Our data demonstrate that non-invasive methods for collecting respiratory samples can be used to identify respiratory viruses with multiplex PCR testing. Detection rates were >50% for most viruses and >80% for RSV. Using NPA as the gold standard, the sensitivity of non-invasive methods ranged from 17%-93% for individual viruses. As with other studies of viral detection, AV had a low detection rate.30–31
In general, anterior nare swabs had higher detection rates and higher sensitivity than facial tissues. For both sample types, specificity was ≥ 95% for all viruses except HRV. These data suggest that, while further investigation is required, non-invasive collection of respiratory samples with viral testing by multiplex PCR may be useful for conducting surveillance or epidemiology studies in community settings where invasive testing is impractical or not feasible.
Other studies have investigated the use of anterior nare swabs for the detection of respiratory viruses using antigen detection, viral culture, and PCR.23–28
Sample collection from the anterior nares with flocked swabs has been shown to be comparable to collection by NPA, 23, 25
although some studies have reported difficulties in the detection of RSV with swabs.24, 26
This included one study in which detection was by culture 26
and one by PCR.24
In the culture-based study, the lability of RSV was hypothesized as a factor decreasing the sensitivity of swabs. In our study, the sensitivity of both swabs (94%) and facial tissue samples (84%) were highest for RSV.
To our knowledge no other studies have looked at the use of facial tissue as a sample collection method for the detection of respiratory viruses in children. Facial tissues are inexpensive, readily available, and in our experience, children generally accept them without significant distress. This method could be particularly beneficial for use in population surveillance, allowing for self-collection by large numbers of individuals quickly in the setting of a public health emergency. In studies where large groups or repeated sampling is involved, facial tissue might be a more practical and acceptable method for obtaining specimens. Sensitivity of facial tissues was lower than that of swabs, and they are not an adequate sample type for individual diagnostics. However, their specificity for viral detection may make them appropriate for community surveillance as the detection of positives likely indicates the pathogen is in the population.
In this study the sensitivity of each sample collection method varied by virus type. While the number of positive specimens for many viruses was too low for comparisons, we could compare RSV and HRV. Sensitivity for the detection of RSV was >80% for both anterior nare swabs and facial tissues while for HRV it was < 60%. The reasons for this are unclear, but could be due to virus or symptom-related factors that would require further investigation 32–33
High specificity for detection of viruses is crucial for surveillance, as it provides confidence that a detected virus is circulating in a population. Some current methods for influenza surveillance are not virus-specific and are performed, for example, in schools through absenteeism data and through sentinel clinics by influenza-like illness (ILI) reporting. Absenteeism can be due to a number of factors unrelated to influenza,34–35
and the specificity of ILI for culture-proven influenza has been shown to range from 35 to 71%.15, 36–38
Use of non-invasive sampling methods combined with molecular detection could offer the potential to broaden population-based testing with the possibility of a significant improvement in data. In other studies of infectious pathogens, non-invasive collection methods combined with molecular detection has improved epidemiologic understanding.39–41
The cost of molecular testing could be considered prohibitive for its use in surveillance settings. However, sample strategies that involve pooling for testing may result in significant savings and further studies of this are warranted.
There are several limitations to our study. The primary limitation was sample size. While 95 participants provided samples, the numbers of each virus detected were small. Our study was not designed to determine the non-inferiority of swabs or tissues for individual diagnostics when compared to NPA. The age range of our participants was biased toward children younger than 2 years who may have had higher respiratory viral loads than older children; therefore, our reported virus detection rates may be higher than would be found for older children. In addition, the young age of our participants may have made it more difficult to evaluate sample collection by facial tissue, as small children cannot blow their noses to adequately expel nasal secretions. Only one brand of facial tissues was tested, and it is possible that others will not perform in the same manner. The recovery of viruses from the facial tissue samples, in particular, may have been affected by the lack of precision in sample collection and transfer to cryovials; however, we believe our results are still useful as our methods reflect what is likely to occur during community epidemiologic studies where this sample-type might be used. Finally, all children tested were in the ED and were thought to be sufficiently ill that viral testing was ordered. These children may have higher respiratory viral loads making detection easier. In surveillance of healthy children who may have low viral loads, non-invasive testing may not perform as well.
Overall, both anterior nare swabs and facial tissues are promising tools for non-invasive diagnostic testing for respiratory viruses in certain circumstances. While not appropriate for patient care, the use of non-invasive respiratory sampling may prove valuable for epidemiologic or surveillance studies in community settings where respiratory diagnostics have been limited.