Prevalence of SARS-COV-2 and other respiratory pathogens among a Jordanian subpopulation during Delta-to-Omicron transition: Winter 2021/2022

Acute respiratory tract infections (ARTIs) during the winter months are associated with higher morbidity and mortality compared to other seasons of the year, with children below five, elderly, and immunocompromised patients being the most susceptible. Influenza A and B viruses, rhinovirus, coronaviruses, respiratory syncytial virus, adenovirus, and parainfluenza viruses, are the most frequently identified causes of viral ARTIs. In addition, the emergence of SARS-CoV-2 in 2019 provided an additional viral cause of ARTIs. The aim of this study was to provide an overview of the epidemiological status of upper respiratory infections, their main causative agents, and reported clinical presentation in the winter months of 2021, during two important surges of COVID-19 in Jordan. Nasopharyngeal samples were collected from 339 symptomatic patients during the period from December 2021 to March 2022, followed by nucleic acid isolation using a Viral RNA/DNA extraction Kit. The causative virus species associated with the patient’s respiratory symptoms was determined utilizing a multiplex real-time PCR targeting 21 viruses, 11 bacteria, and a single fungus. SARS-CoV-2 was identified in 39.2% of the patients (n = 133/339). A total of 15 different pathogens were also identified as co-infections among these 133 patients (n = 67/133). SARS-CoV-2-Bacterial coinfections (37.6%, n = 50/133) were the most frequent, with Bordetella species being the most common, followed by Staphylococcus aureus, and H.influenzae type B. Viral coinfection rate was 27.8% (n = 37/133), with Influenza B virus and Human bocavirus being the most common. In Conclusion, Both SARS-CoV-2, influenza B virus, and Bordetella accounted for the majority of infections in patients with URTI during the winter months of 2021–2022. Interestingly, more than 50% of the patients with symptoms of URTIs were confirmed to have a coinfection with two or more respiratory pathogens, with SARS-CoV-2 and Bordetella coinfection being most predominant.