Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses.
Author(s): Jeong JH, Kim KH, Jeong SH, Park JW, Lee SM, Seo YH
Publication: J Med Virol, 2014, Vol. 86, Page 2122-7
PubMed ID: 24797344 PubMed Review Paper? No
Purpose of Paper
This paper compared detection of respiratory viruses by real-time PCR in sputum and nasopharyngeal swab specimens.
Conclusion of Paper
Sputum specimens had a significantly higher detection rate for respiratory viruses than nasopharyngeal swabs. Influenza A, respiratory syncytial virus A, rhinovirus, coronavirus OC43, and adenovirus were detected more often in sputum samples than in nasopharyngeal swabs but concordance was high between matched specimens for all viruses except adenovirus. Importantly, 27% influenza A infections, 41% respiratory syncytial virus A infections, 23% rhinovirus infections, 38% coronavirus OC43 infections, and 27% adenovirus infections were positive only in sputum.
Studies
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Study Purpose
This study compared detection of respiratory viruses by real-time PCR in sputum and nasopharyngeal swab specimens. Paired nasopharyngeal swabs and sputum were obtained from 154 patients (median age=52 y, 47 males and 107 females) with symptoms of acute respiratory illness defined as cough, rhinorrhoea, nasal congestion, dyspnoea, sputum, or fever. Nasopharyngeal specimens were obtained using flocked swabs and placed in universal transport medium (details not provided). Sputum was obtained by expectoration into sterile containers, delivered to the laboratory within 2 h, diluted with an equal volume of phosphate buffered saline (PBS) and mixed by vortexing for 1 to 5 min. RNA was extracted using the GeneAll Ribospin Kit and an automated system. Sixteen respiratory viruses (bocavirus; enterovirus; influenza virus A and B; parainfluenza virus 1, 2, 3, and 4; respiratory syncytial virus A and B; adenovirus; metapneumovirus; coronavirus OC43, 229E, and NL63; and human rhinovirus A/B/C) were detected using a multiplex real-time RT-PCR assay.
Summary of Findings:
Sputum specimens had a significantly higher detection rate for respiratory viruses than nasopharyngeal swabs (68% versus 53%, P<0.001). Influenza A, respiratory syncytial virus A, rhinovirus, coronavirus OC43, and adenovirus were detected more often in sputum samples than in nasopharyngeal swabs (P<0.001, all) but concordance was high between matched specimensfor all viruses (Kappa= 0.737, Kappa= 0.637, Kappa= 0.854, Kappa= 0.746; respectively) except adenovirus (Kappa= -0.045). Detection of other viruses was too low for statistical analysis. Importantly, 27% (12/44) of influenza A infections, 41% (11/27) of respiratory syncytial virus A infections, 23% (5/22) of rhinovirus infections, 38% (5/13) of coronavirus OC43 infections, and 27% (3/11) of adenovirus infections were positive only in sputum.
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) Real-time qRT-PCR Specific Targeted nucleic acid bocavirus
enterovirus
influenza virus A
influenza virus B
parainfluenza virus 1
parainfluenza virus 2
parainfluenza virus 3
parainfluenza virus 4
respiratory syncytial virus A
respiratory syncytial virus B
adenovirus
metapneumovirus
coronavirus OC43
coronavirus NL63
human rhinovirus A/B/C
Biospecimen Acquisition Biospecimen location Nasopharynx
Sputum