Retrospective testing of respiratory specimens for COVID-19 to assess for earlier SARS-CoV-2 infections in Alberta, Canada

2020 ◽  
Vol COVID-19 ◽  
pp. CO1920200035
Author(s):  
Jamil N Kanji ◽  
Mathew Diggle ◽  
Dennis Bulman ◽  
Stacey Hume ◽  
Sherry Taylor ◽  
...  
Keyword(s):  
Retrospective Testing ◽  
Respiratory Specimens

scholarly journals Infectivity of healthcare workers diagnosed with coronavirus disease 2019 (COVID-19) approximately 2 weeks after onset of symptoms: A cross-sectional study

2021 ◽  
pp. 1-3
Author(s):  
Yves Longtin ◽  
Hugues Charest ◽  
Caroline Quach ◽  
Patrice Savard ◽  
Mariana Baz ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Healthcare Workers ◽  
Positive Culture ◽  
Cross Sectional Study ◽  
Sectional Study ◽  
Cross Sectional ◽  
Viral Shedding ◽  
Viral Culture ◽  
Respiratory Coronavirus ◽  
Respiratory Specimens

Abstract We performed viral culture of respiratory specimens in 118 severe acute respiratory coronavirus virus 2 (SARS-CoV-2)–infected healthcare workers (HCWs), ∼2 weeks after symptom onset. Only 1 HCW (0.8%) had a positive culture. No factors for prolonged viral shedding were identified. Infectivity is resolved in nearly all HCWs ∼2 weeks after symptom onset.

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 Assessment of SARS-CoV-2 infectivity of upper respiratory specimens from COVID-19 patients by virus isolation using VeroE6/TMPRSS2 cells

2021 ◽  
Vol 8 (1) ◽  
pp. e000830
Author(s):  
Souichi Yamada ◽  
Shuetsu Fukushi ◽  
Hitomi Kinoshita ◽  
Makoto Ohnishi ◽  
Tadaki Suzuki ◽  
...  
Keyword(s):  
Virus Isolation ◽  
Laboratory Diagnostics ◽  
Viral Isolation ◽  
Viral Loads ◽  
A Cell ◽  
Blind Passage ◽  
Upper Respiratory ◽  
Novel Coronavirus ◽  
Respiratory Specimens

BackgroundAn outbreak of novel coronavirus (SARS-CoV-2)-associated respiratory infectious diseases (COVID-19) emerged in 2019 and has spread rapidly in humans around the world. The demonstration of in vitro infectiousness of respiratory specimens is an informative surrogate for SARS-CoV-2 transmission from patients with COVID-19; accordingly, viral isolation assays in cell culture are an important aspect of laboratory diagnostics for COVID-19.MethodsWe developed a simple and rapid protocol for isolating SARS-CoV-2 from respiratory specimens using VeroE6/TMPRSS2 cells, a cell line that is highly susceptible to the virus. We also investigated a correlation between isolation of SARS-CoV-2 and viral load detected by real-time RT-PCR (rRT-PCR) using N2 primer/probe set that has been developed for testing of COVID-19 in Japan.ResultsThe SARS-CoV-2 isolation protocol did not require blind passage of inoculated cells and yielded the results of viral isolation within 7 days after inoculation. Specimens with cycle threshold (Ct) values of <20.2, determined by rRT-PCR, were predicted to be isolation-positive. On the other hand, 6.9% of specimens with Ct values >35 were virus isolation-positive, indicating that low viral loads (high Ct values) in upper respiratory specimens do not always indicate no risk of containing transmissible virus.ConclusionIn combination with rRT-PCR, the SARS-CoV-2 isolation protocol provides a means for assessing the potential risk of transmissible virus in upper respiratory specimens.

scholarly journals Lower Recovery of Nontuberculous Mycobacteria from Outdoor Hawai’i Environmental Water Biofilms Compared to Indoor Samples

2021 ◽  
Vol 9 (2) ◽  
pp. 224
Author(s):  
Ravleen Virdi ◽  
Melissa E. Lowe ◽  
Grant J. Norton ◽  
Stephanie N. Dawrs ◽  
Nabeeh A. Hasan ◽  
...  
Keyword(s):  
Pulmonary Disease ◽  
Environmental Samples ◽  
Nontuberculous Mycobacteria ◽  
Phylogenetic Analyses ◽  
Environmental Water ◽  
Rpob Gene ◽  
The United States ◽  
Indoor Environments ◽  
Respiratory Specimens ◽  
Rpob Sequence

Nontuberculous mycobacteria (NTM) are environmental organisms that can cause opportunistic pulmonary disease with species diversity showing significant regional variation. In the United States, Hawai’i shows the highest rate of NTM pulmonary disease. The need for improved understanding of NTM reservoirs led us to identify NTM from patient respiratory specimens and compare NTM diversity between outdoor and indoor locations in Hawai’i. A total of 545 water biofilm samples were collected from 357 unique locations across Kaua’i (n = 51), O’ahu (n = 202), Maui (n = 159), and Hawai’i Island (n = 133) and divided into outdoor (n = 179) or indoor (n = 366) categories. rpoB sequence analysis was used to determine NTM species and predictive modeling applied to develop NTM risk maps based on geographic characteristics between environments. M. chimaera was frequently identified from respiratory and environmental samples followed by M. chelonae and M. abscessus; yet significantly less NTM were consistently recovered from outdoor compared to indoor biofilms, as exemplified by showerhead biofilm samples. While the frequency of M. chimaera recovery was comparable between outdoor and indoor showerhead biofilms, phylogenetic analyses demonstrate similar rpoB gene sequences between all showerhead and respiratory M. chimaera isolates, supporting outdoor and indoor environments as possible sources for pulmonary M. chimaera infections.

scholarly journals Pooling of Upper Respiratory Specimens Using a SARS-CoV-2 Real-time RT-PCR Assay Authorized for Emergency Use in Low-Prevalence Populations for High-Throughput Testing

2020 ◽  
Vol 7 (11) ◽  
Author(s):  
Gwynngelle A Borillo ◽  
Ron M Kagan ◽  
Russell E Baumann ◽  
Boris M Fainstein ◽  
Lamela Umaru ◽  
...  
Keyword(s):  
Real Time ◽  
False Negative ◽  
False Negative Rate ◽  
Nucleic Acid Amplification ◽  
Rt Pcr ◽  
Pooled Testing ◽  
Negative Results ◽  
Single Positive ◽  
Upper Respiratory ◽  
Respiratory Specimens

Abstract Background Nucleic acid amplification testing is a critical tool for addressing the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Specimen pooling can increase throughput and conserve testing resources but requires validation to ensure that reduced sensitivity does not increase the false-negative rate. We evaluated the performance of a real-time reverse transcription polymerase chain reaction (RT-PCR) test authorized by the US Food and Drug Administration (FDA) for emergency use for pooled testing of upper respiratory specimens. Methods Positive specimens were selected from 3 prevalence groups, 1%–3%, &gt;3%–6%, and &gt;6%–10%. Positive percent agreement (PPA) was assessed by pooling single-positive specimens with 3 negative specimens; performance was assessed using Passing-Bablok regression. Additionally, we assessed the distributions of RT-PCR cycle threshold (Ct) values for 3091 positive specimens. Results PPA was 100% for the 101 pooled specimens. There was a linear relationship between Ct values for pooled and single-tested specimens (r = 0.96–0.99; slope ≈ 1). The mean pooled Ct shifts at 40 cycles were 2.38 and 1.90, respectively, for the N1 and N3 targets. The median Cts for 3091 positive specimens were 25.9 (N1) and 24.7 (N3). The percentage of positive specimens with Cts between 40 and the shifted Ct was 1.42% (N1) and 0.0% (N3). Conclusions Pooled and individual testing of specimens positive for SARS-CoV-2 demonstrated 100% agreement, which demonstrates the viability of pooled specimens for SARS-COV-2 testing using a dual-target RT-PCR system. Pooled specimen testing can help increase testing capacity for SARS-CoV-2 with a low risk of false-negative results.

scholarly journals First Evaluation of GenoType MTBDRplus2.0 Performed Directly on Respiratory Specimens in Central America

2016 ◽  
Vol 54 (10) ◽  
pp. 2498-2502 ◽  
Author(s):  
Fedora Lanzas ◽  
Thomas R. Ioerger ◽  
Harita Shah ◽  
William Acosta ◽  
Petros C. Karakousis
Keyword(s):  
Sensitivity And Specificity ◽  
Drug Susceptibility ◽  
Multidrug Resistant ◽  
Content Type ◽  
Appropriate Treatment ◽  
Nitrate Reductase Assay ◽  
Frequent Mutations ◽  
Version 2.0 ◽  
Probe Assay ◽  
Respiratory Specimens

The turnaround times for conventional methods used to detectMycobacterium tuberculosisin sputum samples and to obtain drug susceptibility information are long in many developing countries, including Panama, leading to delays in appropriate treatment initiation and continued transmission in the community. We evaluated the performance of a molecular line probe assay, the Genotype MTBDRplusversion 2.0 assay, in detectingM. tuberculosiscomplex directly in respiratory specimens from smear-positive tuberculosis cases from four different regions in Panama, as well as the most frequent mutations in genes conferring resistance to isoniazid (katGandinhA) and rifampin (rpoB). Our results were confirmed with the nitrate reductase assay and genomic sequencing.M. tuberculosiscomplex was detected by the Genotype MTBDRplus2.0 assay with 100% sensitivity and specificity. The sensitivity and specificity for rifampin resistance were 100% and 100%, respectively, and those for isoniazid resistance were 90.7% and 100%. Isoniazid monoresistance was detected in 5.2% of new cases. Genotype MTBDRplus2.0 is highly accurate in detectingM. tuberculosiscomplex in respiratory specimens and is able to discriminate isoniazid-monoresistant cases from multidrug-resistant cases within 2 days.

scholarly journals Evaluation of a Turbidimetric β-D-Glucan Test for Detection of Pneumocystis jirovecii Pneumonia

2018 ◽  
Vol 56 (7) ◽  
pp. e00286-18 ◽  
Author(s):  
Karl Dichtl ◽  
Ulrich Seybold ◽  
Johannes Wagener
Keyword(s):  
Sensitivity And Specificity ◽  
Test Performance ◽  
Laboratory Diagnosis ◽  
Turnover Time ◽  
Pneumocystis Jirovecii ◽  
Pneumocystis Jirovecii Pneumonia ◽  
Content Type ◽  
Increased Risk ◽  
Turbidimetric Assay ◽  
Respiratory Specimens

ABSTRACT Currently, diagnosis of Pneumocystis jirovecii pneumonia (PJP) relies on analysis of lower respiratory specimens, either by microscopy or quantitative real-time PCR (qPCR). Thus, bronchoscopy is required, which is associated with increased risk of respiratory failure. We assessed the value of noninvasive serologic β-d-glucan (BDG) testing for laboratory diagnosis of PJP using a newly available turbidimetric assay. We identified 73 cases of PJP with positive qPCR results from lower respiratory specimens for Pneumocystis and serology samples dating from 1 week before to 4 weeks after qPCR. In addition, 25 sera from controls with suspected PJP but specimens negative for Pneumocystis by qPCR were identified. Sera were tested with a turbidimetric BDG assay (Fujifilm Wako Chemicals Europe GmbH, Neuss, Germany), using an 11-pg/ml cutoff. Sensitivity and specificity were calculated based on qPCR test results as a reference. The turbidimetric BDG assay identified 63/73 patients with positive or slightly positive qPCR tests for an overall sensitivity of 86%; after exclusion of cases with only slightly positive qPCR results, sensitivity was 91%. No correlation between serum BDG levels and respiratory specimen DNA levels was found. Serologic BDG testing was negative in 25/25 controls with negative qPCR for a specificity of 100% using the predefined cutoff. In 22/25 samples (88%), no BDG was detected. Serologic BDG testing using the turbidimetric assay showed high sensitivity and specificity compared to qPCR of lower respiratory specimens for the diagnosis of PJP. Both turnover time and test performance will allow clinicians to delay or in some cases forego bronchoscopy.

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