27 Surveillance of Severe Acute Respiratory Infections 2 RT-PCR testing Patients were tested for respiratory viruses at the discretion of the treating physician. RT-PCR tests were conducted on upper respiratory tract samples, using either a nasal, nasopharyngeal, or throat swabs. Virology results were recorded in the Global Laboratory Information Management System (GLIMS), which is linked to the EMR. The total number of RT-PCR tests performed for one of the following respiratory viruses were collected: human adenovirus, bocavirus, human coronaviruses (SARSCoV-2, MERS, 229E, HKU1, NL63, OC43), human metapneumovirus, influenza viruses A and B, parainfluenza virus (PIV) 1–4, human rhinovirus and respiratory syncytial virus (RSV). Even though patients were frequently screened for multiple viruses using the multiplex RT-PCR method, we accounted for it as a single RT-PCR test per patient in our analysis. If a patient had more than one (multiplex) RT-PCR test done during hospitalisation, we selected the first test. If a patient tested positive for multiple pathogens within a single RT-PCR test, we included all of the identified pathogens in the virological test results. Only RT-PCR tests that were done 48 h before admission to 48 h after admission were eligible for inclusion to minimise the probability of including hospital-acquired infections. Tests before hospital admission were included to account for patients that were tested, e.g. at the emergency department or in the outpatient clinic, but initially sent home before being readmitted within the next 2 days because of clinical deterioration. RT-PCR test results were reported as positive or negative for each tested virus. Contact and droplet precautions According to the standard procedure in our hospital, contact and droplet precautions are applied for all patients suspected or confirmed to have a respiratory viral infection from one of the viruses mentioned above. However, for rhinoviruses, these precautions are only recommended for immunocompromised patients and neonates. The installation of contact and droplet precautions are recorded in the EMR. The process for recording contact and droplet precautions in our hospital’s system underwent a revision on 1 December 2020. Prior to this date, only the infection control and hospital hygiene department staff could add these precautions to the EMR. Precautions were added to the EMR only after a positive RT-PCR test result. Starting from 1 December 2020, a broader range of healthcare personnel, including nurses and physicians from all departments, could add contact and droplet precautions to the EMR. Precautions were taken and added to the EMR for both suspected or confirmed infections. Only contact and droplet precautions registered within 48 h of hospital admission were counted, in order to minimise the probability of including hospital-acquired infections.
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