The diagnostic accuracy of RT-PCR from self-collected saliva versus nasopharyngeal sampling

AbstractA novel zoonotic coronavirus outbreak is spreading all over the world. This pandemic disease has now been defined as novel coronavirus disease 2019 (COVID-19), and is sustained by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As the current gold standard for the etiological diagnosis of SARS-CoV-2 infection is (real time) reverse transcription polymerase chain reaction (rRT-PCR) on respiratory tract specimens, the diagnostic accuracy of this technique shall be considered a foremost prerequisite. Overall, potential RT-PCR vulnerabilities include general preanalytical issues such as identification problems, inadequate procedures for collection, handling, transport and storage of the swabs, collection of inappropriate or inadequate material (for quality or volume), presence of interfering substances, manual errors, as well as specific aspects such as sample contamination and testing patients receiving antiretroviral therapy. Some analytical problems may also contribute to jeopardize the diagnostic accuracy, including testing outside the diagnostic window, active viral recombination, use of inadequately validated assays, insufficient harmonization, instrument malfunctioning, along with other specific technical issues. Some practical indications can hence be identified for minimizing the risk of diagnostic errors, encompassing the improvement of diagnostic accuracy by combining clinical evidence with results of chest computed tomography (CT) and RT-PCR, interpretation of RT-PCR results according to epidemiologic, clinical and radiological factors, recollection and testing of upper (or lower) respiratory specimens in patients with negative RT-PCR test results and high suspicion or probability of infection, dissemination of clear instructions for specimen (especially swab) collection, management and storage, together with refinement of molecular target(s) and thorough compliance with analytical procedures, including quality assurance.

Download Full-text

Letter to the Editor regarding Leber W, Lammel O, Siebenhofer A, Redlberger-Fritz M, Panovska-Griffiths J, Czypionka T. Comparing the diagnostic accuracy of point-of-care lateral flow antigen testing for SARS-CoV-2 with RT-PCR in primary care (REAP-2)

EClinicalMedicine ◽

10.1016/j.eclinm.2021.101106 ◽

2021 ◽

Vol 40 ◽

pp. 101106

Author(s):

Jonathan J Deeks

Keyword(s):

Primary Care ◽

Diagnostic Accuracy ◽

Point Of Care ◽

Lateral Flow ◽

Rt Pcr ◽

Letter To The Editor ◽

Antigen Testing

Download Full-text

Diagnostic Accuracy of Rapid Antigen Detection Tests for Respiratory Syncytial Virus Infection: Systematic Review and Meta-analysis

Journal of Clinical Microbiology ◽

10.1128/jcm.01816-15 ◽

2015 ◽

Vol 53 (12) ◽

pp. 3738-3749 ◽

Cited By ~ 87

Author(s):

Caroline Chartrand ◽

Nicolas Tremblay ◽

Christian Renaud ◽

Jesse Papenburg

Keyword(s):

Systematic Review ◽

Respiratory Syncytial Virus ◽

Diagnostic Accuracy ◽

Sensitivity And Specificity ◽

Meta Analysis ◽

Reference Standard ◽

Rt Pcr ◽

Test Sensitivity ◽

Subgroup Analyses ◽

Syncytial Virus

Respiratory syncytial virus (RSV) rapid antigen detection tests (RADT) are extensively used in clinical laboratories. We performed a systematic review and meta-analysis to evaluate the accuracy of RADTs for diagnosis of RSV infection and to determine factors associated with accuracy estimates. We searched EMBASE and PubMed for diagnostic-accuracy studies of commercialized RSV RADTs. Studies reporting sensitivity and specificity data compared to a reference standard (reverse transcriptase PCR [RT-PCR], immunofluorescence, or viral culture) were considered. Two reviewers independently extracted data on study characteristics, diagnostic-accuracy estimates, and study quality. Accuracy estimates were pooled using bivariate random-effects regression models. Heterogeneity was investigated with prespecified subgroup analyses. Seventy-one articles met inclusion criteria. Overall, RSV RADT pooled sensitivity and specificity were 80% (95% confidence interval [CI], 76% to 83%) and 97% (95% CI, 96% to 98%), respectively. Positive- and negative-likelihood ratios were 25.5 (95% CI, 18.3 to 35.5) and 0.21 (95% CI, 0.18 to 0.24), respectively. Sensitivity was higher in children (81% [95% CI, 78%, 84%]) than in adults (29% [95% CI, 11% to 48%]). Because of this disparity, further subgroup analyses were restricted to pediatric data (63 studies). Test sensitivity was poorest using RT-PCR as a reference standard and highest using immunofluorescence (74% versus 88%;P< 0.001). Industry-sponsored studies reported significantly higher sensitivity (87% versus 78%;P= 0.01). Our results suggest that the poor sensitivity of RSV RADTs in adults may preclude their use in this population. Furthermore, industry-sponsored studies and those that did not use RT-PCR as a reference standard likely overestimated test sensitivity.

Download Full-text

High Resolution CHEST CT(HRCT) Evaluation in Patients Hospitalized with COVID-19 Infection

10.1101/2020.05.26.20114082 ◽

2020 ◽

Author(s):

Maulin Patel ◽

Junad Chowdhury ◽

Matthew Zheng ◽

Osheen Abramian ◽

Steven Verga ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

High Resolution ◽

Diagnostic Accuracy ◽

Reverse Transcriptase ◽

Retrospective Analysis ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Chain Reaction ◽

Bottom Line ◽

Polymerase Chain

AbstractIntroductionCurrently the main diagnostic modality for COVID-19 (Coronavirus disease-2019) is reverse transcriptase polymerase chain reaction (RT-PCR) via nasopharyngeal swab which has high false negative rates. We evaluated the performance of high-resolution computed tomography (HRCT) imaging in the diagnosis of suspected COVID-19 infection compared to RT-PCR nasopharyngeal swab alone in patients hospitalized for suspected COVID-19 infection.MethodsThis was a retrospective analysis of 324 consecutive patients admitted to Temple University Hospital. All hospitalized patients who had RT-PCR testing and HRCT were included in the study. HRCTs were classified as Category 1, 2 or 3. Patients were then divided into four groups based on HRCT category and RT-PCR swab results for analysis.ResultsThe average age of patients was 59.4 (±15.2) years and 123 (38.9%) were female. Predominant ethnicity was African American 148 (46.11%). 161 patients tested positive by RT-PCR, while 41 tested positive by HRCT. 167 (52.02%) had category 1 scan, 63 (19.63%) had category 2 scan and 91 (28.35%) had category 3 HRCT scans. There was substantial agreement between our radiologists for HRCT classification (κ = 0.64). Sensitivity and specificity of HRCT classification system was 77.6 and 73.7 respectively. Ferritin, LDH, AST and ALT were higher in Group 1 and D-dimers levels was higher in Group 3; differences however were not statistically significant.ConclusionDue to its high infectivity and asymptomatic transmission, until a highly sensitive and specific COVID-19 test is developed, HRCT should be incorporated into the assessment of patients who are hospitalized with suspected COVID-19.Key PointsKey QuestionCan High Resolution CT chest (HRCT) improve diagnostic accuracy of current Nasopharyngeal swab in suspected COVID-19 patients?Bottom LineIn this retrospective analysis, our novel HRCT classification identified 20% of all COVID-19 patients who had negative nasopharyngeal reverse transcriptase polymerase chain reaction (RT-PCR) tests but had HRCT findings consistent with COVID-19 pneumonia. These patients were ruled out for other infections and laboratory markers were similar to other RT-PCR positive patientsWhy Read onOur new HRCT classification when combined with RT-PCR can improve diagnostic accuracy while promptly improving triaging in COVID-19 patients.

Download Full-text

Diagnostic accuracy estimates for COVID-19 RT-PCR and Lateral flow immunoassay tests with Bayesian latent class models

10.21203/rs.3.rs-33243/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Polychronis Kostoulas ◽

Paolo Eusebi ◽

Sonja Hartnack

Keyword(s):

Diagnostic Accuracy ◽

Symptom Onset ◽

Latent Class ◽

Reference Method ◽

Latent Class Models ◽

Lateral Flow ◽

Lateral Flow Immunoassay ◽

Rt Pcr ◽

The Cross ◽

Class Models

Abstract The objective of this work was to estimate the diagnostic accuracy of RT-PCR and Lateral flow immunoassay tests (LFIA) for COVID-19, depending on the time post symptom onset. Based on the cross-classified results of RT-PCR and LFIA, we used Bayesian latent class models (BLCMs), which do not require a gold standard for the evaluation of diagnostics. Data were extracted from studies that evaluated LFIA (IgG and/or IgM) assays using RT-PCR as the reference method. The cross-classified results of LFIA and RT-PCR were analysed separately for the first, second and third week post symptom onset. The SeRT-PCR was 0.695 (95% probability intervals: 0.563; 0.837) for the first week and remained similar for the second and the third week. The SeIgG/M was 0.318 (0.229; 0.416) for the first week and increased steadily. It was 0.755 (0.673; 0.829) and 0.927 (0.881; 0.965) for the second and third week, respectively. Both tests had a high to absolute Sp, with point median estimates for SpRT-PCR being consistently higher. SpRT-PCR was 0.990 (0.980; 0.998) for the first week. The corresponding value for SpIgG/M was 0.962 (0.905; 0.998). Further, Sp estimates for each test did not differ between weeks. BLCMs provide a valid and efficient alternative for evaluating the rapidly evolving diagnostics for COVID-19, under various clinical settings and for different risk profiles.

Download Full-text

Diagnostic accuracy and utility of SARS-CoV-2 antigen lateral flow assays in medical admissions with possible COVID-19

10.1101/2021.01.27.21250428 ◽

2021 ◽

Author(s):

Hamish Houston ◽

Ankur Gupta-Wright ◽

Edward Toke-Bjolgerud ◽

James Biggin-Lamming ◽

Laurence John

Keyword(s):

Diagnostic Accuracy ◽

Hospital Admissions ◽

Case Definition ◽

Acute Hospital ◽

Lateral Flow ◽

Rt Pcr ◽

Lateral Flow Assays ◽

Qualitative Test ◽

The Uk

AbstractWe evaluated diagnostic accuracy of the Innova SARS-CoV-2 Antigen Rapid Qualitative Test compared to SARS-CoV-2 RT-PCR from nasopharyngeal swabs in adult admissions who met the COVID-19 case definition at a busy acute hospital in the UK. We found the Innova SARS-CoV-2 Antigen Rapid Qualitative Test had a good specificity in patients with symptoms of COVID-19 presenting to hospital. The Innova LFA can be used to rapidly identify COVID-19 cases amongst hospital admissions meeting the COVID-19 case definition, allowing patients to be allocated to COVID-19 cohort areas.

Download Full-text

Diagnostic accuracy of two commercial SARS-CoV-2 antigen-detecting rapid tests at the point of care in community-based testing centers

PLoS ONE ◽

10.1371/journal.pone.0248921 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248921

Author(s):

Alice Berger ◽

Marie Therese Ngo Nsoga ◽

Francisco Javier Perez-Rodriguez ◽

Yasmine Abi Aad ◽

Pascale Sattonnet-Roche ◽

...

Keyword(s):

Diagnostic Accuracy ◽

Point Of Care ◽

Rapid Test ◽

Diagnostic Value ◽

Ease Of Use ◽

Lower Sensitivity ◽

Rt Pcr ◽

Test Device ◽

Community Based ◽

Rapid Tests

Objectives Determine the diagnostic accuracy of two antigen-detecting rapid diagnostic tests (Ag-RDT) for SARS-CoV-2 at the point of care and define individuals’ characteristics providing best performance. Methods We performed a prospective, single-center, point of care validation of two Ag-RDT in comparison to RT-PCR on nasopharyngeal swabs. Results Between October 9th and 23rd, 2020, 1064 participants were enrolled. The PanbioTM Covid-19 Ag Rapid Test device (Abbott) was validated in 535 participants, with 106 positive Ag-RDT results out of 124 positive RT-PCR individuals, yielding a sensitivity of 85.5% (95% CI: 78.0–91.2). Specificity was 100.0% (95% CI: 99.1–100) in 411 RT-PCR negative individuals. The Standard Q Ag-RDT (SD Biosensor, Roche) was validated in 529 participants, with 170 positive Ag-RDT results out of 191 positive RT-PCR individuals, yielding a sensitivity of 89.0% (95%CI: 83.7–93.1). One false positive result was obtained in 338 RT-PCR negative individuals, yielding a specificity of 99.7% (95%CI: 98.4–100). For individuals presenting with fever 1–5 days post symptom onset, combined Ag-RDT sensitivity was above 95%. Lower sensitivity of 88.2% was seen on the same day of symptom development (day 0). Conclusions We provide an independent validation of two widely available commercial Ag-RDTs, both meeting WHO criteria of ≥80% sensitivity and ≥97% specificity. Although less sensitive than RT-PCR, these assays could be beneficial due to their rapid results, ease of use, and independence from existing laboratory structures. Testing criteria focusing on patients with typical symptoms in their early symptomatic period onset could further increase diagnostic value.

Download Full-text

RT-PCR Versus Computed Tomography in Early Symptoms of COVID-19: A Systematic Review of Diagnostic Accuracy

SSRN Electronic Journal ◽

10.2139/ssrn.3588538 ◽

2020 ◽

Author(s):

Márcio Duarte ◽

Lucas Ribeiro dos Santos ◽

Andrea Carla de Souza Contenças ◽

Wagner Iared ◽

Maria Stella Peccin

Keyword(s):

Computed Tomography ◽

Systematic Review ◽

Diagnostic Accuracy ◽

Rt Pcr ◽

Early Symptoms

Download Full-text