scholarly journals The Effect of Sample Site, Illness Duration, and the Presence of Pneumonia on the Detection of SARS-CoV-2 by Real-time Reverse Transcription PCR

2020 ◽  
Vol 7 (9) ◽  
Author(s):  
Stephanie Sutjipto ◽  
Pei Hua Lee ◽  
Jun Yang Tay ◽  
Shehara M Mendis ◽  
Mohammad Yazid Abdad ◽  
...  
Keyword(s):  
Real Time ◽  
Reverse Transcription ◽  
Sampling Site ◽  
Upper Respiratory Tract ◽  
Clinical Sensitivity ◽  
Illness Onset ◽  
Reverse Transcription Pcr ◽  
Upper Respiratory ◽  
Polymerase Chain ◽  
Respiratory Specimens

Abstract Background The performance of real-time reverse transcription polymerase chain reaction (rRT-PCR) for SARS-CoV-2 varies with sampling site(s), illness stage, and infection site. Methods Unilateral nasopharyngeal, nasal midturbinate, throat swabs, and saliva were simultaneously sampled for SARS-CoV-2 rRT-PCR from suspected or confirmed cases of COVID-19. True positives were defined as patients with at least 1 SARS-CoV-2 detected by rRT-PCR from any site on the evaluation day or at any time point thereafter, until discharge. Diagnostic performance was assessed and extrapolated for site combinations. Results We evaluated 105 patients; 73 had active SARS-CoV-2 infection. Overall, nasopharyngeal specimens had the highest clinical sensitivity at 85%, followed by throat, 80%, midturbinate, 62%, and saliva, 38%–52%. Clinical sensitivity for nasopharyngeal, throat, midturbinate, and saliva was 95%, 88%, 72%, and 44%–56%, respectively, if taken ≤7 days from onset of illness, and 70%, 67%, 47%, 28%–44% if >7 days of illness. Comparing patients with upper respiratory tract infection (URTI) vs pneumonia, clinical sensitivity for nasopharyngeal, throat, midturbinate, and saliva was 92% vs 70%, 88% vs 61%, 70% vs 44%, 43%–54% vs 26%–45%, respectively. A combination of nasopharyngeal plus throat or midturbinate plus throat specimen afforded overall clinical sensitivities of 89%–92%; this rose to 96% for persons with URTI and 98% for persons ≤7 days from illness onset. Conclusions Nasopharyngeal specimens, followed by throat specimens, offer the highest clinical sensitivity for COVID-19 diagnosis in early illness. Clinical sensitivity improves and is similar when either midturbinate or nasopharyngeal specimens are combined with throat specimens. Upper respiratory specimens perform poorly if taken after the first week of illness or if there is pneumonia.

scholarly journals Ultra-sensitive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antigen Detection for the Diagnosis of Coronavirus Disease 2019 (COVID-19) in Upper Respiratory Samples

2021 ◽  
Author(s):  
Hannah Wang ◽  
Catherine A Hogan ◽  
Michelle Verghese ◽  
Daniel Solis ◽  
Mamdouh Sibai ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Nucleic Acid ◽  
Severe Acute Respiratory Syndrome ◽  
High Throughput ◽  
Reverse Transcription ◽  
Chain Reaction ◽  
Antigen Assay ◽  
Upper Respiratory ◽  
Polymerase Chain ◽  
Respiratory Specimens

Abstract An ultra-sensitive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen assay (S-PLEX, MesoScale Diagnostics) was evaluated in 250 retrospective and 200 prospective upper respiratory specimens. In samples with cycle threshold <35, there was 95%–98% positive and 93%–96% negative percent agreement with reverse transcription-polymerase chain reaction. S-PLEX may provide a high-throughput alternative to nucleic acid-based testing for coronavirus disease 2019 (COVID-19) diagnosis.

scholarly journals Specific detection by real-time reverse-transcription PCR assays of a novel avian influenza A(H7N9) strain associated with human spillover infections in China

2013 ◽  
Vol 18 (16) ◽  
Author(s):  
V M Corman ◽  
M Eickmann ◽  
O Landt ◽  
T Bleicker ◽  
S Brünink ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Real Time ◽  
Reverse Transcription ◽  
Influenza A ◽  
Specific Detection ◽  
Validation Data ◽  
Reverse Transcription Pcr ◽  
Polymerase Chain ◽  
Pcr Assays ◽  
Positive Controls

In response to a recent outbreak in China, detection assays for a novel avian influenza A(H7N9) virus need to be implemented in a large number of public health laboratories. Here we present real-time reverse-transcription polymerase chain reaction (RT-PCR) assays for specific detection of this virus, along with clinical validation data and biologically-safe positive controls.

scholarly journals Declining SARS-CoV-2 PCR sensitivity with time and dependence on clinical features: consequences for control

2020 ◽  
Author(s):  
Barbara J.M. Bergmans ◽  
Chantal B.E.M. Reusken ◽  
Anne J.G. Van Oudheusden ◽  
Gert-Jan Godeke ◽  
Axel A. Bonacic Marinovic ◽  
...  
Keyword(s):  
Disease Severity ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Clinical Sensitivity ◽  
Health Measures ◽  
Supportive Role ◽  
Upper Respiratory ◽  
Polymerase Chain ◽  
Bayesian Statistical Modeling

Real-time reverse transcription-polymerase chain reaction (RT-PCR) on upper respiratory tract (URT) samples is the primary method to diagnose SARS-CoV-2 infections and guide public health measures, with a supportive role for serology. However, the clinical sensitivity of RT-PCR remains uncertain. In the present study, Bayesian statistical modeling was used to retrospectively determine the sensitivity of RT-PCR using SARS-CoV-2 serology in 644 COVID-19-suspected patients with varying degrees of disease severity and duration. The sensitivity of RT-PCR ranged between 79-95%; while increasing with disease severity, it decreased rapidly over time in mild COVID-19 cases. Negative URT RT-PCR results should therefore be interpreted in the context of clinical characteristics, especially with regard to containment of viral transmission based on the 'test, trace and isolate' principle.

1504: Molecular Diagnosis and Staging of Prostate Cancer Using Clusterin in Real Time Reverse Transcription Polymerase Chain Reaction (RT-PCR)

2006 ◽  
Vol 175 (4S) ◽  
pp. 485-486
Author(s):  
Sabarinath B. Nair ◽  
Christodoulos Pipinikas ◽  
Roger Kirby ◽  
Nick Carter ◽  
Christiane Fenske
Keyword(s):  
Prostate Cancer ◽  
Polymerase Chain Reaction ◽  
Real Time ◽  
Molecular Diagnosis ◽  
Reverse Transcription ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals Clinical evaluation of rapid point-of-care antigen tests for diagnosis of SARS-CoV-2 infection

2021 ◽  
Author(s):  
Johannes G. M. Koeleman ◽  
Henk Brand ◽  
Stijn J. de Man ◽  
David S. Y. Ong
Keyword(s):  
Health Care ◽  
Health Care Workers ◽  
Antigen Test ◽  
Duration Of Symptoms ◽  
Large Variability ◽  
Clinical Sensitivity ◽  
Care Workers ◽  
Upper Respiratory ◽  
Antigen Tests ◽  
Respiratory Specimens

AbstractThe RT-qPCR in respiratory specimens is the gold standard for diagnosing acute COVID-19 infections. However, this test takes considerable time before test results become available, thereby delaying patients from being diagnosed, treated, and isolated immediately. Rapid antigen tests could overcome this problem. In the first study, clinical performances of five rapid antigen tests were compared to RT-qPCR in upper respiratory specimens from 40 patients with positive and 40 with negative RTq-PCR results. In the second study, the rapid antigen test with one of the best test characteristics (Romed) was evaluated in a large prospective collection of upper respiratory specimens from 900 different COVID-19-suspected patients (300 emergency room patients, 300 nursing home patients, and 300 health care workers). Test specificities ranged from 87.5 to 100.0%, and test sensitivities from 55.0 to 80.0%. The clinical specificity of the Romed test was 99.8% (95% CI 98.9–100). Overall clinical sensitivity in the study population was 73.3% (95% CI 67.9–78.2), whereas sensitivity in the different patient groups varied from 65.3 to 86.7%. Sensitivity was 83.0 to 86.7% in patients with short duration of symptoms. In a population with a COVID-19 prevalence of 1%, the negative predictive value in all patients was 99.7%. There is a large variability in diagnostic performance between rapid antigen tests. The Romed rapid antigen test showed a good clinical performance in patients with high viral loads (RT-qPCR cycle threshold ≤30), which makes this antigen test suitable for rapid identification of COVID-19-infected health care workers and patients.

scholarly journals Is it enough for COVID-19 screening test? Limitation of swab test and general characteristics of mild symptom patients

2021 ◽  
Vol 104 (2) ◽  
pp. 003685042110261
Author(s):  
Sungwoo Choi ◽  
Hyo Jeong Choi ◽  
Ho Jung Kim
Keyword(s):  
Screening Test ◽  
Community Treatment ◽  
Upper Respiratory Tract ◽  
Test Results ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Positive Rate ◽  
Upper Respiratory ◽  
Polymerase Chain ◽  
Discharge Criteria

The most common method for SARS-CoV-2 testing is throat or nasal swabbing by real-time reverse transcription polymerase chain reaction (RT-PCR) assay. In South Korea, drive-through swab test is used for screening system and community treatment centers (CTCs), which admit and treat confirmed COVID-19 patients with mild symptoms, are being used. This retrospective study was conducted on patients admitted to a CTC on March 6, 2020. A total of 313 patients were admitted. The nasal and throat swabs were collected from the upper respiratory tract, and a sputum test was performed to obtain lower respiratory samples. The positive rate of the first set of test, sputum test was higher than that of the swab test ( p = 0.011). In the second set of test, 1 week after the first ones, the rate of positive swab tests was relatively high ( p = 0.026). In the first set of test, 66 of 152 (43.4%) patients showed 24-h consecutive negative swab test results, when the sputum test results were considered together, that number fell to 29 patients (19.1%) ( p < 0.001). Also, in the second set of test, 63 of 164 (38.4%) patients met the discharge criteria only when the swab test was considered; that number fell to 30 (18.3%) when the sputum test results were also considered ( p < 0.001). Using the swab test alone is insufficient for screening test and discharge decision. Patients who may have positive result in the sputum test can be missed.

scholarly journals Implementation of an in-house real-time reverse transcription-PCR assay to detect the emerging SARS-CoV-2 N501Y variants

2021 ◽  
pp. 104868
Author(s):  
Marielle BEDOTTO ◽  
Pierre-Edouard FOURNIER ◽  
Linda HOUHAMDI ◽  
Philippe COLSON ◽  
Didier RAOULT
Keyword(s):  
Real Time ◽  
Reverse Transcription ◽  
Pcr Assay ◽  
Reverse Transcription Pcr
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