scholarly journals Evaluation of rapid SARS-CoV-2 antigen tests, AFIAS COVID-19 Ag and ichroma COVID-19 Ag, with serial nasopharyngeal specimens from COVID-19 patients

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249972
Author(s):  
Oh Joo Kweon ◽  
Yong Kwan Lim ◽  
Hye Ryoun Kim ◽  
Yoojeong Choi ◽  
Min-Chul Kim ◽  
...  
Keyword(s):  
Early Detection ◽  
Point Of Care ◽  
Molecular Testing ◽  
Test Results ◽  
Molecular Test ◽  
Viral Loads ◽  
Molecular Tests ◽  
Antigen Tests ◽  
Diagnostic Sensitivity And Specificity ◽  
Negative Controls

We evaluated the diagnostic accuracy of two newly developed, point-of-care, rapid antigen tests (RATs) for detecting SARS-CoV-2, the AFIAS COVID-19 Ag and the ichromaTM COVID-19 Ag, and investigated antigen kinetics. A total of 200 serially collected nasopharyngeal (NP) specimens from 38 COVID-19 patients and 122 specimens from negative controls were analyzed. Diagnostic sensitivity and specificity were assessed in comparison to molecular test results and subdivided according to targeted genes (E, RdRP, and N) and days post-symptom onset (PSO). For the kinetics evaluation, cut-off-indices from serial NP specimens were used according to the number of days PSO. Both RATs showed sensitivity of 91.3‒100% for specimens with cycle threshold (Ct) < 25. The specificity of AFIAS was 98.7‒98.9% and that of ichromaTM was 100.0%. The kappa values of AFIAS and ichromaTM for the molecular testing of specimens with Ct < 25 (RdRP) were 0.97 and 1.00, respectively. The sensitivity of AFIAS and ichromaTM for all genes was lower for specimens collected at 8‒14 PSO than for those collected before 7-days PSO. The kinetics profiles showed that antigen levels gradually decreased from ≤ 7-days PSO to > 22-days PSO. Both RATs showed excellent specificity and acceptable sensitivity for NP specimens with higher viral loads and for specimens collected within 7-days PSO. Hence, they have the potential to become useful tools for the early detection of SARS-CoV-2. However, because of concerns about false negativity, RATs should be used in conjunction with molecular tests.

What Every Neuropathologist Needs to Know: Practical Aspects and Pitfalls in Molecular Diagnosis of Brain Tumors

2021 ◽  
Author(s):  
J Stephen Nix ◽  
Cristiane M Ida
Keyword(s):  
Brain Tumors ◽  
Molecular Diagnosis ◽  
Genetic Alterations ◽  
Genetic Alteration ◽  
Molecular Testing ◽  
Test Results ◽  
Molecular Test ◽  
Molecular Tests ◽  
Clinically Significant ◽  
Selection Of

Abstract Molecular testing has become part of the routine diagnostic workup of brain tumors after the implementation of integrated histomolecular diagnoses in the 2016 WHO classification update. It is important for every neuropathologist to be aware of practical preanalytical, analytical, and postanalytical factors that impact the performance and interpretation of molecular tests. Prior to testing, optimizing tumor purity and tumor amount increases the ability of the molecular test to detect the genetic alteration of interest. Recognizing basic molecular testing platform analytical characteristics allows selection of the optimal platform for each clinicopathological scenario. Finally, postanalytical considerations to properly interpret molecular test results include understanding the clinical significance of the detected genetic alteration, recognizing that detected clinically significant genetic alterations are occasionally germline constitutional rather than somatic tumor-specific, and being cognizant that recommended and commonly used genetic nomenclature may differ. Potential pitfalls in brain tumor molecular diagnosis are also discussed.

Clinical Requests for Molecular Tests: The 3-Step Evidence Check

2012 ◽  
Vol 136 (12) ◽  
pp. 1585-1592 ◽  
Author(s):  
Alexis B Carter
Keyword(s):  
Laboratory Tests ◽  
Digital Age ◽  
Molecular Methods ◽  
Molecular Medicine ◽  
Molecular Testing ◽  
Reference Laboratory ◽  
New Wave ◽  
Molecular Test ◽  
Molecular Tests ◽  
The Individual

Laboratory tests performed by molecular methods are increasing in volume and complexity at an unprecedented rate. Molecular tests have a broad set of applications, and most recently have been advocated as the mechanism by which providers can further tailor treatments to the individual patient. As the momentum behind molecular testing continues to increase, pathology practices may find themselves unprepared for the new wave of molecular medicine. This special article has been developed in an effort to provide pathologists who have limited molecular training with a simple and quick algorithm for determining whether a requested molecular test is appropriate for a patient. Additional recommendations for a more intensive and proactive review and management of molecular requests also are included. The principles discussed can easily be applied to requests for any test, including those not using molecular methods, which would be sent to an outside reference laboratory. This special article was developed from a Webinar for the College of American Pathologists targeting education for pathologists about the transformation of pathology practice in the new molecular and digital age.

scholarly journals Decreased Sensitivity of the Serological Detection of Feline Immunodeficiency Virus Infection Potentially Due to Imported Genetic Variants

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 697 ◽  
Author(s):  
Julia Frankenfeld ◽  
Theres Meili ◽  
Marina Meli ◽  
Barbara Riond ◽  
A. Helfer-Hungerbuehler ◽  
...  
Keyword(s):  
Feline Immunodeficiency Virus ◽  
Point Of Care ◽  
Diagnostic Efficiency ◽  
Rt Pcr ◽  
Viral Loads ◽  
Feline Immunodeficiency Virus Infection ◽  
Immunodeficiency Virus ◽  
Screening Assays ◽  
Diagnostic Sensitivity And Specificity ◽  
Point Of Care Tests

Feline immunodeficiency virus (FIV) is a lentivirus of domestic cats worldwide. Diagnosis usually relies on antibody screening by point-of-care tests (POCT), e.g., by enzyme-linked immunosorbent assays (ELISA), and confirmation using Western blot (WB). We increasingly observed ELISA-negative, WB-positive samples and aimed to substantiate these observations using 1194 serum/plasma samples collected from 1998 to 2019 primarily from FIV-suspect cats. While 441 samples tested positive and 375 tested negative by ELISA and WB, 81 samples had discordant results: 70 were false ELISA-negative (WB-positive) and 11 were false ELISA-positive (WB-negative); 297 ambiguous results were not analyzed further. The diagnostic sensitivity and specificity of the ELISA (82% and 91%, respectively) were lower than those reported in 1995 (98% and 97%, respectively). The diagnostic efficiency was reduced from 97% to 86%. False ELISA-negative samples originated mainly (54%) from Switzerland (1995: 0%). Sixty-four false ELISA-negative samples were available for POCT (SNAPTM/WITNESSR): five were POCT-positive. FIV RT-PCR was positive for two of these samples and was weakly positive for two ELISA- and POCT-negative samples. Low viral loads prohibited sequencing. Our results suggest that FIV diagnosis has become more challenging, probably due to increasing travel by cats and the introduction of new FIV isolates not recognized by screening assays.

Outcomes of Indeterminate Thyroid Nodules Managed Nonoperatively after Molecular Testing

2020 ◽  
Author(s):  
Catherine Y Zhu ◽  
Ines Donangelo ◽  
Deepashree Gupta ◽  
Dalena T Nguyen ◽  
Joana E Ochoa ◽  
...  
Keyword(s):  
Thyroid Nodules ◽  
False Negative ◽  
False Negative Rate ◽  
Molecular Testing ◽  
Test Results ◽  
Molecular Test ◽  
Negative Rate ◽  
Indeterminate Nodules

Abstract Context Molecular testing to refine the diagnosis of cytologically indeterminate thyroid nodules has become increasingly popular, but data on long-term durability of test results and the rate of delayed operation are limited. Objective Determine the delayed rate of surgical resection in indeterminate nodules with benign/negative molecular testing and the risk of false-negative molecular test results. Design Prospective follow-up of the Gene Expression Classifier vs Targeted Next-Generation Sequencing in the Management of Indeterminate Thyroid Nodules randomized controlled trial comparing the diagnostic test performance of Afirma Gene Expression Classifier and ThyroSeq v2. Setting University of California, Los Angeles. Participants Patients who underwent thyroid biopsy with indeterminate (Bethesda III/IV) cytology (April 2016 to July 2017). Intervention Ultrasound surveillance. Main Outcome Measure False-negative rate of molecular testing. Results Of 95 indeterminate nodules with negative/benign molecular test results, 12 nodules underwent immediate resection (11 benign nodules, 1 noninvasive follicular thyroid neoplasm nodule with papillary-like nuclear features). Nonoperative management was pursued for 83 (87.4%) nodules. The median surveillance was 26.7 months. Ten nodules were resected during surveillance and malignancy was identified in 4 nodules (overall false-negative rate of 5.8%). In the 4 malignant nodules that underwent delayed operation, surgery was prompted by sonographic changes during surveillance. Conclusions The majority of indeterminate nodules with negative molecular testing have a stable clinical course over 3 years of follow-up, but our finding of a 6% false-negative rate highlights the importance of continuing sonographic surveillance. Long-term studies are needed to determine the optimal length of follow-up.

scholarly journals Evaluation of Rapid Antigen Tests Using Nasal Samples to Diagnose SARS-CoV-2 in Symptomatic Patients

2022 ◽  
Vol 9 ◽  
Author(s):  
Manaf Alqahtani ◽  
Abdulkarim Abdulrahman ◽  
Fathi Mustafa ◽  
Abdulla I. Alawadhi ◽  
Batool Alalawi ◽  
...  
Keyword(s):  
Early Detection ◽  
Nasal Swab ◽  
Cost Effective ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Rapid Antigen Detection Test ◽  
Viral Loads ◽  
Antigen Tests ◽  
Stratified Analysis ◽  
Potential Use

IntroductionThe best way to mitigate an outbreak besides mass vaccination is via early detection and isolation of infected cases. As such, a rapid, cost-effective test for the early detection of COVID-19 is required.MethodsThe study included 4,183 mildly symptomatic patients. A nasal and nasopharyngeal sample obtained from each patient was analyzed to determine the diagnostic ability of the rapid antigen detection test (RADT, nasal swab) in comparison with the current gold-standard (RT-PCR, nasopharyngeal swab).ResultsThe calculated sensitivity and specificity of the RADT was 82.1 and 99.1%, respectively. Kappa's coefficient of agreement between the RADT and RT-PCR was 0.859 (p &lt; 0.001). Stratified analysis showed that the sensitivity of the RADT improved significantly when lowering the cut-off RT-PCR Ct value to 24.ConclusionOur study's results support the potential use of nasal swab RADT as a screening tool in mildly symptomatic patients, especially in patients with higher viral loads.

scholarly journals Salivary SARS-CoV-2 antigen rapid detection: a prospective cohort study

2020 ◽  
Author(s):  
Daniela Basso ◽  
Ada Aita ◽  
Andrea Padoan ◽  
Chiara Cosma ◽  
Filippo Navaglia ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Point Of Care ◽  
High Viral Load ◽  
Antigen Detection ◽  
Molecular Testing ◽  
Pharyngeal Swab ◽  
Viral Loads ◽  
Optimal Value ◽  
Antigen Testing ◽  
Limited Sensitivity

AbstractBackgroundSARS-CoV-2 quick testing and reporting are now considered relevant for the containment of new pandemic waves. Antigen testing in self-collected saliva might be useful. We compared the diagnostic performance of salivary and naso-pharyngeal swab (NPS) SARS-CoV-2 antigen detection by a rapid chemiluminescent assay (CLEIA) and two different point-of-care (POC) immunochromatographic assays, with that of molecular testing.Methods234 patients were prospectively enrolled. Paired self-collected saliva (Salivette) and NPS were obtained to perform rRT-PCR, chemiluminescent (Lumipulse G) and POC (NPS: Fujirebio and Abbott; saliva: Fujirebio) for SARS-CoV-2 antigen detection.ResultsThe overall agreement between NPS and saliva rRT-PCR was 78.7%, reaching 91.7% at the first week from symptoms onset. SARS-CoV-2 CLEIA antigen was highly accurate in distinguishing between positive and negative NPS (ROC-AUC=0.939, 95%CI:0.903-0.977), with 81.6% sensitivity and 93.8% specificity. This assay on saliva had an overall good accuracy (ROC-AUC=0.805, 95%CI:0.740-0.870), reaching the optimal value within 7 days from symptom onset (Sensitivity: 72%; Specificity: 97%). POC antigen in saliva had a very limited sensitivity (13%), performing better in NPS (Sensitivity: 48% and 66%; Specificity: 100% and 99% for Espline and Abbott respectively), depending on viral loads.ConclusionsSelf-collected saliva is a valid alternative to NPS for SARS-CoV-2 detection not only by molecular, but also by CLEIA antigen testing, for which the highest diagnostic accuracy was achieved in the first week from symptom onset. Saliva is not suitable for POC, although the accuracy of these tests appears satisfactory for NPS with high viral load.

scholarly journals ImplemeNting SARS-CoV-2 Rapid antigen testing in the Emergency wArd of a Swiss univErsity hospital: the INCREASE study

2021 ◽  
Author(s):  
Giorgia Caruana ◽  
Antony Croxatto ◽  
Eleftheria Kampouri ◽  
Antonios Kritikos ◽  
Onya Opota ◽  
...  
Keyword(s):  
University Hospital ◽  
Lower Sensitivity ◽  
Clinical Settings ◽  
Rt Pcr ◽  
Emergency Ward ◽  
Viral Loads ◽  
Molecular Tests ◽  
One Step ◽  
Antigen Tests ◽  
Second Wave

BackgroundWhile facing a second wave in SARS-CoV-2 pandemic, in November 2020 the Swiss Federal Office of Public Health (FOPH) authorized the use of rapid antigen tests (RATs) in addition to the gold-standard reverse transcription-polymerase chain reaction (RT-PCR).MethodsWe implemented the use of RAT in the emergency ward of our university hospital for rapid patients’ triaging and compared performances of four different antigen tests. All results were compared to SARS-CoV-2 specific RT-PCR (reference standard).ResultsTriaging patients using RAT in association with RT-PCR allowed us to isolate promptly positive patients and to save resources, in a context of rapid RT-PCR reagents shortage. Among 532 patients with valid results, overall sensitivities were 48.3% for One Step Exdia and 41.2% for Standard Q®, Panbio−and BD Veritor. All four antigen tests exhibited specificity above 99%. Sensitivity increased up to 74.6%, 66.2%, 66.2% and 64.8% for One Step Exdia, Standard Q, Panbio, and BD Veritor respectively, when considering viral loads above 105copies/ml, up to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/ml and 100% (for all tests) when considering viral loads above 107 copies/ml. Sensitivity was significantly higher for patients presenting with symptoms onset within 4 days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with evolution of symptoms for more than 4 days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Sensitivities of all RAT assays were of only 33% among hospitalized patients without COVID-19 symptoms.ConclusionRAT might represent a useful epidemiological resource in selected clinical settings as a complementary tool to the molecular tests for rapid patients triaging, but the lower sensitivity compared to RT-PCR, especially in late presenters and subjects without COVID-19 symptoms, must be taken into account in order to correctly use RAT for triaging.

QUALITY OF LIFE FOLLOWING MOLECULAR MARKER TESTING FOR INDETERMINATE THYROID NODULES

2020 ◽  
Vol 26 (9) ◽  
pp. 960-966
Author(s):  
Calvin W. Wong ◽  
Max A. Schumm ◽  
Catherine Y. Zhu ◽  
Chi-Hong Tseng ◽  
Aarthi Arasu ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Thyroid Nodules ◽  
Needle Aspiration ◽  
Patient Reported Outcome ◽  
Molecular Testing ◽  
Test Results ◽  
Molecular Test ◽  
Fine Needle ◽  
Patient Reported

Objective: Thyroid cancer has a disproportionately negative effect on the quality of life (QOL) compared to malignancies with a worse prognosis. The QOL of patients with indeterminate thyroid nodules has not been previously evaluated. We aimed to assess the impact of molecular test results on the QOL of patients with indeterminate thyroid nodules. Methods: A short version of the Thyroid-Related Patient-Reported Outcome (ThyPro-39) was used to assess the QOL of patients who underwent thyroid fine needle aspiration (FNA) biopsy throughout UCLA Health from May, 2016, to June, 2017. All patients with indeterminate biopsy results underwent molecular testing with either Afirma Gene Expression Classifier or ThyroSeq v2 at the time of the initial biopsy. The QOL associated with symptoms of goiter, anxiety, depression, and impaired daily life were analyzed. Results: Of 825 consented patients, 366 completed the assessment (44.4% response rate). FNA results included 76% benign, 7% malignant, and 17% indeterminate. There were no differences in QOL between patients with a benign FNA and patients with an indeterminate result with benign molecular testing. In patients with an indeterminate FNA, symptoms of goiter (20.5 versus 10.4; P = .033) and depression (33.3 versus 21.0; P = .026) were worse for patients with suspicious versus benign molecular test results; however, no significant differences were observed in anxiety or impaired daily life. Conclusion: A benign molecular test result may provide reassurance for patients with indeterminate thyroid nodules that the risk of malignancy is low. Long-term follow-up is necessary to determine if benign molecular test results maintain improved QOL. Abbreviations: FNA = fine needle aspiration; GEC = gene expression classifier; QOL = quality of life; ThyPro-39 = thyroid-related patient-reported outcome; TSH = thyroid-stimulating hormone

scholarly journals Accuracy of a rapid molecular test for tuberculosis in sputum samples, bronchoalveolar lavage fluid, and tracheal aspirate obtained from patients with suspected pulmonary tuberculosis at a tertiary referral hospital

2019 ◽  
Vol 45 (2) ◽  
Author(s):  
Tatiane Maria da Silva ◽  
Valéria Martins Soares ◽  
Mariana Gontijo Ramos ◽  
Adriana dos Santos
Keyword(s):  
Clinical Status ◽  
Public Health Problem ◽  
Tracheal Aspirate ◽  
Lavage Fluid ◽  
Major Public Health Problem ◽  
Test Results ◽  
Molecular Test ◽  
Tertiary Referral Hospital ◽  
Molecular Tests ◽  
Belo Horizonte

ABSTRACT Tuberculosis continues to be a major public health problem worldwide. The aim of the present study was to evaluate the accuracy of the Xpert MTB/RIF rapid molecular test for tuberculosis, using pulmonary samples obtained from patients treated at the Júlia Kubitschek Hospital, which is operated by the Hospital Foundation of the State of Minas Gerais, in the city of Belo Horizonte, Brazil. This was a retrospective study comparing the Xpert MTB/RIF test results with those of standard culture for Mycobacterium tuberculosis and phenotypic susceptibility tests. Although the Xpert MTB/RIF test showed high accuracy for the detection of M. tuberculosis and its resistance to rifampin, attention must be given to the clinical status of the patient, in relation to the test results, as well as to the limitations of molecular tests.

scholarly journals Predictive molecular pathology in the time of coronavirus disease (COVID-19) in Europe

2020 ◽  
pp. jclinpath-2020-206957 ◽  
Author(s):  
Umberto Malapelle ◽  
Pasquale Pisapia ◽  
Antonino Iaccarino ◽  
Massimo Barberis ◽  
Claudio Bellevicine ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Liquid Biopsy ◽  
Predictive Biomarker ◽  
Turnaround Time ◽  
Molecular Testing ◽  
Advanced Stage ◽  
Molecular Test ◽  
Rt Pcr ◽  
Molecular Tests ◽  
Advanced Stage Lung Cancer

AimsLung cancer predictive biomarker testing is essential to select advanced-stage patients for targeted treatments and should be carried out without delays even during health emergencies, such as the coronavirus (COVID-19) outbreak.MethodsFifteen molecular laboratories from seven different European countries compared 4 weeks of national lockdown to a corresponding period in 2019, in terms of tissue and/or plasma-based molecular test workload, analytical platforms adopted, number of cases undergoing programmed death-ligand1 (PD-L1) expression assessment and DNA-based molecular tests turnaround time.ResultsIn most laboratories (80.0%), tissue-based molecular test workload was reduced. In 40.0% of laboratories (6/15), the decrease was >25%, and in one, reduction was as high as 80.0%. In this instance, a concomitant increase in liquid biopsy was reported (60.0%). Remarkably, in 33.3% of the laboratories, real-time PCR (RT-PCR)-based methodologies increased, whereas highly multiplexing assays approaches decreased. Most laboratories (88.9%) did not report significant variations in PD-L1 volume testing.ConclusionsThe workload of molecular testing for patients with advanced-stage lung cancer during the lockdown showed little variations. Local strategies to overcome health emergency-related issues included the preference for RT-PCR tissue-based testing methodologies and, occasionally, for liquid biopsy.

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