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2.
In Vivo ; 36(6): 2823-2827, 2022.
Article in English | MEDLINE | ID: covidwho-2100683

ABSTRACT

BACKGROUND/AIM: COVID-19 is a concerning issue among in-center hemodialysis (HD) patients. To prevent COVID-19 diffusion in our HD facility, weekly rapid nasal antigen test screening was performed for all asymptomatic patients on chronic HD. This study aimed to assess the performance of weekly rapid antigen test in detecting SARS-CoV-2 infection among asymptomatic patients receiving HD. PATIENTS AND METHODS: A retrospective analysis was conducted in HD patients who underwent rapid antigen test screening from December 2021 to March 2022. The diagnosis of COVID-19 with rapid antigen test was always confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS: During the observational period, 1,748 rapid antigen tests were performed in 220 HD patients. Mean age was 68.4±14.6 years. Fifteen (8.5%) patients resulted positive for SARS-CoV-2 infection using rapid antigen tests. The diagnosis was subsequently confirmed in 14 (93.3%) patients by RT-PCR. During the same period, 12 (5.4%) symptomatic patients, regularly screened with weekly rapid antigen test, resulted positive for SARS-CoV-2 infection using RT-PCR. Overall, weekly rapid antigen test screening identified 14 out of 26 (53.8%) COVID-19 cases and showed a positive predictive value of 93%. CONCLUSION: Weekly antigen test screening of asymptomatic patients on chronic HD detected around half of the COVID-19 cases in our population.


Subject(s)
COVID-19 , Humans , Middle Aged , Aged , Aged, 80 and over , COVID-19/diagnosis , COVID-19/epidemiology , SARS-CoV-2 , Retrospective Studies , COVID-19 Testing , Renal Dialysis , Sensitivity and Specificity
3.
Ann Intern Med ; 175(11): JC131, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2100329

ABSTRACT

SOURCE CITATION: Goodall BL, LeBlanc JJ, Hatchette TF, et al. Investigating the sensitivity of nasal or throat swabs: combination of both swabs increases the sensitivity of SARS-CoV-2 rapid antigen tests. Microbiol Spectr. 2022;10:e0021722 35762772.


Subject(s)
COVID-19 , Humans , Adult , SARS-CoV-2 , Pharynx , Sensitivity and Specificity
4.
J Clin Microbiol ; 60(1): e0174221, 2022 01 19.
Article in English | MEDLINE | ID: covidwho-2097916

ABSTRACT

Point-of-care antigen tests are an important tool for SARS-CoV-2 detection. Antigen tests are less sensitive than real-time reverse transcriptase PCR (rRT-PCR). Data on the performance of the BinaxNOW antigen test compared to rRT-PCR and viral culture by symptom and known exposure status, timing during disease, or exposure period and demographic variables are limited. During 3 to 17 November 2020, we collected paired upper respiratory swab specimens to test for SARS-CoV-2 by rRT-PCR and Abbott BinaxNOW antigen test at two community testing sites in Pima County, Arizona. We administered a questionnaire to capture symptoms, known exposure status, and previous SARS-CoV-2 test results. Specimens positive by either test were analyzed by viral culture. Previously we showed overall BinaxNOW sensitivity was 52.5%. Here, we showed BinaxNOW sensitivity increased to 65.7% among currently symptomatic individuals reporting a known exposure. BinaxNOW sensitivity was lower among participants with a known exposure and previously symptomatic (32.4%) or never symptomatic (47.1%) within 14 days of testing. Sensitivity was 71.1% in participants within a week of symptom onset. In participants with a known exposure, sensitivity was highest 8 to 10 days postexposure (75%). The positive predictive value for recovery of virus in cell culture was 56.7% for BinaxNOW-positive and 35.4% for rRT-PCR-positive specimens. Result reporting time was 2.5 h for BinaxNOW and 26 h for rRT-PCR. Point-of-care antigen tests have a shorter turnaround time than laboratory-based nucleic acid amplification tests, which allows for more rapid identification of infected individuals. Antigen test sensitivity limitations are important to consider when developing a testing program.


Subject(s)
COVID-19 , SARS-CoV-2 , Antigens, Viral , Humans , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity
5.
Scand J Trauma Resusc Emerg Med ; 28(1): 66, 2020 Jul 13.
Article in English | MEDLINE | ID: covidwho-2098371

ABSTRACT

BACKGROUND: There is a need for validated clinical risk scores to identify patients at risk of severe disease and to guide decision-making during the covid-19 pandemic. The National Early Warning Score 2 (NEWS2) is widely used in emergency medicine, but so far, no studies have evaluated its use in patients with covid-19. We aimed to study the performance of NEWS2 and compare commonly used clinical risk stratification tools at admission to predict risk of severe disease and in-hospital mortality in patients with covid-19. METHODS: This was a prospective cohort study in a public non-university general hospital in the Oslo area, Norway, including a cohort of all 66 patients hospitalised with confirmed SARS-CoV-2 infection from the start of the pandemic; 13 who died during hospital stay and 53 who were discharged alive. Data were collected consecutively from March 9th to April 27th 2020. The main outcome was the ability of the NEWS2 score and other clinical risk scores at emergency department admission to predict severe disease and in-hospital mortality in covid-19 patients. We calculated sensitivity and specificity with 95% confidence intervals (CIs) for NEWS2 scores ≥5 and ≥ 6, quick Sequential Organ Failure Assessment (qSOFA) score ≥ 2, ≥2 Systemic Inflammatory Response Syndrome (SIRS) criteria, and CRB-65 score ≥ 2. Areas under the curve (AUCs) for the clinical risk scores were compared using DeLong's test. RESULTS: In total, 66 patients (mean age 67.9 years) were included. Of these, 23% developed severe disease. In-hospital mortality was 20%. Tachypnoea, hypoxemia and confusion at admission were more common in patients developing severe disease. A NEWS2 score ≥ 6 at admission predicted severe disease with 80.0% sensitivity and 84.3% specificity (Area Under the Curve (AUC) 0.822, 95% CI 0.690-0.953). NEWS2 was superior to qSOFA score ≥ 2 (AUC 0.624, 95% CI 0.446-0.810, p < 0.05) and other clinical risk scores for this purpose. CONCLUSION: NEWS2 score at hospital admission predicted severe disease and in-hospital mortality, and was superior to other widely used clinical risk scores in patients with covid-19.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Early Warning Score , Hospital Mortality , Patient Admission , Pneumonia, Viral/epidemiology , Adult , Aged , Aged, 80 and over , COVID-19 , Cohort Studies , Female , Humans , Male , Middle Aged , Norway/epidemiology , Pandemics , Risk Assessment , SARS-CoV-2 , Sensitivity and Specificity , Severity of Illness Index
6.
BMC Infect Dis ; 22(1): 810, 2022 Oct 31.
Article in English | MEDLINE | ID: covidwho-2098319

ABSTRACT

BACKGROUND: There is limited information to compare the qualitative and semi-quantitative performance of rapid diagnostic tests (RDT) and serology for the assessment of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, the objective of the study was (a) to compare the efficacy of SARS-CoV-2 antibody detection between RDT and laboratory serology, trying to identify appropriate semi-quantitative cut-offs for RDT in relation with quantitative serology values and to (b) evaluate diagnostic accuracy of RDT compared to the NAAT gold standard in an unselected adult population. METHODS: SARS-CoV-2 antibodies were simultaneously measured with lateral flow immunochromatographic assays (LFA), the Cellex qSARS-CoV-2 IgG/IgM Rapid Test (by capillary blood), the iFlash-SARS-CoV-2 IgG/IgM chemiluminescent immunoassay (CLIA) (by venous blood) and the nucleic acid amplification test (NAAT) in samples from in- and out-patients with confirmed, suspected and negative diagnosis of coronavirus disease 2019 (COVID-19) attending Udine Hospital (Italy) (March-May 2020). Interpretation of RDT was qualitative (positive/negative) and semi-quantitative based on a chromatographic intensity scale (negative, weak positive, positive). RESULTS: Overall, 720 paired antibody measures were performed on 858 patients. The qualitative and semiquantitative agreement analysis performed in the whole sample between LFA and CLIA provided a Kendall's tau of 0.578 (p < 0.001) and of 0.623 (p < 0.001), respectively, for IgM and IgG. In patients with a diagnosis of COVID-19, accordance between LFA and CLIA was maintained as a function of time from the onset of COVID-19 disease and the severity of disease both for qualitative and semi-quantitative assessments. RDT compared to the NAAT gold standard in 858 patients showed 78.5% sensitivity (95% CI 75.1%-81.7%) and 94.1% specificity (95% CI 90.4%-96.8%), with variable accordance depending on the timing from symptom onset. CONCLUSION: The RDT used in our study can be a non-invasive and reliable alternative to serological tests and facilitate both qualitative and a semi-quantitative antibody detection in COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , Humans , COVID-19/diagnosis , Prospective Studies , Immunoglobulin M , Sensitivity and Specificity , Antibodies, Viral , Immunoglobulin G , Immunoassay/methods
7.
Int J Mol Sci ; 23(21)2022 Oct 28.
Article in English | MEDLINE | ID: covidwho-2090209

ABSTRACT

Consistently emerging variants and the life-threatening consequences of SARS-CoV-2 have prompted worldwide concern about human health, necessitating rapid and accurate point-of-care diagnostics to limit the spread of COVID-19. Still, However, the availability of such diagnostics for COVID-19 remains a major rate-limiting factor in containing the outbreaks. Apart from the conventional reverse transcription polymerase chain reaction, loop-mediated isothermal amplification-based (LAMP) assays have emerged as rapid and efficient systems to detect COVID-19. The present study aims to develop RT-LAMP-based assay system for detecting multiple targets in N, ORF1ab, E, and S genes of the SARS-CoV-2 genome, where the end-products were quantified using spectrophotometry, paper-based lateral-flow devices, and electrochemical sensors. The spectrophotometric method shows a LOD of 10 agµL-1 for N, ORF1ab, E genes and 100 agµL-1 for S gene in SARS-CoV-2. The developed lateral-flow devices showed an LOD of 10 agµL-1 for all four gene targets in SARS-CoV-2. An electrochemical sensor developed for N-gene showed an LOD and E-strip sensitivity of log 1.79 ± 0.427 pgµL-1 and log 0.067 µA/pg µL-1/mm2, respectively. The developed assay systems were validated with the clinical samples from COVID-19 outbreaks in 2020 and 2021. This multigene target approach can effectively detect emerging COVID-19 variants using combination of various analytical techniques at testing facilities and in point-of-care settings.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , Sensitivity and Specificity , Nucleic Acid Amplification Techniques/methods , Molecular Diagnostic Techniques/methods , RNA, Viral/genetics
8.
Euro Surveill ; 27(42)2022 10.
Article in English | MEDLINE | ID: covidwho-2089697

ABSTRACT

BackgroundCountries worldwide are focusing to mitigate the ongoing SARS-CoV-2 pandemic by employing public health measures. Laboratories have a key role in the control of SARS-CoV-2 transmission. Serology for SARS-CoV-2 is of critical importance to support diagnosis, define the epidemiological framework and evaluate immune responses to natural infection and vaccine administration.AimThe aim of this study was the assessment of the actual capability among laboratories involved in sero-epidemiological studies on COVID-19 in EU/EEA and EU enlargement countries to detect SARS-CoV-2 antibodies through an external quality assessment (EQA) based on proficiency testing.MethodsThe EQA panels were composed of eight different, pooled human serum samples (all collected in 2020 before the vaccine roll-out), addressing sensitivity and specificity of detection. The panels and two EU human SARS-CoV-2 serological standards were sent to 56 laboratories in 30 countries.ResultsThe overall performance of laboratories within this EQA indicated a robust ability to establish past SARS-CoV-2 infections via detection of anti-SARS-CoV-2 antibodies, with 53 of 55 laboratories using at least one test that characterised all EQA samples correctly. IgM-specific test methods provided most incorrect sample characterisations (24/208), while test methods detecting total immunoglobulin (0/119) and neutralising antibodies (2/230) performed the best. The semiquantitative assays used by the EQA participants also showed a robust performance in relation to the standards.ConclusionOur EQA showed a high capability across European reference laboratories for reliable diagnostics for SARS-CoV-2 antibody responses. Serological tests that provide robust and reliable detection of anti-SARS-CoV-2 antibodies are available.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Laboratories , Antibodies, Viral , Sensitivity and Specificity , Immunoglobulin M , Antibodies, Neutralizing
9.
Anal Chem ; 94(44): 15472-15480, 2022 Nov 08.
Article in English | MEDLINE | ID: covidwho-2087112

ABSTRACT

Integrated clustered regularly interspaced short palindromic repeat (CRISPR)-loop-mediated amplification (LAMP) technology is of great importance in CRISPR-based diagnostic systems, which urgently needs to be developed to improve diagnostic accuracy. A labor-free, contamination-free, and fully automated droplet manipulation platform for the CRISPR-LAMP technology has not been developed before. Herein, we propose a fully automated CRISPR-LAMP platform, which can precisely manipulate the CRISPR-LAMP droplet and perform combined reactions with high sensitivity and specificity. SARS-CoV-2 Spike T478K, D614G, P681R, and P681H mutations, typical point mutations of B.1.617.2 (Delta) and Omicron variants, are monitored with this platform with a detection limit of 102 copies/µL. Allele discrimination between the mutants and wild type is significant with the designed one/two-mismatch CRISPR RNA (crRNA) at a limit of 102 copies/µL. Chemically synthesized and modified crRNAs greatly increase the CRISPR-LAMP signal, which advance the wide application. Combined with the previously developed RdRp CRISPR-LAMP assay, clinical results showed that Spike T478K and P681H can discriminate the mutant type form the wild type with 70% (49.66-85.50%, 95% confidence interval) and 78% (57.27-90.62%, 95% confidence interval) sensitivity, respectively, and 100% specificity (51.68-100%, 95% confidence interval), and the RdRp target can detect SARS-CoV-2 strains with 85% sensitivity (65.39-95.14%, 95% confidence interval) and 100% specificity (51.68-100%, 95% confidence interval). We believe that this automatic digital microfluid (DMF) system can advance the integrated CRISPR-LAMP technology with higher stability, sensitivity, and practicability, also for other CRISPR-associated diagnostic platforms.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , Nucleic Acid Amplification Techniques/methods , RNA-Dependent RNA Polymerase , Sensitivity and Specificity
10.
Anal Biochem ; 659: 114960, 2022 Dec 15.
Article in English | MEDLINE | ID: covidwho-2085839

ABSTRACT

COVID-19 pandemic highlighted the demand for the fast and reliable detection of viral RNA. Although various methods for RNA amplification and detection have been proposed, some limitations, including those caused by reverse transcription (RT), need to be overcome. Here, we report on the direct detection of specific RNA by conventional polymerase chain reaction (PCR) requiring no prior RT step. It was found that Hemo KlenTaq (HKTaq), which is posed as DNA-dependent DNA polymerase, possesses reverse transcriptase activity and provides reproducible amplification of RNA targets with an efficiency comparable to common RT-PCR. Using nasopharyngeal swab extracts from COVID-19-positive patients, the high reliability of SARS-CoV-2 detection based on HKTaq was demonstrated. The most accurate detection of specific targets are provided by nearby primers, which allow to determine RNA in solutions affected to multiple freeze-thaw cycles. HKTaq can be used for elaboration of simplified amplification techniques intended for the analysis of any specific RNA and requiring only one DNA polymerase.


Subject(s)
COVID-19 , RNA, Viral , Humans , Clinical Laboratory Techniques/methods , COVID-19 Testing , Nucleic Acid Amplification Techniques/methods , Pandemics , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction , RNA, Viral/genetics , RNA, Viral/analysis , RNA-Directed DNA Polymerase/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity , Taq Polymerase/metabolism
11.
Int J Mol Sci ; 23(21)2022 Oct 25.
Article in English | MEDLINE | ID: covidwho-2081940

ABSTRACT

In order to assess SARS-CoV-2 real time quantitative polymerase chain reaction (RT-qPCR) results in a real-life setting, three independent laboratories in Graz (Austria) set up a continuous cross comparison schedule. The following test systems were used: The QIAGEN NeuMoDx SARS-CoV-2 Assay, the Allplex™ 2019-nCoV Assay (Seegene) on a MicroLab Nimbus (Hamilton) platform combined with RealStar SARS-CoV-2 RT-PCR Assay (Altona Diagnostics GmbH), and the cobas SARS-CoV-2 test on a fully automated cobas 6800 system (Roche). A total of 200 samples were analysed, 184 (92%) were found to be concordant with all testing platforms, 14 (7%) discordant. Two (1%) samples tested invalid on a single platform and were excluded from further analysis. Discordant results were distributed randomly across the assays. The Ct values from all assays correlated closely with each other. All discordant samples showed Ct values ≥ 26. SARS-CoV-2 RT-qPCR assays may show considerable variability, especially in samples with low viral RNA concentrations. Decision makers should thus balance the advantages and disadvantages of RT-qPCR for mass screening and adopt suitable strategies that ensure a rational management of positive samples with high Ct values.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , RNA, Viral/genetics , COVID-19 Testing , COVID-19/diagnosis , Real-Time Polymerase Chain Reaction/methods , Sensitivity and Specificity
12.
Clin Lab ; 68(10)2022 Oct 01.
Article in English | MEDLINE | ID: covidwho-2080871

ABSTRACT

BACKGROUND: Diagnosis with reverse transcriptase polymerase chain reaction (RT-PCR) test is a very important step for the control of the COVID-19 pandemic. The aim of this study is to compare the RT-PCR results of the samples taken directly from the viral transport medium (VTM) without extraction with the RT-PCR results of two different extraction methods, one automated and the other manual, in the diagnosis of COVID-19. METHODS: Among the respiratory tract samples sent to Sakarya Training and Research Hospital Microbiology Laboratory for COVID-PCR study, 20 negative and 43 positive samples with different cycle threshold (CT) values were included in the study. Both manual nucleic acid isolation with the vNAT isolation kit (Bioeksen, Turkey) and automatic nucleic acid isolation with the EZ1 Virus Mini Kit v2.0 in the isolation device were performed simulta-neously from the patient samples included in the study and the results were compared. RESULTS: The mean Ct values of the samples were found to be 21.58 using manual vNAT as the extraction method, 17.63 using the automated magnetic bead method, and 21.45 in PCR from direct VTM without extraction. When the automatic magnetic beads extraction method was taken as the reference method, the sensitivity of direct PCR was 97.3%, the specificity was 95%, the positive predictive value was 97.3%, and the negative predictive value was 95%. Phi coefficients were found to be 0.927 between vNAT and direct PCR, 1 between vNAT and EZ1, and 0.922 between direct PCR and EZ1. CONCLUSIONS: Direct PCR has advantages such as eliminating RNA extraction and purification steps, providing a shorter detection time, and using less labor and less consumables without reducing the diagnostic accuracy. It is thought that this method can help as a useful process management for the control of the epidemic in countries with limited resources.


Subject(s)
COVID-19 , Nucleic Acids , COVID-19/diagnosis , COVID-19 Testing , Humans , Pandemics , RNA , RNA, Viral/analysis , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/genetics , Sensitivity and Specificity
13.
Clin Lab ; 68(10)2022 Oct 01.
Article in English | MEDLINE | ID: covidwho-2080870

ABSTRACT

BACKGROUND: We retrospectively examined all initial positive SARS-CoV-2 test results using three real-time PCR tests from patients without a history of COVID-19 collected from September to October 2021 at a university-affiliated hospital. METHODS: We defined a possible false-positive (PFP) case as a positive case that showed negative results upon per-forming a confirmatory test on the same specimen. Positivity% and PFP% were defined as the number of first positive and the number of PFP cases divided by the total test numbers, respectively. RESULTS: The positivity%/PFP% values were 0.76%/0.10%, 0.29%/0.02%, and 0.21%/0.03% for the Xpert, Allplex, and cobas tests, respectively. Six (75%) cobas PFP cases were RdRp-only positive. All PFP cases analyzed by Xpert except one had cycle threshold values ≥ 40. Contamination during extraction was suspected in five of the 10 PFP cases analyzed by Allplex, which requires a separate extraction step. CONCLUSIONS: Care must be taken when analyzing first-positive cases as these may be false-positive signals.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/diagnosis , COVID-19 Testing , Real-Time Polymerase Chain Reaction , Retrospective Studies , SARS-CoV-2/genetics , Sensitivity and Specificity
15.
Biotechniques ; 73(4): 193-203, 2022 10.
Article in English | MEDLINE | ID: covidwho-2079900

ABSTRACT

Dried blood spots (DBSs) provide an alternative sample input for serologic testing. We evaluated DBSs for the ARCHITECT® hepatitis B surface antigen (HBsAg) NEXT, hepatitis B e-antigen (HBeAg), anti-hepatitis B core antigen (anti-HBc II), HIV antigen/antibody (Ag/Ab) Combo and AdviseDx SARS-CoV-2 IgG II assays. Assay performance with DBSs was assessed with or without assay modification and compared with on-market assay with plasma samples. DBS stability was also determined. HBsAg NEXT and HIV Ag/Ab Combo assays using DBSs showed sensitivity and specificity comparable to that of on-market assays. Modified HBeAg, anti-HBc II and SARS-CoV-2 IgG II DBS assays achieved performance comparable to on-market assays. Use of DBSs as input for high-throughput serologic assays is expected to have significant implications for improving population surveillance and increasing access to diagnostic testing.


Subject(s)
COVID-19 , HIV Infections , Humans , Hepatitis B Surface Antigens , Hepatitis B e Antigens , COVID-19/diagnosis , SARS-CoV-2 , Hepatitis B Antibodies , Sensitivity and Specificity , HIV Infections/diagnosis , Immunoglobulin G
16.
PLoS One ; 17(10): e0276464, 2022.
Article in English | MEDLINE | ID: covidwho-2079770

ABSTRACT

The study aimed to shorten multiplex RT-PCR run time for detection of SARS CoV-2 N1 and N2 sequences and human RNase P (RP) sequence as internal mRNA control using conventional and designated real time thermal cycler systems. Optimization of Fast PCR protocol using plasmid-based N1 and N2 positive control and synthetic version of human RP was done on Applied Biosystems (ABI) QuantStudioTM5 (conventional), ABI 7500 Fast Dx (designated), and CFX96 Touch Real Time Detection System, Bio-Rad (conventional). Finally, a performance evaluation of Fast PCR was performed in terms of sensitivity, specificity, and precision. For a 40-cycle PCR with optimized Fast PCR protocols on QuantStudioTM5, ABI 7500 Fast Dx, and CFX96 Touch (conventional), standard/regular versus Fast PCR run times (min) were 84 vs. 49, 96 vs. 48, and 103 vs. 61, thereby saving 35, 48, and 43 min, respectively. For each thermal cycler, Standard and Fast PCR generated identical shapes of fluorescence curves, Ct values, and (3) R2 (0.95 to 0.99) for 5 10-log dilution panels of each positive control. The fast PCR approach generated results with 100% sensitivity and specificity. Median test comparisons between standard PCR and Fast PCR Cts of COVID-19 samples did not produce significance (p>0.5), suggesting that Fast PCR and Standard PCR were comparable. Also, the median and mean of each target had closely-related values, further suggesting that the two approaches were comparable. That is, there is an equivalency between Conventional and Fast PCR instruments for detection of COVID-19.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , Ribonuclease P , Real-Time Polymerase Chain Reaction/methods , Sensitivity and Specificity , Multiplex Polymerase Chain Reaction/methods , RNA, Messenger
17.
PLoS One ; 17(10): e0268160, 2022.
Article in English | MEDLINE | ID: covidwho-2079683

ABSTRACT

BACKGROUND: Rapid diagnostics are vital for curving the transmission and control of the COVID-19 pandemic. Although many commercially available antigen-based rapid diagnostic tests (Ag-RDTs) for the detection of SARS-CoV-2 are recommended by the WHO, their diagnostic performance has not yet been assessed in Ethiopia. So far, the vast majority of studies assessing diagnostic accuracies of rapid antigen tests considered RT-PCR as a reference standard, which inevitably leads to bias when RT-PCR is not 100% sensitive and specific. Thus, this study aimed to evaluate the diagnostic performance of Panbio™ jointly with the RT-PCR for the detection of SARS-CoV-2. METHODS: A prospective cross-sectional study was done from July to September 2021 in Addis Ababa, Ethiopia, during the third wave of the pandemic involving two health centers and two hospitals. Diagnostic sensitivity and specificity of Panbio™ and RT-PCR were obtained using Bayesian Latent-Class Models (BLCM). RESULTS: 438 COVID-19 presumptive clients were enrolled, 239 (54.6%) were females, of whom 196 (44.7%) had a positive RT-PCR and 158 (36.1%) were Panbio™ positive. The Panbio™ and RT-PCR had a sensitivity (95% CrI) of 99.6 (98.4-100) %, 89.3 (83.2-97.6) % and specificity (95% CrI) of 93.4 (82.3-100) %, and 99.1 (97.5-100) %, respectively. Most of the study participants, 318 (72.6%) exhibited COVID-19 symptoms; the most reported was cough 191 (43.6%). CONCLUSION: As expected the RT-PCR performed very well with a near-perfect specificity and a high, but not perfect sensitivity. The diagnostic performance of Panbio™ is coherent with the WHO established criteria of having a sensitivity ≥80% for Ag-RDTs. Both tests displayed high diagnostic accuracies in patients with and without symptoms. Hence, we recommend the use of the Panbio™ for both symptomatic and asymptomatic individuals in clinical settings for screening purposes.


Subject(s)
COVID-19 , SARS-CoV-2 , Female , Humans , Male , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19/epidemiology , Reverse Transcriptase Polymerase Chain Reaction , Pandemics , Cross-Sectional Studies , Ethiopia/epidemiology , Bayes Theorem , Prospective Studies , Sensitivity and Specificity , Antigens, Viral/analysis
18.
Acta Clin Belg ; 77(3): 647-652, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-2077515

ABSTRACT

PURPOSE: In the context of the current COVID-19 pandemic, multiple serological assays for the detection of severe acute respiratory syndrome 2 (SARS-CoV-2) immune response are currently being developed. This study compares the FRENDTM COVID-19 IgG/IgM Duo (NanoEntec) a point of care (POCT) assay with the automated Elecsys anti-SARS-CoV-2 electrochemiluminescent assay (Roche Diagnostics). METHODS: Serum samples (n = 81) from PCR-confirmed SARS-CoV-2 positive patients at different time points after the onset of symptoms were analyzed with both assays. An additional 24 serum samples with cross reactivity potential were also included. RESULTS: The sensitivity of the COVID-19 IgG/IgM Duo assay was higher as compared to the Elecsys anti-SARS-CoV-2 assay, especially when using the combined IgM/IgG result in samples analyzed within 6 days after the onset of symptoms (46.2% vs. 15.4%). The sensitivity of both assays increased with increasing time interval after the onset of symptoms and reached 100% for the COVID-19 IgG/IgM Duo assay in samples taken 14 days or more after symptom onset. Specificity of the COVID-19 IgG/IgM Duo assay was 95.8% for IgM, 91.7% for IgG and 87.5% for the combination of both. CONCLUSION: This study shows that the sensitivity of both assays was highly dependent on the time interval between the onset of the COVID-19 symptoms and serum sampling. Furthermore, rapid serological testing for SARS-CoV-2 antibodies by means of the FRENDTM COVID-19 IgG/IgM Duo POCT assay showed a comparable diagnostic performance as the reference automated immunoassay.


Subject(s)
COVID-19 , Antibodies, Viral , COVID-19/diagnosis , Humans , Immunoassay , Immunoglobulin G , Immunoglobulin M , Pandemics , Point-of-Care Testing , SARS-CoV-2 , Sensitivity and Specificity
19.
Crit Care ; 26(1): 311, 2022 10 14.
Article in English | MEDLINE | ID: covidwho-2079529

ABSTRACT

BACKGROUND: The sublingual microcirculation presumably exhibits disease-specific changes in function and morphology. Algorithm-based quantification of functional microcirculatory hemodynamic variables in handheld vital microscopy (HVM) has recently allowed identification of hemodynamic alterations in the microcirculation associated with COVID-19. In the present study we hypothesized that supervised deep machine learning could be used to identify previously unknown microcirculatory alterations, and combination with algorithmically quantified functional variables increases the model's performance to differentiate critically ill COVID-19 patients from healthy volunteers. METHODS: Four international, multi-central cohorts of critically ill COVID-19 patients and healthy volunteers (n = 59/n = 40) were used for neuronal network training and internal validation, alongside quantification of functional microcirculatory hemodynamic variables. Independent verification of the models was performed in a second cohort (n = 25/n = 33). RESULTS: Six thousand ninety-two image sequences in 157 individuals were included. Bootstrapped internal validation yielded AUROC(CI) for detection of COVID-19 status of 0.75 (0.69-0.79), 0.74 (0.69-0.79) and 0.84 (0.80-0.89) for the algorithm-based, deep learning-based and combined models. Individual model performance in external validation was 0.73 (0.71-0.76) and 0.61 (0.58-0.63). Combined neuronal network and algorithm-based identification yielded the highest externally validated AUROC of 0.75 (0.73-0.78) (P < 0.0001 versus internal validation and individual models). CONCLUSIONS: We successfully trained a deep learning-based model to differentiate critically ill COVID-19 patients from heathy volunteers in sublingual HVM image sequences. Internally validated, deep learning was superior to the algorithmic approach. However, combining the deep learning method with an algorithm-based approach to quantify the functional state of the microcirculation markedly increased the sensitivity and specificity as compared to either approach alone, and enabled successful external validation of the identification of the presence of microcirculatory alterations associated with COVID-19 status.


Subject(s)
COVID-19 , Critical Illness , Artificial Intelligence , Humans , Microcirculation/physiology , Sensitivity and Specificity
20.
J Occup Environ Med ; 64(9): e575-e578, 2022 09 01.
Article in English | MEDLINE | ID: covidwho-2077945

ABSTRACT

OBJECTIVE: The aim of this study was to determine whether mid-turbinate specimens reliably detect active infection in asymptomatic adults undergoing regular COVID-19 PCR testing. METHODS: Qualitative agreement between 2481 paired nasopharyngeal and mid-turbinate PCR results was assessed. Mean cycle threshold values for each positive result were evaluated as an indicator of active infection. RESULTS: Overall agreement between nasopharyngeal and mid-turbinate tests was 98.4%. Positive percent agreement was 37.2%, and negative percent agreement was ~100%. Test pairs with lower cycle thresholds (≤30 and ≤25) reached 67% and 100% positive percent agreement, respectively. CONCLUSIONS: SARS-CoV-2 infections with high viral loads were detected regardless of specimen type. Mid-turbinate swabs reduced staff discomfort and may decrease repeated positive test results weeks or months after initial infection. Discordant pairs generally had high cycle threshold values (>30) indicating low viral load and little risk of transmitting COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , COVID-19/diagnosis , COVID-19 Testing , Humans , Nasopharynx , Polymerase Chain Reaction , Sensitivity and Specificity , Turbinates
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