ABSTRACT
From the onset of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/COVID-19 pandemic, there has been a major emphasis on molecular laboratory tests for the virus. Shortages in various testing supplies, the desire to increase testing capacity, and a push to make point-of-care or home-based testing available have fostered considerable innovation for SARS-CoV-2 molecular diagnostics, advancements likely to be applicable to other diagnostic uses. The authors attempt to cover some of the most compelling novel types of molecular assays or novel approaches in adapting established molecular methodologies for SARS-CoV-2 detection or characterization.
Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , PandemicsABSTRACT
Maybe 2021 wasn't so bad after all! It was like 2020, but with COVID vaccines and better access to plastic pipette tips, and clearly, 2022 is getting off to a bad start. Even better, 2021 had some exciting papers in clinical microbiology, which is what is highlighted in this 2021 year in review. None of them are about COVID-19. Of course, there were some interesting discoveries about SARS-CoV-2 and COVID-19, but this review is completely COVID-19 free (almost).
Subject(s)
COVID-19 , Clinical Laboratory Techniques , Pandemics , COVID-19/diagnosis , Humans , SARS-CoV-2ABSTRACT
CONTEXT.: We implemented multiple nucleic acid amplification test platforms because of the limited availability of test kits for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the early stages of the pandemic. Interpretation of results generated by different platforms and prioritization for testing algorithms required cross-comparison. OBJECTIVE.: To compare the analytical sensitivity of 3 commercial SARS-CoV-2 molecular assays, selected samples were studied in parallel with Cobas SARS-CoV-2 test, NxTAG CoV Extended Panel, and ID NOW COVID-19 assays. DESIGN.: A total of 8043 SARS-CoV-2 tests performed from March 22 to April 19, 2020, were included in this study. For all 1794 positive specimens detected by the cobas SARS-CoV-2 assay, the cycle threshold (Ct) values were manually tracked and plotted to demonstrate the distribution of sample viral levels. Additionally, 50 and 63 low-positive specimens (Ct values >32) as well as 50 and 61 consecutive positive specimens by the cobas assay were tested with NxTAG and ID NOW, respectively, to estimate their relative sensitivities. RESULTS.: The Ct values of cobas SARS-CoV-2-positive samples were evenly distributed throughout ranges of 13.32 to 39.50 (mean, 25.06) and 13.60 to 42.49 (mean, 26.45) for ORF1 and E gene targets, respectively. NxTAG reliably detected only specimens with E gene Ct values lower than 33, and is estimated to detect 89.4% of positive specimens detected by cobas assay. ID NOW had performance variation independent of Ct value and is estimated to detect 83.5% of cobas positives. CONCLUSIONS.: Clinical specimens exhibit a wide range of viral burden, with a significant portion at low levels. Analytical sensitivity of testing platforms is critical for reliable detection of SARS-CoV-2 and uniform care to patients.
Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Pneumonia, Viral/diagnosis , Severe Acute Respiratory Syndrome/diagnosis , Severe acute respiratory syndrome-related coronavirus/genetics , Adult , Betacoronavirus/isolation & purification , Betacoronavirus/physiology , COVID-19 , Clinical Laboratory Techniques/methods , Coronavirus Infections/virology , Diagnosis, Differential , Early Diagnosis , Female , Humans , Male , Middle Aged , Nasopharynx/pathology , Nasopharynx/virology , Pandemics , Pneumonia, Viral/virology , Severe acute respiratory syndrome-related coronavirus/isolation & purification , Severe acute respiratory syndrome-related coronavirus/physiology , SARS-CoV-2 , Sensitivity and Specificity , Severe Acute Respiratory Syndrome/virology , Specimen Handling/instrumentation , Specimen Handling/methodsABSTRACT
Frequent, low-cost, universal testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with quarantine of those with a positive result has been suggested as a strategy to address the coronavirus disease 2019 (COVID-19) pandemic in the United States. Specifically, home or community use of tests that use paper strip detection devices, which may have reduced sensitivity for SARS-CoV-2, has been advocated. There are several potential challenges or problems with this strategy, including the limited availability of such tests, consequences of incorrect test results, difficulties with adherence to testing, and the questionable accuracy of such tests for detection of infectious people. Because of these, we think it is premature to strongly advocate for such a testing strategy, as the adverse consequences may outweigh any benefits. High-quality outcome data demonstrating the efficacy of this testing strategy are needed before widespread implementation.