Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses

Abstract

Diagnostic tests for respiratory viral infections use traditionally either nasopharyngeal washes or swabs. Sputum is representative of the lower respiratory tract but is used rarely for viral testing. The aim of this study was to compare the detection rates of respiratory viruses from nasopharyngeal swabs and sputum using a multiplex real-time reverse transcription-polymerase chain reaction (RT-PCR). Adults who were admitted or presented to the clinics of Gil Medical Center with acute respiratory symptoms were recruited from 1 November 2012 to 31 March 2013. Paired specimens of nasopharyngeal swabs and sputum were obtained from 154 subjects, and RNA was extracted and tested for 16 different respiratory viruses using the Anyplex II RV16 Detection kit (Seegene, Seoul, Korea). The positive rate was 53% (81/154) for nasopharyngeal swabs and 68% (105/154) for sputum (P < 0.001). One hundred thirty-four viruses were identified for 107 illnesses. Influenza A virus, RSV A, HRV, coronavirus OC43, and adenovirus were detected more frequently in sputum samples than in nasopharyngeal swabs (P < 0.001). Importantly, 12 of 44 (27%) influenza A infections and 11 of 27 (41%) RSV infections were positive in only sputum samples. The detection rates of respiratory viruses from sputum samples were significantly higher than those from nasopharyngeal swabs in adults using real-time multiplex RT-PCR. These findings suggest that sputum would benefit for the detection of respiratory viruses by nucleic acid amplification tests (NAATs) in patients who produce sputum. Further studies are needed to establish standardized RNA extraction methods from sputum samples.

Diagnostic performance of multiplex PCR on pulmonary samples versus nasopharyngeal aspirates in community-acquired severe lower respiratory tract infections

“…Here, we investigated the diagnostic efficacy of nasopharyngeal aspirates versus pulmonary samples in a well-defined adult population of community-acquired severed LRTI and found that both diagnostic approaches gave similar diagnostic yield for respiratory viruses. This is discordant with several studies that have reported better performance for LRT samples for the diagnosis of viral infections in adults [10,11]. These studies where based on nasal, throat, or nasopharyngeal swabs.…”

“…The superiority of lower over upper respiratory tract samples for the diagnosis of severe infuenza has been suggested by several authors [11,13]. We did not see such difference in our study, since 27 of 29 influenza virus infections were diagnosed in both specimens.…”

Effectiveness of inactivated influenza vaccine against laboratory-confirmed influenza pneumonia among adults aged ≥65 years in Japan

“…The use of sputum samples in our study may also explain our high IVE estimate. Identification of influenza from sputum samples may be more sensitive and specific than that from upper respiratory tract samples in diagnosing influenza pneumonia and may provide less biased IVE estimates [17,30,31]. Consistent findings in our sensitivity analyses also support the robustness of our IVE estimates.…”

Viral load is strongly associated with length of stay in adults hospitalised with viral acute respiratory illness

“…Real-time PCR Ct values are now considered by many to be a robust surrogate for quantified viral load and are increasingly reported in published studies of acute viral illness including those examining respiratory viruses [6,32] and also in the recent Ebola virus pandemic [33,34]. Furthermore, the use of protocolised sampling techniques, processing by dedicated research staff and the removal of inter-operator variability of results interpretation (as all samples were analysed by the same scientists in the same laboratory) gives reassurance as to the robustness of the Ct result in this study.…”