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1.
Nat Commun ; 12(1): 1152, 2021 02 19.
Article in English | MEDLINE | ID: covidwho-1091492

ABSTRACT

The humoral immune response to SARS-CoV-2 is a benchmark for immunity and detailed analysis is required to understand the manifestation and progression of COVID-19, monitor seroconversion within the general population, and support vaccine development. The majority of currently available commercial serological assays only quantify the SARS-CoV-2 antibody response against individual antigens, limiting our understanding of the immune response. To overcome this, we have developed a multiplex immunoassay (MultiCoV-Ab) including spike and nucleocapsid proteins of SARS-CoV-2 and the endemic human coronaviruses. Compared to three broadly used commercial in vitro diagnostic tests, our MultiCoV-Ab achieves a higher sensitivity and specificity when analyzing a well-characterized sample set of SARS-CoV-2 infected and uninfected individuals. We find a high response against endemic coronaviruses in our sample set, but no consistent cross-reactive IgG response patterns against SARS-CoV-2. Here we show a robust, high-content-enabled, antigen-saving multiplex assay suited to both monitoring vaccination studies and facilitating epidemiologic screenings for humoral immunity towards pandemic and endemic coronaviruses.


Subject(s)
Antibodies, Viral/immunology , /immunology , Cross Reactions , Immunity, Humoral , /diagnosis , Humans , Immunoassay , Immunoglobulin G/immunology , Phosphoproteins/immunology , Sensitivity and Specificity , Spike Glycoprotein, Coronavirus/immunology
2.
BMC Infect Dis ; 21(1): 187, 2021 Feb 18.
Article in English | MEDLINE | ID: covidwho-1090687

ABSTRACT

BACKGROUND: Thresholds for SARS-CoV-2 antibody assays have typically been determined using samples from symptomatic, often hospitalised, patients. In this setting the sensitivity and specificity of the best performing assays can both exceed 98%. However, antibody assay performance following mild infection is less clear. METHODS: We assessed quantitative IgG responses in a cohort of healthcare workers in Oxford, UK, with a high pre-test probability of Covid-19, in particular the 991/11,475(8.6%) who reported loss of smell/taste. We use anosmia/ageusia and other risk factors as probes for Covid-19 infection potentially undiagnosed by immunoassays by investigating their relationship with antibody readings either side of assay thresholds. RESULTS: The proportion of healthcare workers reporting anosmia/ageusia increased at antibody readings below diagnostic thresholds using an in-house ELISA (n = 9324) and the Abbott Architect chemiluminescent microparticle immunoassay (CMIA; n = 11,324): 426/906 (47%) reported anosmia/ageusia with a positive ELISA, 59/449 (13.1%) with high-negative and 326/7969 (4.1%) with low-negative readings. Similarly, by CMIA, 518/1093 (47.4%) with a positive result reported anosmia/ageusia, 106/686 (15.5%) with a high-negative and 358/9563 (3.7%) with a low-negative result. Adjusting for the proportion of staff reporting anosmia/ageusia suggests the sensitivity of both assays in mild infection is lower than previously reported: Oxford ELISA 89.8% (95%CI 86.6-92.8%) and Abbott CMIA 79.3% (75.9-82.7%). CONCLUSION: Following mild SARS-CoV-2 infection 10-30% of individuals may have negative immunoassay results. While lowered diagnostic thresholds may result in unacceptable specificity, our findings have implications for epidemiological analyses and result interpretation in individuals with a high pre-test probability. Samples from mild PCR-confirmed infections should be included in SARS-CoV-2 immunoassay evaluations.


Subject(s)
Antibodies, Viral/analysis , /diagnosis , Immunoglobulin G/analysis , Adult , Ageusia/virology , Asymptomatic Infections , Enzyme-Linked Immunosorbent Assay/standards , Female , Health Personnel , Humans , Immunoassay/standards , Male , Middle Aged , Sensitivity and Specificity , Undiagnosed Diseases , United Kingdom
3.
Biochem Med (Zagreb) ; 31(1): 010708, 2021 Feb 15.
Article in English | MEDLINE | ID: covidwho-1084994

ABSTRACT

Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological tests have been suggested as an additional diagnostic tool in highly suspected cases with a negative molecular test and determination of seroprevalence in population. We compared the diagnostic performance of eight commercial serological assays for IgA, IgM, and IgG antibodies to the SARS-CoV-2 virus. Materials and methods: The comparison study was performed on a total of 76 serum samples: 30 SARS-CoV-2 polymerase chain reaction (PCR)-negative and 46 SARS-CoV-2 PCR-positive patients with asymptomatic to severe disease and symptoms duration from 3-30 days. The study included: three rapid lateral flow immunochromatographic assays (LFIC), two enzyme-linked immunosorbent assays (ELISA), and three chemiluminescence immunoassays (CLIA). Results: Agreement between IgM assays were minimal to moderate (kappa 0.26 to 0.63) and for IgG moderate to excellent (kappa 0.72 to 0.92). Sensitivities improved with > 10 days of symptoms and were: 30% to 89% for IgM; 89% to 100% for IgG; 96% for IgA; 100% for IgA/IgM combination; 96% for total antibodies. Overall specificities were: 90% to 100% for IgM; 85% to 100% for IgG; 90% for IgA; 70% for IgA/IgM combination; 100% for total antibodies. Diagnostic accuracy for IgG ELISA and CIA assays were excellent (AUC ≥ 0.90), without significant difference. IgA showed significantly better diagnostic accuracy than IgM (P < 0.001). Conclusion: There is high variability between IgM assays independently of the assay format, while IgG assays showed moderate to perfect agreement. The appropriate time for testing is crucial for the proper immunity investigation.


Subject(s)
/methods , /diagnosis , /virology , Humans , Sensitivity and Specificity , Serologic Tests/methods
4.
Ann Med ; 53(1): 337-344, 2021 12.
Article in English | MEDLINE | ID: covidwho-1084096

ABSTRACT

BACKGROUND: To minimise the risk of COVID-19 transmission, an ambulant screening protocol for COVID-19 in patients before admission to the hospital was implemented, combining the SARS CoV-2 reverse-transcriptase polymerase chain reaction (RT-PCR) on a nasopharyngeal swab, a chest computed tomography (CT) and assessment of clinical symptoms. The aim of this study was to evaluatethe diagnostic yield and the proportionality of this pre-procedural screeningprotocol. METHODS: In this mono-centre, prospective, cross-sectional study, all patients admitted to the hospital between 22nd April 2020 until 14th May 2020 for semi-urgent surgery, haematological or oncological treatment, or electrophysiological investigationunderwent a COVID-19 screening 2 days before their procedure. At a 2-week follow-up, the presence of clinical symptoms was evaluated by telephone as a post-hoc evaluation of the screening approach.Combined positive RT-PCR assay and/or positive chest CT was used as gold standard. Post-procedural outcomes of all patients diagnosed positive for COVID-19 were assessed. RESULTS: In total,528 patients were included of which 20 (3.8%) were diagnosed as COVID-19 positive and 508 (96.2%) as COVID-19 negative. 11 (55.0%) of COVID-19 positive patients had only a positive RT-PCR assay, 3 (15.0%) had only a positive chest CT and 6 (30%) had both a positive RT-PCR assay and chest CT. 10 out of 20 (50.0%) COVID-19 positive patients reported no single clinical symptom at the screening. At 2 week follow-up, 50% of these patients were still asymptomatic. 37.5% of all COVID-19 negative patients were symptomatic at screening. In the COVID-19 negative group without symptoms at screening, 78 (29.3%) patients developed clinical symptoms at a 2-week follow-up. CONCLUSION: This study suggests that routine chest CT and assessment of self-reported symptoms have limited value in the preprocedural COVID-19 screening due to low sensitivity and/or specificity.


Subject(s)
/methods , Mass Screening/methods , Patient Admission , Adult , Aged , Cross-Sectional Studies , Female , Follow-Up Studies , Humans , Male , Middle Aged , Prospective Studies , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Tomography, X-Ray Computed
5.
PLoS One ; 16(2): e0246864, 2021.
Article in English | MEDLINE | ID: covidwho-1083475

ABSTRACT

BACKGROUND: The presence of neutralizing antibodies (NAbs) is an indicator of protective immunity for most viral infections. A newly developed surrogate viral neutralization assay (sVNT) offers the ability to detect total receptor binding domain-targeting NAbs in an isotype-independent manner, increasing the test sensitivity. Thus, specimens with low IgM/ IgG antibody levels showed strong neutralization activity in sVNT. METHODS: This study aimed to measure the %inhibition of NAbs measured by sVNT in PCR-confirmed COVID-19 patients. The sensitivity of sVNT for the diagnosis of SARS-CoV-2 infection and its kinetics were determined. RESULTS: Ninety-seven patients with PCR-confirmed SARS-CoV-2 infection were included in this study. Majority of the patients were 21-40 years old (67%) and 63% had mild symptoms. The sensitivity of sVNT for the diagnosis of SARS-CoV-2 infection was 99% (95% confidence interval (CI) 94.4-100%) and the specificity was 100% (95% CI 98.3-100%). The negative predictive value of sVNT from the samples collected before and after 7 days of symptom onset was 99.5% (95% CI 97.4-100%) and 100% (95% CI 93.8-100%), respectively. The level of inhibition at days 8-14 were significantly higher than days 0-7 (p<0.001). The median %inhibition values by severity of COVID-19 symptoms were 79.9% (interquartile range (IQR) 49.7-91.8%); 89.0% (IQR 71.2-92.4%); and 86.6% (IQR 69.5-92.8%), for mild, moderate and severe/critical symptoms respectively. The median level of sVNT %inhibition of severe was significantly higher than the mild group (p = 0.05). CONCLUSION: The sVNT is a practical and robust serological test for SARS-CoV-2 infection and does not require specialized biosafety containment. It can be used clinically to aid diagnosis in both early and late infection especially in cases when the real-time RT-PCR results in weakly negative or weakly positive, and to determine the protective immune response from SARS-CoV-2 infection in patients.


Subject(s)
Antibodies, Neutralizing/isolation & purification , /diagnosis , Neutralization Tests/methods , /physiology , Adult , Antibodies, Neutralizing/analysis , Antibodies, Viral/isolation & purification , Female , Humans , Male , Middle Aged , Sensitivity and Specificity , Serologic Tests , Spike Glycoprotein, Coronavirus/chemistry , Thailand , Young Adult
6.
Swiss Med Wkly ; 151: w20471, 2021 02 01.
Article in English | MEDLINE | ID: covidwho-1081785

ABSTRACT

OBJECTIVES: To develop and validate a screening tool designed to identify detained people at increased risk for COVID-19 mortality, the COVID-19 Inmate Risk Appraisal (CIRA). DESIGN: Cross-sectional study with a representative sample (development) and a case-control sample (validation). SETTING: The two largest Swiss prisons. PARTICIPANTS: (1) Development sample: all male persons detained in Pöschwies, Zurich (n = 365); (2) Validation sample: case-control sample of male persons detained in Champ-Dollon, Geneva (n = 192, matching 1:3 for participants at risk for severe course of COVID-19 and participants without risk factors). MAIN OUTCOME MEASURES: The CIRA combined seven risk factors identified by the World Health Organization and the Swiss Federal Office of Public Health as predictive of severe COVID-19 to derive an absolute risk increase in mortality rate: Age ≥60 years, cardiovascular disease, diabetes, hypertension, chronic respiratory disease, immunodeficiency and cancer. RESULTS: Based on the development sample, we proposed a three-level classification: average (<3.7), elevated (3.7-5.7) and high (>5.7) risk. In the validation sample, the CIRA identified all individuals identified as vulnerable by national recommendations (having at least one risk factor). The category “elevated risk” maximised sensitivity (1) and specificity (0.97). The CIRA had even higher capacity in discriminating individuals vulnerable according to clinical evaluation (a four-level risk categorisation based on a consensus of medical staff). The category “elevated risk” maximised sensitivity and specificity (both 1). When considering the individuals classified as extremely high risk by medical staff, the category “high risk” had a high discriminatory capacity (sensitivity =0.89, specificity =0.97). CONCLUSIONS: The CIRA scores have a high discriminative ability and will be important in custodial settings to support decisions and prioritise actions using a standardised valid assessment method. However, as knowledge on risk factors for COVID-19 mortality is still limited, the CIRA may be considered preliminary. Underlying data will be updated regularly on the website (http://www.prison-research.com), where the CIRA algorithm is freely available.


Subject(s)
/etiology , Decision Support Techniques , Mass Screening/standards , Prisoners/statistics & numerical data , Risk Assessment/standards , Adult , Aged , Case-Control Studies , Cross-Sectional Studies , Female , Humans , Male , Mass Screening/methods , Middle Aged , Prisons , Reproducibility of Results , Risk Assessment/methods , Risk Factors , Sensitivity and Specificity , Switzerland
7.
Front Public Health ; 8: 593491, 2020.
Article in English | MEDLINE | ID: covidwho-1081109

ABSTRACT

Background: SARS-CoV-2-infected subjects have been proven contagious in the symptomatic, pre-symptomatic and asymptomatic phase. The identification of these patients is crucial in order to prevent virus circulation. No reliable data on the sensitivity of nasopharyngeal swabs (NPS) are available because of the lack of a shared reference standard to identify SARS-CoV-2 infected patients. The aim of our study was to collect data on patients with a known diagnosis of COVID-19 who underwent serial testing to assess NPS sensitivity. Methods: The study was a multi-center, observational, retrospective clinical study with consecutive enrollment. We enrolled patients who met all of the following inclusion criteria: clinical recovery, documented SARS-CoV-2 infection (≥1 positive rRT-PCR result) and ≥1 positive NPS among the first two follow-up swabs. A positive NPS not preceded by a negative nasopharyngeal swab collected 24-48 h earlier was considered a true positive. A negative NPS followed by a positive NPS collected 24-48 h later was regarded as a false negative. The primary outcome was to define sensitivity of SARS-CoV-2 detection with NPS. Results: Three hundred and ninety three NPS were evaluated in 233 patients; the sensitivity was 77% (95% CI, 73 to 81%). Sensitivity of the first follow-up NPS (n = 233) was 79% (95% CI, 73 to 84%) with no significant variations over time. We found no statistically significant differences in the sensitivity of the first follow-up NPS according to time since symptom onset, age, sex, number of comorbidities, and onset symptoms. Conclusions: NPS utility in the diagnostic algorithm of COVID-19 should be reconsidered.


Subject(s)
/methods , Nasopharynx/virology , /isolation & purification , Adult , Aged , /instrumentation , Chi-Square Distribution , Female , Humans , Male , Middle Aged , RNA, Viral/analysis , Retrospective Studies , Sensitivity and Specificity , Viral Load
8.
J Am Osteopath Assoc ; 121(2): 141-148, 2021 02 01.
Article in English | MEDLINE | ID: covidwho-1076286

ABSTRACT

Current testing for the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 virus), which causes the novel coronavirus 2019 (COVID-19) infection, is typically reliant upon collection of nasal swab samples from subjects. These tests (reverse transcription polymerase chain reaction [RT-PCR] and antigen) are intrusive, can take significant time to process, and can give deleterious false negative and false positive results. Alternative methods for COVID-19 testing and screening are being studied, including the use of trained scent detection dogs to detect volatile organic compounds (VOCs) associated with the COVID virus. In August 2020 and October 2020, the first author (T.D.) searched MEDLINE/PubMed, Cochrane Library, Google Scholar, and additional news articles using keyword phrases including "COVID scent dogs," "COVID sniffer dogs," and "COVID detection dog," returning a total of 13 articles, nine of which were duplicates. Four remaining peer-reviewed studies dedicated to determining the feasibility and efficacy of detecting and screening individuals who may be infected by the COVID-19 virus with scent detection dogs were then examined. In this narrative review, the authors describe the methodologies and results of the remaining four studies, which demonstrated that the sensitivity, specificity, and overall success rates reported by the summarized scent detection studies are comparable to or better than the standard RT-PCR and antigen testing procedures, meaning that scent detection dogs can likely be effectively employed to nonintrusively screen and identify individuals infected with the COVID-19 virus in hospitals, senior care facilities, schools, universities, airports, and even large public gatherings for sporting events and concerts.


Subject(s)
/methods , /diagnosis , Animals , Dogs , Humans , Sensitivity and Specificity , Volatile Organic Compounds
11.
Medicina (Kaunas) ; 57(2)2021 Feb 06.
Article in English | MEDLINE | ID: covidwho-1069846

ABSTRACT

Background and objective: Serologic testing is a useful additional method for the diagnosis of COVID-19. It is also used for population-based seroepidemiological studies. The objective of the study was to determine SARS-CoV-2 seroprevalence in healthcare workers of Kaunas hospitals and to compare two methods for specific SARS-CoV-2 antibody testing. Materials and Methods: A total of 432 healthcare workers in Kaunas hospitals were enrolled in this study. Each participant filled a questionnaire including questions about their demographics, contact with suspected or confirmed COVID-19, acute respiratory symptoms, and whether they contacted their general practitioner, could not come to work, or had to be hospitalized. Capillary blood was used to test for SARS-CoV-2 specific immunoglobulin G (IgG) and immunoglobulin M (IgM) a lateral flow immunoassay. Serum samples were used to test for specific IgG and IgA class immunoglobulins using semiquantitative enzyme-linked immunosorbent assay (ELISA) method. Results: 24.77% of study participants had direct contact with a suspected or confirmed case of COVID-19. A total of 64.81% of studied individuals had at least one symptom representing acute respiratory infection, compatible with COVID-19. Lateral flow immunoassay detected SARS-CoV-2 specific IgG class immunoglobulins in 1.16% of the tested group. Fever, cough, dyspnea, nausea, diarrhea, headache, conjunctivitis, muscle pain, and loss of smell and taste predominated in the anti-SARS-CoV-2 IgG-positive group. Using ELISA, specific IgG were detected in 1.32% of the tested samples. Diarrhea, loss of appetite, and loss of smell and taste sensations were the most predominant symptoms in anti-SARS-CoV-2 IgG-positive group. The positive percent agreement of the two testing methods was 50%, and negative percent agreement was 99.66%. Conclusions: 1.16% of tested healthcare workers of Kaunas hospitals were anti-SARS-CoV-2 IgG-positive. The negative percent agreement of the lateral flow immunoassay and ELISA exceeded 99%.


Subject(s)
/epidemiology , Immunoglobulin G/blood , Personnel, Hospital , /immunology , Adult , Aged , /diagnosis , Enzyme-Linked Immunosorbent Assay , Female , Humans , Immunoassay/methods , Immunoglobulin M/blood , Lithuania/epidemiology , Male , Middle Aged , Sensitivity and Specificity , Seroepidemiologic Studies
12.
PLoS One ; 16(2): e0246536, 2021.
Article in English | MEDLINE | ID: covidwho-1069627

ABSTRACT

We examined the usefulness of five COVID-19 antibody detection tests using 114 serum samples at various time points from 34 Japanese COVID-19 patients. We examined Elecsys Anti-SARS-CoV-2 from Roche, and four immunochromatography tests from Hangzhou Laihe Biotech, Artron Laboratories, Chil, and Nadal. In the first week after onset, Elecsys had 40% positivity in Group S (severe cases) but was negative in Group M (mild-moderate cases). The immunochromatography kits showed 40-60% and 0-8% positivity in Groups S and M, respectively. In the second week, Elecsys showed 75% and 50% positivity, and the immunochromatography tests showed 5-80% and 50-75% positivity in Groups S and M, respectively. After the third week, Elecsys showed 100% positivity in both groups. The immunochromatography kits showed 100% positivity in Group S. In Group M, positivity decreased to 50% for Chil and 75-89% for Artron and Lyher. Elecsys and immunochromatography kits had 91-100% specificity. Elecsys had comparable chronological change of cut-off index values in the two groups from the second week to the sixth week. The current SARS-CoV-2 antibody detection tests do not provide meaningful interpretation of severity and infection status. Its use might be limited to short-term epidemiological studies.


Subject(s)
Antibodies, Viral/immunology , /diagnosis , /immunology , Adult , Aged , Female , Humans , Male , Middle Aged , Reagent Kits, Diagnostic , Sensitivity and Specificity
13.
Epidemiol Prev ; 44(5-6 Suppl 2): 193-199, 2020.
Article in English | MEDLINE | ID: covidwho-1068139

ABSTRACT

BACKGROUND: facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. Although RT-PCR is the most reliable technique to detect ongoing infections, serological tests are frequently proposed as tools in heterogeneous screening strategies. OBJECTIVES: to analyse the performance of a screening strategy proposed by the local government of Tuscany (Central Italy), which first uses qualitative rapid tests for antibody detection, and then RT-PCR tests on the positive subjects. METHODS: a simulation study is conducted to investigate the number of RT-PCR tests required by the screening strategy and the undetected ongoing infections in a pseudo-population of 500,000 subjects, under different prevalence scenarios and assuming a sensitivity of the serological test ranging from 0.50 to 0.80 (specificity 0.98). A compartmental model is used to predict the number of new infections generated by the false negatives two months after the screening, under different values of the infection reproduction number. RESULTS: assuming a sensitivity equal to 0.80 and a prevalence of 0.3%, the screening procedure would require on average 11,167 RT-PCR tests and would produce 300 false negatives, responsible after two months of a number of contagions ranging from 526 to 1,132, under the optimistic scenario of a reproduction number between 0.5 to 1. Resources and false negatives increase with the prevalence. CONCLUSIONS: the analysed screening procedure should be avoided unless the prevalence and the rate of contagion are very low. The cost and effectiveness of the screening strategies should be evaluated in the actual context of the epidemic, accounting for the fact that it may change over time.


Subject(s)
Antibodies, Viral/blood , Computer Simulation , Mass Screening/methods , Models, Theoretical , Pandemics , /immunology , Basic Reproduction Number , /transmission , /methods , Cost-Benefit Analysis , False Negative Reactions , False Positive Reactions , Humans , Italy/epidemiology , Mass Screening/economics , Monte Carlo Method , Point-of-Care Testing/economics , Prevalence , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity
14.
Epidemiol Prev ; 44(5-6 Suppl 2): 184-192, 2020.
Article in English | MEDLINE | ID: covidwho-1068138

ABSTRACT

BACKGROUND: since the beginning of the COVID-19 pandemic, the importance of developing a serological test has emerged and a debate on test accuracy and reliability become an issue widely discussed in the media. The importance of communication during this pandemic has been strongly underlined by public health experts, epidemiologists, media expert, psychologists, sociologists. In the case of serological tests, there are several aspects that have to be considered: why we perform the test, what population is tested, which are the parameters conditioning the results and their interpretation. OBJECTIVES: to show how to quantify the uncertainty related to the validity of the serological test with respect to its predictive value and in particular the positive predictive value. METHODS: the evaluation of a qualitative diagnostic test includes four distinct assessments: accuracy, empirical evidence, practical importance, and prevalence of the pathology. Accuracy is measured by the sensitivity and specificity of the test; empirical evidence is quantified by the likelihood ratio, respectively for a positive and negative test result; the practical importance of the result of a diagnostic test is assessed by the positive or negative predictive value. Prevalence of COVID-19 is substantial uncertainty and it is possible to estimate the apparent prevalence starting from the results obtained with a diagnostic test. RESULTS: at the moment, the knowledge about the accuracy of serological tests is limited and little attention is paid to confidence interval on point estimates. In terms of practical importance of testing at individual level, while negative predictive values are high whatever the level of sensitivity of the test, the interpretation of a positive results is very cumbersome. Positive predictive values above 90% can be reached only by tests with specificity above 99% at the expected prevalence rate of 5%. There is a linear relationship between apparent - testing positive - prevalence and real prevalence. The apparent prevalence in the context of serological test for COVID-19 is always larger than real prevalence. The level of specificity is crucial. CONCLUSIONS: the main applications of the serological test in the epidemic contest are: to study the seroprevalence of the virus antibodies in the general population; to screen the healthcare workers for the early identification of contagious subjects' health care settings and to screen the general population in order to identify new incident cases. In the first two cases, seroprevalence study and screening of a high-risk population, the consequences of the uncertainty associated to the statistics are already accounted for in the first situation, or are overcome by repeating the screening on the healthcare workers, and using the molecular test to verify the presence of the virus in those tested positive. The case of screening of general population is more complex and of major interest for the implication it may have on individual behaviours and on the implementation of public health interventions by the political decision makers. A positive result has, per se, no practical value for individuals since the probability of being really infected by the virus is low. The uncertainty associated with the different estimates (sensitivity, specificity and disease prevalence) play a double role: it is a key factor in defining the informative content of the test result and it might guide the individual actions and the public policy decisions.


Subject(s)
Antibodies, Viral/blood , Communication , Immunoassay , Luminescent Measurements , Medical Overuse , Pandemics , /immunology , /epidemiology , Confidence Intervals , Decision Making , Enzyme-Linked Immunosorbent Assay , False Positive Reactions , Health Policy , Humans , Italy/epidemiology , Likelihood Functions , Mass Screening , Predictive Value of Tests , Prevalence , Sensitivity and Specificity , Seroepidemiologic Studies , Uncertainty
15.
Diagn Microbiol Infect Dis ; 99(3): 115260, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1065005

ABSTRACT

The BioFire® COVID-19 Test and Respiratory Panel 2.1 (RP2.1) are rapid, fully automated assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swabs. In the case of the RP2.1, an additional 21 viral and bacterial pathogens can be detected. Both tests have received emergency use authorization from the U.S. Food & Drug Administration and Interim Order authorization from Health Canada for use in clinical laboratories. We evaluated the performance characteristics of these tests in comparison to a laboratory-developed real-time PCR assay targeting the viral RNA-dependent RNA polymerase and E genes. A total of 78 tests were performed using the BioFire COVID-19 Test, including 30 clinical specimens and 48 tests in a limit of detection study; 57 tests were performed using the RP2.1 for evaluation of SARS-CoV-2 detection, including 30 clinical specimens and 27 tests for limit of detection. Results showed 100% concordance between the BioFire assays and the laboratory-developed test for all clinical samples tested, and acceptable performance of both BioFire assays at their stated limits of detection. Conclusively, the BioFire COVID-19 Test and RP2.1 are highly sensitive assays that can be effectively used in the clinical laboratory for rapid SARS-CoV-2 testing.


Subject(s)
/methods , Nasopharynx/virology , /isolation & purification , /standards , Clinical Laboratory Techniques/methods , Diagnostic Tests, Routine , Humans , Limit of Detection , Multiplex Polymerase Chain Reaction , Real-Time Polymerase Chain Reaction/methods , Reproducibility of Results , Sensitivity and Specificity
16.
Viruses ; 13(2)2021 Jan 20.
Article in English | MEDLINE | ID: covidwho-1067779

ABSTRACT

Accurate and rapid diagnostic tools are needed for management of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Antibody tests enable detection of individuals past the initial phase of infection and help examine vaccine responses. The major targets of human antibody response in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are the spike glycoprotein (SP) and nucleocapsid protein (NP). We have developed a rapid homogenous approach for antibody detection termed LFRET (protein L-based time-resolved Förster resonance energy transfer immunoassay). In LFRET, fluorophore-labeled protein L and antigen are brought to close proximity by antigen-specific patient immunoglobulins of any isotype, resulting in TR-FRET signal. We set up LFRET assays for antibodies against SP and NP and evaluated their diagnostic performance using a panel of 77 serum/plasma samples from 44 individuals with COVID-19 and 52 negative controls. Moreover, using a previously described SP and a novel NP construct, we set up enzyme linked immunosorbent assays (ELISAs) for antibodies against SARS-CoV-2 SP and NP. We then compared the LFRET assays with these ELISAs and with a SARS-CoV-2 microneutralization test (MNT). We found the LFRET assays to parallel ELISAs in sensitivity (90-95% vs. 90-100%) and specificity (100% vs. 94-100%). In identifying individuals with or without a detectable neutralizing antibody response, LFRET outperformed ELISA in specificity (91-96% vs. 82-87%), while demonstrating an equal sensitivity (98%). In conclusion, this study demonstrates the applicability of LFRET, a 10-min "mix and read" assay, to detection of SARS-CoV-2 antibodies.


Subject(s)
/methods , Immunoassay/methods , /isolation & purification , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , /immunology , Humans , Phosphoproteins/immunology , Sensitivity and Specificity , Spike Glycoprotein, Coronavirus/immunology
17.
PLoS One ; 16(1): e0243554, 2021.
Article in English | MEDLINE | ID: covidwho-1067394

ABSTRACT

With COVID-19 N95 shortages, frontline medical personnel are forced to reuse this disposable-but sophisticated-multilayer respirator. Widely used to decontaminate nonporous surfaces, UV-C light has demonstrated germicidal efficacy on porous, non-planar N95 respirators when all surfaces receive ≥1.0 J/cm2 dose. Of utmost importance across disciplines, translation of empirical evidence to implementation relies upon UV-C measurements frequently confounded by radiometer complexities. To enable rigorous on-respirator measurements, we introduce a photochromic indicator dose quantification technique for: (1) UV-C treatment design and (2) in-process UV-C dose validation. While addressing outstanding indicator limitations of qualitative readout and insufficient dynamic range, our methodology establishes that color-changing dosimetry can achieve the necessary accuracy (>90%), uncertainty (<10%), and UV-C specificity (>95%) required for UV-C dose measurements. In a measurement infeasible with radiometers, we observe a striking ~20× dose variation over N95s within one decontamination system. Furthermore, we adapt consumer electronics for accessible quantitative readout and use optical attenuators to extend indicator dynamic range >10× to quantify doses relevant for N95 decontamination. By transforming photochromic indicators into quantitative dosimeters, we illuminate critical considerations for both photochromic indicators themselves and UV-C decontamination processes.


Subject(s)
Decontamination/methods , Respiratory Protective Devices/microbiology , /prevention & control , Dose-Response Relationship, Radiation , Equipment Contamination/prevention & control , Equipment Contamination/statistics & numerical data , Equipment Reuse/statistics & numerical data , Humans , Indicators and Reagents/radiation effects , Radiometry/methods , Sensitivity and Specificity , Ultraviolet Rays , Ventilators, Mechanical/microbiology
18.
Virol J ; 18(1): 13, 2021 01 09.
Article in English | MEDLINE | ID: covidwho-1067245

ABSTRACT

BACKGROUND: COVID-19 is diagnosed via detection of SARS-CoV-2 RNA using real time reverse-transcriptase polymerase chain reaction (rtRT-PCR). Performance of many SARS-CoV-2 rtRT-PCR assays is not entirely known due to the lack of a gold standard. We sought to evaluate the false negative rate (FNR) and sensitivity of our laboratory-developed SARS-CoV-2 rtRT-PCR targeting the envelope (E) and RNA-dependent RNA-polymerase (RdRp) genes. METHODS: SARS-CoV-2 rtRT-PCR results at the Public Health Laboratory (Alberta, Canada) from January 21 to April 18, 2020 were reviewed to identify patients with an initial negative rtRT-PCR followed by a positive result on repeat testing within 14 days (defined as discordant results). Negative samples from these discordant specimens were re-tested using three alternate rtRT-PCR assays (targeting the E gene and N1/N2 regions of the nucleocapsid genes) to assess for false negative (FN) results. RESULTS: During the time period specified, 95,919 patients (100,001 samples) were tested for SARS-CoV-2. Of these, 49 patients were found to have discordant results including 49 positive and 52 negative swabs. Repeat testing of 52 negative swabs found five FNs (from five separate patients). Assuming 100% specificity of the diagnostic assay, the FNR and sensitivity in this group of patients with discordant testing was 9.3% (95% CI 1.5-17.0%) and 90.7% (95% CI 82.6-98.9%) respectively. CONCLUSIONS: Studies to understand the FNR of routinely used assays are important to confirm adequate clinical performance. In this study, most FN results were due to low amounts of SARS-CoV-2 virus concentrations in patients with multiple specimens collected during different stages of infection. Post-test clinical evaluation of each patient is advised to ensure that rtRT-PCR results are not the only factor in excluding COVID-19.


Subject(s)
/diagnosis , Real-Time Polymerase Chain Reaction , /isolation & purification , Adult , Aged , Aged, 80 and over , /statistics & numerical data , Canada , False Negative Reactions , Female , Humans , Male , Middle Aged , Molecular Diagnostic Techniques/statistics & numerical data , Sensitivity and Specificity
19.
BMC Infect Dis ; 21(1): 148, 2021 Feb 05.
Article in English | MEDLINE | ID: covidwho-1067202

ABSTRACT

BACKGROUND: One-fifth of COVID-19 patients are seriously and critically ill cases and have a worse prognosis than non-severe cases. Although there is no specific treatment available for COVID-19, early recognition and supportive treatment may reduce the mortality. The aim of this study is to develop a functional nomogram that can be used by clinicians to estimate the risk of in-hospital mortality in patients hospitalized and treated for COVID-19 disease, and to compare the accuracy of model predictions with previous nomograms. METHODS: This retrospective study enrolled 709 patients who were over 18 years old and received inpatient treatment for COVID-19 disease. Multivariable Logistic Regression analysis was performed to assess the possible predictors of a fatal outcome. A nomogram was developed with the possible predictors and total point were calculated. RESULTS: Of the 709 patients treated for COVID-19, 75 (11%) died and 634 survived. The elder age, certain comorbidities (cancer, heart failure, chronic renal failure), dyspnea, lower levels of oxygen saturation and hematocrit, higher levels of C-reactive protein, aspartate aminotransferase and ferritin were independent risk factors for mortality. The prediction ability of total points was excellent (Area Under Curve = 0.922). CONCLUSIONS: The nomogram developed in this study can be used by clinicians as a practical and effective tool in mortality risk estimation. So that with early diagnosis and intervention mortality in COVID-19 patients may be reduced.


Subject(s)
/mortality , Hospital Mortality , Nomograms , Adult , Age Factors , Aged , Aged, 80 and over , Female , Hospitals, University , Humans , Male , Middle Aged , Predictive Value of Tests , Prognosis , ROC Curve , Retrospective Studies , Risk Assessment , Sensitivity and Specificity , Turkey , Young Adult
20.
mSphere ; 6(1)2021 01 13.
Article in English | MEDLINE | ID: covidwho-1066824

ABSTRACT

Information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread in Africa is limited by insufficient diagnostic capacity. Here, we assessed the coronavirus disease (COVID-19)-related diagnostic workload during the onset of the pandemic in the central laboratory of Benin, Western Africa; characterized 12 SARS-CoV-2 genomes from returning travelers; and validated the Da An RT-PCR-based diagnostic kit that is widely used across Africa. We found a 15-fold increase in the monthly laboratory workload due to COVID-19, dealt with at the cost of routine activities. Genomic surveillance showed near-simultaneous introduction of distinct SARS-CoV-2 lineages termed A.4 and B.1, including the D614G spike protein variant potentially associated with higher transmissibility from travelers from six different European and African countries during March-April 2020. We decoded the target regions within the ORF1ab and N genes of the Da An dual-target kit by MinION-based amplicon sequencing. Despite relatively high similarity between SARS-CoV-2 and endemic human coronaviruses (HCoVs) within the ORF1ab target domain, no cross-detection of high-titered cell culture supernatants of HCoVs was observed, suggesting high analytical specificity. The Da An kit was highly sensitive, detecting 3.2 to 9.0 copies of target-specific in vitro transcripts/reaction. Although discrepant test results were observed in low-titered clinical samples, clinical sensitivity of the Da An kit was at least comparable to that of commercial kits from affluent settings. In sum, virologic diagnostics are achievable in a resource-limited setting, but unprecedented pressure resulting from COVID-19-related diagnostics requires rapid and sustainable support of national and supranational stakeholders addressing limited laboratory capacity.IMPORTANCE Months after the start of the COVID-19 pandemic, case numbers from Africa are surprisingly low, potentially because the number of SARS-CoV-2 tests performed in Africa is lower than in other regions. Here, we show an overload of COVID-19-related diagnostics in the central laboratory of Benin, Western Africa, with a stagnating average number of positive samples irrespective of daily sample counts. SARS-CoV-2 genomic surveillance confirmed a high genomic diversity in Benin introduced by travelers returning from Europe and other African countries, including early circulation of the D614G spike mutation associated with potentially higher transmissibility. We validated a widely used RT-PCR kit donated by the Chinese Jack Ma Foundation and confirmed high analytical specificity and clinical sensitivity equivalent to tests used in affluent settings. Our assessment shows that although achievable in an African setting, the burden from COVID-19-related diagnostics on national reference laboratories is very high.


Subject(s)
/diagnosis , /isolation & purification , Adult , Benin/epidemiology , /transmission , /methods , Developing Countries , Female , Genome, Viral , Health Resources/supply & distribution , Health Services Accessibility/statistics & numerical data , Humans , Male , Middle Aged , Sensitivity and Specificity , Travel-Related Illness , Workload/statistics & numerical data
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