Incidence of common respiratory pathogens among patients with severe acute respiratory infection during COVID-19 pandemic in Egypt

Severe Acute Respiratory Infection poses a significant threat to human health being a major cause of morbidity and mortality. The rate of co-infection among the underlying pathogens is unknown. During COVID-19 pandemic, reports for respiratory pathogens co-circulations in developing countries were limited. Identification of respiratory pathogens is paramount for effective patient management as early detection decreases the risk of mortality and morbidity. This is the first report to investigate the incidence of respiratory pathogens co-infection among patients with SARI during COVID-19 pandemic in Egypt. Clinically SARI patients were recruited from October 2020 to June 2022. Nasopharyngeal swabs were collected to detect SARS-CoV-2 followed by 33 respiratory pathogens identification using RT-PCR. Of 599 samples tested, 27% (158/599) patients were positive for COVID-19, in which 75.9% (120/158) patients were co-infected with other respiratory pathogens. In total, 31 pathogens were identified with a detection rate of 75% (450/599) among positive and negative COVID-19 patients. Bacterial co-infections rate was 39%, in which Klebsiella pneumoniae (5.3%) is the most common, while viral co-infections rate was 61%, in which Human Coronavirus HKU1 (6.2%) is the most common. Adenovirus, human rhinovirus and RSV were only detected in 70/11.7%, 50/8.3% and 41/6.8% of cases, respectively. Early detection and management of respiratory pathogens co-infection are crucial for effective patient management and preparedness for future pandemics.