Comparison of nasopharyngeal aspirate and saliva in the detection of live influenza virus

Abstract

Influenza virus is of great concern for healthcare practitioners and scientists due to the high transmissibility, mortality and morbidity. Influenza virus can cause severe viral pneumonia. Several epidemic and pandemic outbreaks were found to be caused by influenza virus, including H1N1 pandemic in 1918, H2N2 pandemic in 1957, H3N2 pandemic in 1968 and H1N1 pandemic in 2009. Clinical specimens commonly used for detection of influenza virus include nasopharyngeal aspirate/swab and throat swab. The collection procedure would also cause discomfort to patients and pose risks for both patients and healthcare workers. Several groups have studied the use of saliva as an alternative specimen for detection of influenza viruses with molecular methods. However, viral culture was not performed in those studies. Therefore, it was unclear whether live virus was present in the saliva. In this study, we aim to evaluate the performance of nasopharyngeal aspirate and saliva in culturing influenza virus. Saliva and NPA specimens from 82 adult patients were collected from February, 2015 to February, 2016. Among them, 40 participants were female and 42 were male. Fifty of them were aged >65 years and 32 of them were aged between 18 and 65 years. The result of viral culture in this study was similar in both NPA and saliva specimen. The positive rate for NPA was 28%(23/82) and that for saliva was 24%(20/82). Viral culture was positive in NPA only for 11%(9/82) and saliva only for 7%(6/82). The positive rate for viral culture would be increased by 26% if both NPA and saliva specimens were collected for viral culture when compared with NPA alone. Gene sequencing showed that one patient had a threonine at amino acid position 160 of the haemagglutinin (HA) protein from the NPA specimen, but a mixed population of threonine and lysine was found at the same position in the saliva specimen of the same patient. The findings in this study suggest that viral culture using both saliva and NPA will increase the positive rate of viral culture of influenza virus. Furthermore, viral culture from saliva may also identify virus quasispecies that are not present in the NPA.