Additional molecular testing of saliva specimens improves the detection of respiratory viruses

Abstract

Emerging infectious diseases in humans are often caused by respiratory viruses such as pandemic or avian influenza viruses and novel coronaviruses. Microbiological testing for respiratory viruses is important for patient management, infection control and epidemiological studies. Nasopharyngeal specimens are frequently tested, but their sensitivity is suboptimal. This study evaluated the incremental benefit of testing respiratory viruses in expectorated saliva using molecular assays. A total of 258 hospitalized adult patients with suspected respiratory infections were included. Their expectorated saliva was collected without the use of any special devices. In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Seventeen percent of the patients (27/159) had higher viral loads in the saliva than in the NPA. The second cohort consisted of 99 patients whose NPAs tested negative for respiratory viruses using a direct immunofluorescence assay. Their NPA and saliva specimens were additionally tested using multiplex PCR. In these patients, the concordance rate by multiplex PCR between NPA and saliva was 83.8%. Multiplex PCR detected viruses in saliva samples from 16 patients, of which nine (56.3%) had at least one virus that was not detected in the NPA. Decisions on antiviral or isolation precautions would be affected by salivary testing in six patients. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients.

Figure 1

Study design. nasopharyngeal aspirate, NPA; quantitative PCR with reverse transcription, qRT-PCR. ^aRoutine clinical testing was performed using antigen detection by the DFA, which included the influenza A and B viruses, parainfluenza virus types 1–3, respiratory syncytial virus, human metapneumovirus and adenovirus. From 1 March to 8 April 2015 (during the peak influenza A virus season), monoplex real-time RT-PCR for the influenza A M gene was performed for patients admitted to the general medical ward. ^bPatients whose NPA specimens either tested negative for respiratory viruses by DFA or had insufficient NPCs for DFA during routine clinical testing. Insufficient NPCs is defined as <20 NPCs in the entire well.

Figure 2

Viral loads in the NPA and the saliva specimens for all patients in the first cohort. The number of patients infected with each of the respiratory viruses is outlined in Table 2. (A) Comparison of viral loads between the NPA and saliva specimens. (B) Comparison of the saliva viral load of influenza A and influenza B in patients with saliva collected before and after oseltamivir treatment. (C) Comparison of the saliva viral loads in patients with or without pneumonia. Medians, quartiles, and ranges are shown. nasopharyngeal aspirate, NPA.