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
Open Access
- 3 August 2020
- journal article
- research article
- Published by Oxford University Press (OUP) in Open Forum Infectious Diseases
- Vol. 7 (9), ofaa335
- https://doi.org/10.1093/ofid/ofaa335
Abstract
The performance of rRT-PCR for SARS-CoV-2 varies with sampling site(s), illness stage and infection site. Unilateral nasopharyngeal, nasal mid-turbinate, throat swabs, and saliva were simultaneously sampled for SARS-CoV-2 rRT-PCR from suspect or confirmed cases of COVID-19.True positives were defined as patients with at least one SARS-CoV-2 detected by rRT-PCR from any site on the evaluation day or at any time point thereafter, till discharge. Diagnostic performance was assessed and extrapolated for site combinations. 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%, mid-turbinate, 62%, and saliva, 38-52%. Clinical sensitivity for nasopharyngeal, throat, mid-turbinate and saliva was 95%, 88%, 72%, and 44-56% if taken ≤7 days from onset of illness, and 70%, 67%, 47%, 28-44% if >7 days of illness. Comparing patients with URTI vs. pneumonia, clinical sensitivity for nasopharyngeal, throat, mid-turbinate and saliva was 92% vs 70%, 88% vs 61%, 70% vs 44%, 43-54% vs 26-45%. A combination of nasopharyngeal plus throat or mid-turbinate 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. Nasopharyngeal followed by throat specimens offer the highest clinical sensitivity for COVID-19 diagnosis in early illness. Clinical sensitivity improves and is similar when either mid-turbinate 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.This publication has 25 references indexed in Scilit:
- SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected PatientsThe New England Journal of Medicine, 2020
- Consistent Detection of 2019 Novel Coronavirus in SalivaClinical Infectious Diseases, 2020
- Accuracy and Discomfort of Different Types of Intranasal Specimen Collection Methods for Molecular Influenza Testing in Emergency Department PatientsAnnals of Emergency Medicine, 2018
- Comparison of Nasal and Nasopharyngeal Swabs for Influenza Detection in AdultsClinical Medicine & Research, 2012
- Current Best Practices for Respiratory Virus TestingJournal of Clinical Microbiology, 2011
- Performance of the BD GeneOhm MRSA Achromopeptidase Assay for Real-Time PCR Detection of Methicillin-Resistant Staphylococcus aureus in Nasal SpecimensJournal of Clinical Microbiology, 2011
- Epithelial Cells Lining Salivary Gland Ducts Are Early Target Cells of Severe Acute Respiratory Syndrome Coronavirus Infection in the Upper Respiratory Tracts of Rhesus MacaquesJournal of Virology, 2011
- Pitfalls in Diagnosis of Pandemic (Novel) A/H1N1 2009 InfluenzaJournal of Clinical Microbiology, 2010
- Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early DiagnosisEmerging Infectious Diseases, 2004
- Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. A first step in understanding SARS pathogenesisThe Journal of Pathology, 2004