Investigation of the factors that cause respiratory tract infection during the COVID-19 pandemic in Afyonkarahisar, Turkey  (2020-2021).

Background Respiratory tract infections are a significant cause of morbidity and mortality worldwide. In particular, closely monitoring pathogens with pandemic potential is essential for early diagnosis and control of possible pandemics. In this study, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and viruses that most commonly cause respiratory tract infections in patients with similar clinical symptoms during the COVID-19 pandemic were examined; Influenza A/Influenza B; influenza A H1/H3/H5/H7; Human MetapneumoVirus (HMPV), Human respiratory syncytial virus (HRSV) A/B, Human rhinovirus (HRV); human bocavirus (HBoV); The simultaneous presence of Human enterovirus (HEV), Human parechvirus (HPeV), Human adenovirus (AV), Human coronavirus (HCoV) HKU/NL63/OC43/229E and Parainfluenza (PIV) 1/2/3/4 viruses were investigated. Methods Nasopharyngeal swab samples taken from 100 patients were analyzed using the multiplex single-step reverse transcription polymerase chain reaction (Multiplex RT qPCR) method. Results SARS-CoV-2 was detected in two (1%) of 50 samples taken from pediatric patients, and Human coronavirus (HCoV) OC43 was positive in one. While 14 samples (28%) were found to be positive for SARS-CoV-2 in the adult patient group, other respiratory tract viruses were not detected. Conclusions Although the study was carried out during the high season of influenza and other respiratory viral pathogens, they were found to be at low numbers and ratios. The reason for the low detection rate of SARS-CoV-2 virus and other respiratory tract viruses was interpreted as taking personal precautions and quarantine measures during the COVID-19 pandemic. It was thought that SARS-CoV-2 activity and its effect on seasonal influenza and other respiratory tract virus activities should be followed closely in the coming years.