Abstract
In this review, we summarize the current status of nucleic acid and antigen testing required for diagnosing SARS-CoV-2 infection and COVID-19 disease. Nucleic acid amplification (NAAT) and antigen-detection (Ag) tests occupy a critically important frontline of defense against SARS-CoV-2 in clinical and public health settings. In early stages of this outbreak, we observed that identifying the causative agent of a new illness of unknown origin was greatly accelerated by characterizing the nucleic acid signature of the novel coronavirus. Results from nucleic acid sequencing led to the development of highly sensitive RT-PCR testing for use in clinical settings and to informing best practices for patient care, and in public health settings to the development of strategies for protecting populations. As the current COVID-19 pandemic has evolved, we have seen how NAAT performance has been used to guide and optimize specimen collection, inform patient triage decisions, reveal unexpected clinical symptoms, clarify risks of transmission within patient care facilities, and guide appropriate treatment strategies. For public health settings during the earliest stages of the pandemic, NAATs served as the only tool available for studying the epidemiology of this new disease by identifying infected individuals, studying transmission patterns, modeling population impacts, and enabling disease control organizations and governments to make challenging disease mitigation recommendations to protect the expanding breadth of populations at risk. With time, the nucleic acid signature has provided the information necessary to understand SARS-CoV-2 protein expression for further development of antigen-based point-of-care (POC) diagnostic tests. The advent of massive parallel sequencing (ie, next generation sequencing) has afforded the characterization of this novel pathogen, informed the sequences best adapted for RT-PCR assays, guided vaccine production, and is currently used for tracking and monitoring SARS-CoV-2 variants.
Highlights
In this review, we summarize the current status of nucleic acid and antigen testing required for diagnosing SARS-CoV-2 infection and COVID-19 disease
In the sections provided below, we discuss the specimens, collection methods, diagnostic strategies, and the interpretation and significance of test positivity in relation to the prevalence of disease and onset of symptoms. This latter point has become the central concern for diagnosis of SARS-Cov-2 infection and associated COVID-19 illness because of the challenges posed to limiting transmission within and outside clinical settings
We studied pooling in asymptomatic patients with COVID-19 and demonstrated an 85% correlation between direct testing and those pooled 10:1, which meets the FDA criteria for pooling [84]
Summary
AFFILIATED INSTITUTIONS 1C enter for Global Health and Diseases, Case Western Reserve University, Cleveland , Ohio 2C enter for Medical Mycology and Integrated Microbiome Core, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio 3D epartment of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio; Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio; and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, Ohio 4C leveland Clinic, Cleveland, Ohio #Contributed to this work. SUGGESTED CITATION Zimmerman PA, King CL, Ghannoum M, Bonomo RA and Procop GW. Molecular Diagnosis of SARS-CoV-2: Assessing and Interpreting Nucleic Acid and Antigen Tests.
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