The effect of COVID-19 pandemic on the epidemiology of respiratory tract viral agents

Acute respiratory tract infections are most commonly caused by viruses. Viruses primarily cause upper respiratory tract infections; however, they can also cause infections with high mortality in small children, the elderly, people with underlying conditions, and immunocompromised individuals by affecting the lower respiratory tract. The identification of viral agents causing respiratory tract infections is critical for both guiding treatment and monitoring viral agent epidemiology. The aim of this study was to investigate at the impact of the COVID-19 pandemic on the epidemiology of respiratory tract viral agents. This study comprised all nasopharyngeal swab samples that were sent between January 1, 2018, and February 28, 2023, to the Medical Microbiology Laboratory of Aydın Adnan Menderes University Hospital for the molecular investigation of respiratory tract viral agents and stored under appropriate conditions. The first COVID-19 case reported in our country was reported on March 11, 2020, and this day was officially recognized as the pandemic's beginning. Retrospective data from the hospital information management system (HBYS) (MIA-MED automation information system) were used in the study. The 202 Magnesia Viral DNA/RNA Extraction Kit on the Magnesia 16 (Anatolia, Turkey) device was used in the study to extract nucleic acid from the samples, and presence of viral nucleic acid was investigated by multiplex Real time PCR method using the Bosphore Respiratory Pathogens Panel Kit v4 (Anatolia, Turkey). Statistical data were obtained by applying the chi-square test using the SPSS 21.0 program. For statistical significance, a p value less than 0.05 was required. Of the 2550 patients included in our study, 1161 (45.5%) were female and 1389 (54.5%) were male. The age range of the patients in the study group was 0-99 years. Nucleic acid belonging to at least one virus in the panel was detected in 1422 (48.6%) of the 2924 samples analyzed. Enterovirus/Rhinovirus, RSV A/B, Influenza A were the most frequently detected respiratory viruses in both sexes, respectively. In our study, the percentage of respiratory virus detection was 60.6% before the pandemic and 37.3% during the pandemic. The percentage of respiratory tract virus detection was found to be statistically significantly lower during the pandemic period compared to the pre-pandemic period. Respiratory viruses causing co-infection were EV/RV, RSV A/B and Influenza A, respectively. The frequency of co-infection was statistically significantly higher in patients under 18 years of age (mean 13%) than in patients over 18 years of age (mean 1.8%). Co-infection rates were statistically significantly higher in the pre-pandemic period compared to the pandemic period. In our study, it was determined that EV/RV continued to be detected between the dates when schools were closed and partial normalization began, while other respiratory viruses were largely withdrawn from circulation. Results of our study: The frequency of viral agents in respiratory tract infections decreased in the pandemic period compared to the pre-pandemic period. EV/RV is the most frequently detected viral agent in respiratory tract infections in both the pre-pandemic and pandemic periods in all patients over two years of age, hospitalized/outpatient. In patients aged 0-1 years, the most frequently detected viral agent is RSV A/B. The detection frequency of EV/RV and Bocavirus among all viruses increased statistically significantly in the pandemic period. Enterovirus/Rhinovirus is the most common viruses causing co-infection. The pandemic had little effect on this circumstance. Viral co-infections are more common in children. The frequency of viral co-infection decreased during the pandemic period. Viral agents were detected most in winter and least in summer. This situation has not changed with the pandemic. The most frequently detected viral agent in winter is RSV A/B; in spring, summer and autumn, it is EV/RV. This situation has not changed with the pandemic. As a limitation of our study, data from a single center were presented. In addition, our results could not be evaluated together with patient symptoms and clinical findings. Therefore, it was not possible to reach a clear conclusion as to whether the viruses detected were causative or not, especially when evaluating co-infections. In addition, in our study, simultaneous SARS-CoV-2 examination could not be performed in patient samples during the pandemic period. Therefore, SARS-CoV-2 data could not be presented and it could not be determined whether SARS-CoV-2 accompanied co-infections during the pandemic period. It is considered important to continue studies investigating the distribution of respiratory viral agents by examining patient symptoms and clinical findings. However, it is thought that studies designed to determine the respiratory viral microbiota are needed in order to fully understand whether the viruses detected by molecular methods in patient samples are infectious agents.