Table 2. Detection of viruses using quantitative real-time reverse transcription PCR in the first cohort of patients.
| Virus | Number of patients with the virus detected in the NPA during routine clinical testinga | Saliva-positive, number (%) | Higher viral load in saliva than in NPA, number (%) |
|---|---|---|---|
| Influenza A virus | 99b,c | 95 (96.0) | 17 (17.2) |
| Respiratory syncytial virus | 18 | 15 (83.3) | 1 (5.6) |
| Human metapneumovirus | 14 | 11 (78.6) | 2 (14.3) |
| Influenza B virus | 12 | 10 (83.3) | 3 (25) |
| Parainfluenza virus type 3 | 8 | 8 (100) | 2 (25.0) |
| Parainfluenza virus type 1 | 5 | 4 (80) | 1 (20.0) |
| Parainfluenza virus type 2 | 3 | 3 (100) | 1 (33.3) |
| All viruses | 159 | 146 (91.8) | 27 (17.0)d |
Abbreviations: direct immunofluorescence, DFA; nasopharyngeal aspirate, NPA; PCR with reverse transcription, RT-PCR.
Routine clinical testing was performed using antigen detection by DFA, which included 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 season of influenza A virus), monoplex real-time RT-PCR for influenza A M gene was performed for patients admitted to the general medical ward. Among patients recruited in this study, there were no patients with adenovirus detected in their NPA during routine clinical testing.
Eighty-four patients were infected with H3 subtype, while 15 patients were infected with H1 subtype.
Eighty-seven patients (87.9%) were tested positive for influenza A virus using antigen detection by direct immunofluorescence. Twelve patients (12.1% all infected with H3 subtype) admitted to the general medical ward during the peak influenza season were tested by RT-PCR for influenza virus M gene only during the routine clinical testing.
The denominator includes those patients for whom their saliva specimens were tested negative for respiratory viruses. This is because these patients may have a low quantity of respiratory virus present in their saliva specimens but below the detection limit of the assay.