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2.
BMJ ; 376: e066871, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1707375

ABSTRACT

OBJECTIVES: To investigate the proportion of lateral flow tests (LFTs) that produce negative results in those with a high risk of infectiousness from SARS-CoV-2, to investigate the impact of the stage and severity of disease, and to compare predictions made by influential mathematical models with findings of empirical studies. DESIGN: Linked data analysis combining empirical evidence of the accuracy of the Innova LFT, the probability of positive viral culture or transmission to secondary cases, and the distribution of viral loads of SARS-CoV-2 in individuals in different settings. SETTING: Testing of individuals with symptoms attending NHS Test-and-Trace centres across the UK, residents without symptoms attending municipal mass testing centres in Liverpool, and students without symptoms screened at the University of Birmingham. PARTICIPANTS: Evidence for the sensitivity of the Innova LFT, based on 70 individuals with SARS-CoV-2 and LFT results. Infectiousness was based on viral culture rates on 246 samples (176 people with SARS-CoV-2) and secondary cases among 2 474 066 contacts; distributions of cycle threshold (Ct) values from 231 497 index individuals attending NHS Test-and-Trace centres; 70 people with SARS-CoV-2 detected in Liverpool and 62 people with SARS-CoV-2 in Birmingham (54 imputed). MAIN OUTCOME MEASURES: The predicted proportions who were missed by LFT and viral culture positive and missed by LFT and sources of secondary cases, in each of the three settings. Predictions were compared with those made by mathematical models. RESULTS: The analysis predicted that of those with a viral culture positive result, Innova would miss 20% attending an NHS Test-and-Trace centre, 29% without symptoms attending municipal mass testing, and 81% attending university screen testing without symptoms, along with 38%, 47%, and 90% of sources of secondary cases. In comparison, two mathematical models underestimated the numbers of missed infectious individuals (8%, 10%, and 32% in the three settings for one model, whereas the assumptions from the second model made it impossible to miss an infectious individual). Owing to the paucity of usable data, the inputs to the analyses are from limited sources. CONCLUSIONS: The proportion of infectious people with SARS-CoV-2 missed by LFTs is substantial enough to be of clinical importance. The proportion missed varied between settings because of different viral load distributions and is likely to be highest in those without symptoms. Key models have substantially overestimated the sensitivity of LFTs compared with empirical data. An urgent need exists for additional robust well designed and reported empirical studies from intended use settings to inform evidence based policy.


Subject(s)
COVID-19 Serological Testing/standards , COVID-19/epidemiology , Antibodies, Viral/blood , COVID-19/diagnosis , False Negative Reactions , False Positive Reactions , Humans , Pandemics , Reverse Transcriptase Polymerase Chain Reaction/standards , SARS-CoV-2 , Sensitivity and Specificity , Viral Load
3.
Sci Rep ; 12(1): 2806, 2022 02 18.
Article in English | MEDLINE | ID: covidwho-1699734

ABSTRACT

Saliva is an attractive sample for coronavirus disease 2019 testing due its ease of collection and amenability to detect viral RNA with minimal processing. Using a direct-to-RT-PCR method with saliva self-collected from confirmed COVID-19 positive volunteers, we observed 32% false negative results. Confirmed negative and healthy volunteer samples spiked with 106 genome copies/mL of heat-inactivated severe acute respiratory syndrome coronavirus 2 showed false negative results of 10% and 13%, respectively. Additional sample heating or dilution of the false negative samples conferred only modest improvements. These results highlight the potential to significantly underdiagnose COVID-19 infections when testing directly from minimally processed heterogeneous saliva samples.


Subject(s)
COVID-19 Nucleic Acid Testing , SARS-CoV-2/isolation & purification , Saliva/virology , False Negative Reactions , Healthy Volunteers , Humans , Point-of-Care Testing
4.
Sci Rep ; 12(1): 1614, 2022 01 31.
Article in English | MEDLINE | ID: covidwho-1661979

ABSTRACT

As the SARS-CoV-2 pandemic persists, methods that can quickly and reliably confirm infection and immune status is extremely urgently and critically needed. In this contribution we show that combining laser induced breakdown spectroscopy (LIBS) with machine learning can distinguish plasma of donors who previously tested positive for SARS-CoV-2 by RT-PCR from those who did not, with up to 95% accuracy. The samples were also analyzed by LIBS-ICP-MS in tandem mode, implicating a depletion of Zn and Ba in samples of SARS-CoV-2 positive subjects that inversely correlate with CN lines in the LIBS spectra.


Subject(s)
COVID-19/blood , COVID-19/diagnosis , Immunity , Lasers , Pandemics , SARS-CoV-2/immunology , Spectrophotometry, Atomic/methods , Barium/analysis , COVID-19/epidemiology , COVID-19/virology , Data Accuracy , Discriminant Analysis , False Negative Reactions , False Positive Reactions , Humans , Machine Learning , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Sensitivity and Specificity , Zinc/analysis
5.
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
6.
J Clin Lab Anal ; 36(2): e24226, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1611241

ABSTRACT

INTRODUCTION: RT-PCR is widely used as a diagnostic test for the detection of SARS-CoV-2. In this study, we aim to describe the clinical utility of serial PCR testing in the final detection of COVID-19. METHOD: We collected multiple nasopharyngeal swab samples from patients who had negative RT-PCR test on the first day after hospitalization. RT-PCR tests were performed on the second day for all patients with initial negative result. For the patients with secondary negative results on day 2, tertiary RT-PCR tests were performed on day 3 after hospitalization. RESULT: Among 68 patients with initial negative test results, at the end of follow-up, the mortality number was 20 (29.4%). About 33.8% of patients had subsequent positive PCR test results for the second time and 17.4% of the patients who performed third PCR test had positive result. CONCLUSION: Based on this study, serial RT-PCR testing is unlikely to yield additional information.


Subject(s)
COVID-19/diagnosis , Molecular Diagnostic Techniques , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , Aged , Aged, 80 and over , False Negative Reactions , Female , Humans , Male , Middle Aged , Molecular Diagnostic Techniques/methods , Molecular Diagnostic Techniques/standards , Molecular Diagnostic Techniques/statistics & numerical data , Real-Time Polymerase Chain Reaction/methods , Real-Time Polymerase Chain Reaction/standards , Real-Time Polymerase Chain Reaction/statistics & numerical data , SARS-CoV-2/isolation & purification
7.
Viruses ; 13(12)2021 12 10.
Article in English | MEDLINE | ID: covidwho-1572657

ABSTRACT

The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , Coronavirus Nucleocapsid Proteins/genetics , SARS-CoV-2/isolation & purification , Brazil/epidemiology , COVID-19/epidemiology , Coronavirus RNA-Dependent RNA Polymerase/genetics , DNA Primers , False Negative Reactions , Genome, Viral/genetics , Humans , Mutation , Phosphoproteins/genetics , RNA, Viral/genetics , SARS-CoV-2/genetics
8.
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
9.
J Med Virol ; 93(12): 6512-6518, 2021 12.
Article in English | MEDLINE | ID: covidwho-1544296

ABSTRACT

There is a great demand for more rapid tests for SARS-CoV-2 detection to reduce waiting time, boost public health strategies for combating disease, decrease costs, and prevent overwhelming laboratory capacities. This study was conducted to assess the performance of 10 lateral flow device viral antigen immunoassays for the detection of SARS-CoV-2 in nasopharyngeal swab specimens. We analyzed 231 nasopharyngeal samples collected from October 2020 to December 2020, from suspected COVID-19 cases and contacts of positive cases at Biotechnology Research Center laboratories, Tripoli, Libya. The performance of 10 COVID-19 Antigen (Ag) rapid test devices for the detection of SARS-CoV-2 antigen was compared to a quantitative reverse transcription-polymerase chain reaction (RT-qPCR). In this study, 161 cases had symptoms consistent with COVID-19. The mean duration from symptom onset was 6.6 ± 4.3 days. The median cycle threshold (Ct ) of positive samples was 25. Among the 108 positive samples detected by RT-qPCR, the COVID-19 antigen (Ag) tests detected 83 cases correctly. All rapid Ag test devices used in this study showed 100% specificity. While tests from six manufacturers had an overall sensitivity range from 75% to 100%, the remaining four tests had a sensitivity of 50%-71.43%. Sensitivity during the first 6 days of symptoms and in samples with high viral loads (Ct < 25), was 100% in all but two of the test platforms. False-negative samples had a median Ct of 34 and an average duration of onset of symptoms of 11.3 days (range = 5-20 days). Antigen test diagnosis has high sensitivity and specificity in early disease when patients present less than 7 days of symptom onset. Patients are encouraged to test as soon as they get COVID-19-related symptoms within 1 week and to seek medical advice within 24 h if they develop disturbed smell/taste. The use of rapid antigen tests is important for controlling the COVID-19 pandemic and reducing the burden on molecular diagnostic laboratories.


Subject(s)
Antigens, Viral/analysis , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Immunoassay/methods , Adult , COVID-19 Serological Testing/economics , False Negative Reactions , Female , Humans , Immunoassay/economics , Male , Nasopharynx/virology , Prospective Studies , SARS-CoV-2/immunology , Sensitivity and Specificity , Time Factors , Viral Load
10.
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
11.
Eur J Clin Invest ; 52(2): e13706, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1501402

ABSTRACT

BACKGROUND: Molecular-based tests used to identify symptomatic or asymptomatic patients infected by SARS-CoV-2 are characterized by high specificity but scarce sensitivity, generating false-negative results. We aimed to estimate, through a systematic review of the literature, the rate of RT-PCR false negatives at initial testing for COVID-19. METHODS: We systematically searched Pubmed, Embase and CENTRAL as well as a list of reference literature. We included observational studies that collected samples from respiratory tract to detect SARS-CoV-2 RNA using RT-PCR, reporting the number of false-negative subjects and the number of final patients with a COVID-19 diagnosis. Reported rates of false negatives were pooled in a meta-analysis as appropriate. We assessed the risk of bias of included studies and graded the quality of evidence according to the GRADE method. All information in this article is current up to February 2021. RESULTS: We included 32 studies, enrolling more than 18,000 patients infected by SARS-CoV-2. The overall false-negative rate was 0.12 (95%CI from 0.10 to 0.14) with very low certainty of evidence. The impact of misdiagnoses was estimated according to disease prevalence; a range between 2 and 58/1,000 subjects could be misdiagnosed with a disease prevalence of 10%, increasing to 290/1,000 misdiagnosed subjects with a disease prevalence of 50%. CONCLUSIONS: This systematic review showed that up to 58% of COVID-19 patients may have initial false-negative RT-PCR results, suggesting the need to implement a correct diagnostic strategy to correctly identify suspected cases, thereby reducing false-negative results and decreasing the disease burden among the population.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , SARS-CoV-2/genetics , Diagnostic Errors , False Negative Reactions , Humans , RNA, Viral
12.
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
13.
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
14.
Emerg Microbes Infect ; 10(1): 2090-2097, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1479918

ABSTRACT

Since December 2019, coronavirus disease 2019 (COVID-19) caused by SARS coronavirus 2 (SARS-CoV-2) has spread and threatens public health worldwide. The recurrence of SARS-CoV-2 RNA detection in patients after discharge from hospital signals a risk of transmission from such patients to the community and challenges the current discharge criteria of COVID-19 patients. A wide range of clinical specimens has been used to detect SARS-CoV-2. However, to date, a consensus has not been reached regarding the most appropriate specimens to use for viral RNA detection in assessing COVID-19 patients for discharge. An anal swab sample was proposed as the standard because of prolonged viral detection. In this retrospective longitudinal study of viral RNA detection in 60 confirmed COVID-19 patients, we used saliva, oropharyngeal/nasopharyngeal swab (O/N swab) and anal swab procedures from admission to discharge. The conversion times of saliva and anal swab were longer than that of O/N swab. The conversion time of hyper sensitive-CRP was the shortest and correlated with that of CT scanning and viral detection. Some patients were found to be RNA-positive in saliva while RNA-negative in anal swab while the reverse was true in some other patients, which indicated that false negatives were inevitable if only the anal swab is used for evaluating suitability for discharge. These results indicated that double-checking for viral RNA using multiple and diverse specimens was essential, and saliva could be a candidate to supplement anal swabs to reduce false-negative results and facilitate pandemic control.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/isolation & purification , Saliva/virology , Adult , Anal Canal/virology , False Negative Reactions , Female , Humans , Male , Middle Aged , Nasopharynx/virology , Oropharynx/virology , Patient Discharge , RNA, Viral/analysis , Retrospective Studies , Young Adult
15.
Comput Math Methods Med ; 2021: 6636396, 2021.
Article in English | MEDLINE | ID: covidwho-1476878

ABSTRACT

Group testing (or pool testing), for example, Dorfman's method or grid method, has been validated for COVID-19 RT-PCR tests and implemented widely by most laboratories in many countries. These methods take advantages since they reduce resources, time, and overall costs required for a large number of samples. However, these methods could have more false negative cases and lower sensitivity. In order to maintain both accuracy and efficiency for different prevalence, we provide a novel pooling strategy based on the grid method with an extra pool set and an optimized rule inspired by the idea of error-correcting codes. The mathematical analysis shows that (i) the proposed method has the best sensitivity among all the methods we compared, if the false negative rate (FNR) of an individual test is in the range [1%, 20%] and the FNR of a pool test is closed to that of an individual test, and (ii) the proposed method is efficient when the prevalence is below 10%. Numerical simulations are also performed to confirm the theoretical derivations. In summary, the proposed method is shown to be felicitous under the above conditions in the epidemic.


Subject(s)
COVID-19 Testing/methods , COVID-19 Testing/standards , COVID-19/diagnosis , Algorithms , Computer Simulation , False Negative Reactions , Humans , Laboratories/standards , Models, Theoretical , Prevalence , Probability , Reproducibility of Results
16.
Pan Afr Med J ; 39: 244, 2021.
Article in English | MEDLINE | ID: covidwho-1468747

ABSTRACT

Numerous genetic tests for the detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, including those based on the ever-popular real-time polymerase chain reaction (RT-qPCR) technique, have been reported. These diagnostic tests give false negatives particularly during the early and late stages of COVID-19 clearly indicating inadequate test sensitivity. The entire COVID-19 diagnostic workflow is often overlooked and given very little attention. Herein, we propose that volumetric modifications to COVID-19 workflows would significantly improve detection limits. We would therefore encourage researchers to adopt a holistic approach, in which all the steps of a COVID-19 diagnostic workflow, are carefully scrutinised, particularly those upstream factors at the viral sampling and pre-analytical stages.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Real-Time Polymerase Chain Reaction/methods , COVID-19 Testing/standards , False Negative Reactions , Humans , Limit of Detection , Real-Time Polymerase Chain Reaction/standards , Sensitivity and Specificity , Specimen Handling
17.
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
19.
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
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