The impact of COVID-19 pandemic on surveillance of influenza and influenza-like viruses: a single center experience

Abstract

Aims: Influenza and the agents responsible for influenza-like illness (ILI) are a significant cause of upper and lower respiratory tract infections, with a notable pattern of seasonal incidence. The surveillance of influenza and agents causing ILI is important for the developmentof a prophylaxis approach and infection control. In the present study, we utilize the Reverse transcription-polymerase chain reaction (RT-PCR) method to identify the presence of influenza virus and other agents associated with ILI in nasopharyngeal smears obtained from patients exhibiting symptoms of influenza and ILI. The study sample included patients who were admitted to multiple clinics and intensive care units (ICU) of the Health Sciences University Ankara Training and Research Hospital in the period preceding, and in the initial months and first year following the coronavirus disease 2019 (COVID-19) outbreak. Throughthe comparisons made in the study, the intention is to gain a better understanding of the influence of the COVID-19 pandemic on other viral infectious agents transmitted via the respiratory tract.
 Methods: Included in the study were 257 admitted to different wards and ICUs of our hospital due to symptoms of upper or lower respiratory tract infection and ILI between 2015 and 2021 (excluding data from 2017–2018). The study was conducted prospectively within the scope of the Global Influenza Hospital Surveillance Network project. Using sterile swabs, nasopharyngeal swab samples were collected from inpatients who provided informed consent for their participation in the study, and the samples were placed in a viral transport medium. The presence of influenza viruses (Influenza A, subtypes of Influenza A and Influenza B) and agents causing ILI (i.e. respiratory syncytial virus, coronavirus) was investigated with an RT-PCR approach.
 Results: The most common symptoms among the 257 patients included in the study with pre-diagnoses of influenza and ILI were cough (82.2%), fever (67.7%), shortness of breath (66.1%) and myalgia (40%). The RT-PCR detected a viral agent in 60 (23.3%) of the 257 patients, whereas no agent could be detected in 197 (76.6%) patients. Furthermore, 51 (18.5%) tested positive for influenza virus, five (1.9%) for respiratory syncytial virus (RSV), and four (1.5%) for SARS-CoV-2. An analysis of the results within two distinct time frames, namely prior to the COVID-19 pandemic (2016–2017, 2019–prior to December 10, 2020) and during the COVID-19 pandemic (between December 11, 2020 and 2021), influenza viruses (influenza A H1N1 and influenza A H3N2), RSV and influenza type B were identified as the dominant viruses before the COVID-19 pandemic, while the predominant viruses were a single influenza strain and four SARS-CoV-2 variants during the COVID-19 pandemic.A significant difference was noted in the distribution of viruses between the two time frames – prior to the pandemic and during the pandemic. Of the patients, 199 (77.4%) were discharged with full recovery while 58 patients died (22.6%). Of the 58 patients that died, 25 were female (25/131 females) and 33 were male (33/126 males), 11 had tested positive for influenza virus andone for RSV, while no infectious agent could be identified in 46 patients. 
 Conclusion: The implementation of molecular testing methods for the identification of viral infectious agents among inpatients during influenza and ILI outbreaks, administering antiviral and prophylactic treatments targeting influenza, RSV and SARS-CoV-2 infections, and adopting infection control measures, could significantly decrease mortality and morbidity rates while mitigating the complications associated with these infectious agents.