Viral infection diagnostics have been revolutionized by the development of RT-PCR, and the substantial burden of these ubiquitous pathogens is now being increasingly recognized (1
). However, some fundamental issues, including the utility of swabs versus washes, nose versus throat versus nasopharyngeal samples, and flocked versus regular swabs, remain regarding the determination of the optimal specimens for viral testing (24
). Throughout those debates, the use of sputum has rarely been considered and none of the currently available commercial RT-PCR assays for respiratory virus detection are approved for sputum testing (10
). The observation that viruses can be detected in sputum by RT-PCR has been previously reported from studies of patients with COPD and asthma (3
). However, the use of sputum as a diagnostic tool for patient care has likely been ignored because of difficulties in procuring adequate samples and because of its highly viscous nature, which makes processing difficult. The fact that sputum was obtained in only 73% of cases highlights the difficulties presented by sputum collection. Yet our data show that these difficulties are not insurmountable and that the added diagnostic yield of sputum can be substantial if it can be collected.
The association of a positive NTS RT-PCR result with the presence of upper respiratory tract symptoms and a shorter duration of illness prior to evaluation suggests that our findings reflect a progression of virus from the upper to the lower airways rather than sampling issues or random detection of low levels of RNA. It is possible that the decreased sensitivity of NTS RT-PCR in hospitalized patients is due in part to drying of the nasal mucosa secondary to nasal prong oxygen administration.
The accurate diagnosis of influenza is immediately useful for appropriate isolation and treatment of hospitalized patients. During the H1N1 2009 influenza pandemic, a number of investigators reported the utility of RT-PCR testing using lower respiratory tract samples from patients with negative nasopharyngeal swabs (4
). In most instances, BAL fluid or endotracheal secretions were tested. Since the majority of influenza patients do not require intubation or bronchoscopy, our data suggest that sputum is a reasonable alternative. The identification of specific viral infections other than influenza virus infections is also important for the institution of appropriate infection control policies for immunocompromised patients, particularly in hospital settings. Lastly, accurate detection of all viruses is important for epidemiologic research and vaccine and therapeutic trials.
Our data indicate that NTS and sputum testing yield complementary results. The most cost-effective method of viral testing would likely involve combining samples rather than performing separate RT-PCR assays. It might be possible to use the viral transport media from the NTS swab to dilute the sputum sample. Alternatively, a swab might be dipped in the sputum sample and combined in the viral transport media with the NTS. In acute care settings, simple procedures are most likely to be implemented; thus, further studies of combined sample testing and specimen processing are needed.
Our study has several limitations. Quantitative RT-PCR data would have been useful to help address the question of active replication in the lower airways versus low residual levels of RNA from a prior infection. We did not test for rhinovirus or adenoviruses, and it is possible that testing for these viruses would have provided different results for the yields of NTS and sputum RT-PCR. Finally, the use of flocked swabs for collection of nasal secretions might have increased the yield from NTS specimens, resulting in fewer significant differences between NTS and sputum samples (18
In conclusion, we found that inclusion of RT-PCR using sputum samples significantly increased the diagnostic yield for respiratory viral infections. Our data indicate that RT-PCR testing of sputum has merit and should be considered in studies of respiratory illnesses. As RT-PCR assays are validated and become commercially available, better methods to process and test sputum would be worthwhile.