Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously.
Author(s): Wang X, Tan L, Wang X., Liu W, Lu Y, Cheng L, Sun Z
Publication: Int J Infect Dis, 2020, Vol. 94, Page 107-109
PubMed ID: 32315809 PubMed Review Paper? No
Purpose of Paper
This paper compared detection of SARS-CoV-2, the virus that causes the novel 2019 coronavirus disease (COVID, COVID-19, COVID19) by real-time PCR using oropharyngeal specimens to nasopharyngeal specimens.
Conclusion of Paper
The rate of detection of SARS-CoV-2 was higher for nasopharyngeal than oropharyngeal swabs when all cases were considered and when broken down by inpatient and outpatient cases and for males. Using both specimen types resulted in slightly higher rate of detection of SARS-CoV-2 than using nasopharyngeal swabs alone in all cases and when outpatient and inpatient cases were analyzed separately. Concordance was poor between oropharyngeal and nasopharyngeal swabs with 66% of cases positive in oropharyngeal swabs also positive in the nasopharyngeal swab and 73.1% of cases positive in nasopharyngeal swabs also positive in the oropharyngeal swab (Kappa= 0.308).
Studies
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Study Purpose
This study compared detection of SARS-CoV-2 by real-time PCR using oropharyngeal specimens to nasopharyngeal specimens. Specimens were collected from 353 patients (median age = 54 years; male=176, female= 177; 192 outpatients, 161 inpatients) with COVID-19 like symptoms, such as fever, cough, and fatigue initially screened in community hospitals for fever and chest X-ray abnormality. Nasopharyngeal swab specimens were obtained from a single nostril (details not provided). Oropharyngeal swabs were collected from both sides of the throat (details not provided). RNA was extracted using an automatic nucleic acid extraction system. SARS-CoV-2 nucleocapsid protein and open reading frame 1ab (ORF1ab) genes were detected using a multiplex real-time RT-PCR assay.
Summary of Findings:
The SARS-CoV-2 detection rates were higher for nasopharyngeal than oropharyngeal swabs when all cases were considered (19.0% versus 7.6%) and when broken down by inpatient and outpatient cases (7.3% versus 6.3% and 32.9% versus 9.3%; respectively). SARS-CoV-2 rates were significantly higher in males than females when all cases were considered and in outpatient nasopharyngeal swab specimens (P=0.20 and P=0.004, respectively) but not oropharyngeal swabs. Using both specimen types resulted in slightly higher rates of SARS-CoV-2 detection than using nasopharyngeal swabs alone in total, outpatient, and inpatient cases (21.5% versus 19.0%, 9.9% versus 7.3%, and 35.4% versus 32.9%; respectively). Concordance was poor between oropharyngeal and nasopharyngeal swabs with 66% (18/27) of cases positive in oropharyngeal swabs also positive in the nasopharyngeal swab and 73.1% (49/67) of cases positive in nasopharyngeal swabs also positive in the oropharyngeal swab (Kappa= 0.308).
Biospecimens
Preservative Types
- None (Fresh)
Diagnoses:
- Pneumonia/Respiratory Infection
Platform:
Analyte Technology Platform RNA Real-time qRT-PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Preaquisition Patient gender Female
Male
Preaquisition Diagnosis/ patient condition Inpatient
Outpatient
Real-time qRT-PCR Specific Targeted nucleic acid SARS-CoV-2 nucleocapsid protein
SARS-CoV-2 open reading frame 1ab (ORF1ab) gene
Biospecimen Acquisition Biospecimen location Nasopharynx
Oropharynx