/virology , Pharyngitis/diagnosis , Pharyngitis/etiology , Pharyngitis/virology , Polymerase Chain Reaction , SARS-CoV-2/genetics , State Medicine
14.
Hum Cell ; 34(6): 1744-1754, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1437343

ABSTRACT

Positive retests of COVID-19 represent a public health concern because of the increased risk of transmission. This study explored whether factors other than the nucleic acid amplification test (NAAT) contribute to positive retest results. Patients with COVID-19 admitted to the Guanggu district of the Hubei Maternal and Child Health Hospital between February 17 and March 28, 2020, were retrospectively included. The patients were grouped into the negative (n = 133) and positive (n = 51) retest groups. The results showed that the proportion of patients presenting with cough was higher (P < 0.001) and the proportion of patients with dyspnea was lower (P = 0.018) in the positive than in the negative retest group. The positive retest group showed shorter durations between symptom onset and hospitalization (P < 0.001) and symptom onset and the first positive NAAT (P = 0.033). The positive retest group had higher basophil counts (P = 0.023) and direct bilirubin (P = 0.032) and chlorine concentrations (P = 0.023) but lower potassium concentrations (P = 0.001) than the negative retest group. Multivariable regression analysis showed that coughing (OR = 7.59, 95% CI 2.28-25.32, P = 0.001) and serum chloride concentrations (OR = 1.38, 95% CI 1.08-1.77, P = 0.010) were independently associated with a positive retest result. Coughing and serum chloride concentrations were independent risk factors for positive NAAT retest results. Patients with a hospital stay of < 2 weeks or a short incubation period should stay in isolation and be monitored to reduce transmission. These results could help identify patients who require closer surveillance.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Adult , Aged , COVID-19/prevention & control , Chlorides/blood , Cough , False Positive Reactions , Female , Humans , Male , Middle Aged , Risk Factors , Sensitivity and Specificity
15.
Rev Esp Quimioter ; 34(6): 618-622, 2021 Dec.
Article in Spanish | MEDLINE | ID: covidwho-1436597

ABSTRACT

OBJECTIVE: To assess the validity of SARS-CoV-2 Antigen (Ag) detection for the diagnosis of SARS-CoV-2 infection in mildly infected or asymptomatic patients. METHODS: Observational study to evaluate diagnostic tests. Non-hospitalized patients with indication for diagnostic testing for SARS-CoV-2 infection were included. The diagnostic test to be evaluated was the determination of Ag and as a reference standard to determine the presence of viral RNA the RT-PCR was used. RESULTS: A total of 494 patients were included. Of these 71.5% (353/494) had symptoms and 28.5% (141/494) were asymptomatic (presurgery screening (35/494) and confirmed case-contact (106/494). The overall sensitivity of the Ag test was 61.1% and the specificity was 99.7%. The sensitivity and specificity in the asymptomatic group were 40% and 100% respectively, and in the symptomatic group 63.5% and 99.6% respectively. In turn, the sensitivity and specificity in the group of symptomatic patients varied according to the time of symptom evolution: in patients with recent symptoms, they were 71.4% and 99.6% respectively, while in patients with symptoms of more than 5 days of evolution, they were 26.7% and 100% respectively. In all groups studied, the presence of antigen is associated with a high viral load (Ct<30 cycles). CONCLUSIONS: The use of Ag detection test is not indicated for the diagnosis of SARS-CoV-2 infection in asymptomatic patients or with symptoms of more than 5 days of evolution, but it could be useful in patients with symptoms of 1-5 days of evolution.


Subject(s)
COVID-19 , SARS-CoV-2 , False Positive Reactions , Humans , Reference Standards , Sensitivity and Specificity
16.
Microbiol Spectr ; 9(2): e0031321, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1410326

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic has brought about the unprecedented expansion of highly sensitive molecular diagnostics as a primary infection control strategy. At the same time, many laboratories have shifted focus to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) research and diagnostic development, leading to large-scale production of SARS-CoV-2 nucleic acids that can interfere with these tests. We have identified multiple instances, in independent laboratories, in which nucleic acids generated in research settings are suspected to have caused researchers to test positive for SARS-CoV-2 in surveillance testing. In some cases, the affected individuals did not work directly with these nucleic acids but were exposed via a contaminated surface or object. Though researchers have long been vigilant of DNA contaminants, the transfer of these contaminants to SARS-CoV-2 testing samples can result in anomalous test results. The impact of these incidents stretches into the public sphere, placing additional burdens on public health resources, placing affected researchers and their contacts in isolation and quarantine, removing them from the testing pool for 3 months, and carrying the potential to trigger shutdowns of classrooms and workplaces. We report our observations as a call for increased stewardship over nucleic acids with the potential to impact both the use and development of diagnostics. IMPORTANCE To meet the challenges imposed by the COVID-19 pandemic, research laboratories shifted their focus and clinical diagnostic laboratories developed and utilized new assays. Nucleic acid-based testing became widespread and, for the first time, was used as a prophylactic measure. We report 15 cases of researchers at two institutes testing positive for SARS-CoV-2 on routine surveillance tests, in the absence of any symptoms or transmission. These researchers were likely contaminated with nonhazardous nucleic acids generated in the laboratory in the course of developing new SARS-CoV-2 diagnostics. These contaminating nucleic acids were persistent and widespread throughout the laboratory. We report these findings as a cautionary tale to those working with nucleic acids used in diagnostic testing and as a call for careful stewardship of diagnostically relevant molecules. Our conclusions are especially relevant as at-home COVID-19 testing gains traction in the marketplace and these amplicons may impact on the general public.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , DNA Contamination , DNA, Viral/genetics , SARS-CoV-2/genetics , False Positive Reactions , Humans , Molecular Diagnostic Techniques , RNA, Viral/genetics , SARS-CoV-2/isolation & purification
17.
PLoS One ; 16(9): e0253407, 2021.
Article in English | MEDLINE | ID: covidwho-1398926

ABSTRACT

Surveillance testing for infectious disease is an important tool to combat disease transmission at the population level. During the SARS-CoV-2 pandemic, RT-PCR tests have been considered the gold standard due to their high sensitivity and specificity. However, RT-PCR tests for SARS-CoV-2 have been shown to return positive results when performed to individuals who are past the infectious stage of the disease. Meanwhile, antigen-based tests are often treated as a less accurate substitute for RT-PCR, however, new evidence suggests they may better reflect infectiousness. Consequently, the two test types may each be most optimally deployed in different settings. Here, we present an epidemiological model with surveillance testing and coordinated isolation in two congregate living settings (a nursing home and a university dormitory system) that considers test metrics with respect to viral culture, a proxy for infectiousness. Simulations show that antigen-based surveillance testing coupled with isolation greatly reduces disease burden and carries a lower economic cost than RT-PCR-based strategies. Antigen and RT-PCR tests perform different functions toward the goal of reducing infectious disease burden and should be used accordingly.


Subject(s)
Antigens, Viral/immunology , COVID-19 Serological Testing/methods , COVID-19/diagnosis , SARS-CoV-2/genetics , SARS-CoV-2/immunology , COVID-19/virology , False Negative Reactions , False Positive Reactions , Humans , Immunologic Surveillance/immunology , Nursing Homes , Pandemics/prevention & control , Reverse Transcriptase Polymerase Chain Reaction/methods , Sensitivity and Specificity , Universities
19.
J Infect ; 83(1): 119-145, 2021 07.
Article in English | MEDLINE | ID: covidwho-1386031

ABSTRACT

We performed a retrospective screening of 428 serum samples for anti-SARS-CoV-2  immunoglobulin during a period of low prevalence. Employing two different serological tests yielded discrepant results for 10 samples; highlighting an increased risk of potential  false positive results and the need for further confirmatory testing before publication of data.


Subject(s)
COVID-19 , SARS-CoV-2 , Brazil , False Positive Reactions , Humans , Immunoglobulins , Prevalence , Retrospective Studies , Sensitivity and Specificity
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