Background Globally, viral pathogens are the leading cause of acute respiratory infection in children under-five years. We aim to describe the epidemiology of viral respiratory pathogens in hospitalized children under-two years of age in Eastern Province of Sierra Leone, during the second year of the SARS-CoV-2 pandemic. Methods We conducted a prospective study of children hospitalized with respiratory symptoms between October 2020 and October 2021. We collected demographic and clinical characteristics and calculated each participant´s respiratory symptom severity. Nose and throat swabs were collected at enrollment. Total nucleic acid was purified and tested for multiple respiratory viruses. Statistical analysis was performed using R version 4.2.0 software. Results 502 children less than two-years of age were enrolled. 376 (75%) had at least one respiratory virus detected. The most common viruses isolated were HRV/EV (28.2%), RSV (19.5%) and PIV (13.1%). Influenza and SARS-CoV-2 were identified in only 9.2% and 3.9% of children, respectively. Viral co-detection was common. Human metapneumovirus and RSV had more than two-fold higher odds of requiring O2 therapy while hospitalized. Conclusion Viral pathogen prevalence was high (75%) in our study population. Despite this, 100% of children received antibiotics, underscoring a need to expand laboratory diagnostic capacity and to revisit clinical guidelines implementation in these children. Continuous surveillance and serologic studies among more diverse age groups, with greater geographic breadth, are needed in Sierra Leone to better characterize the long-term impact of COVID-19 on respiratory virus prevalence and to better characterize the seasonality of respiratory viruses in Sierra Leone.

BackgroundWheezing is a continuous musical sound that can be produced by oscillation of opposing walls of an airway that is narrowed almost to the point of closure 1; it affects approximately one-third of children at least once by the age of nine and is a significant cause of morbidity and mortality in young children worldwide2,3. While wheezing is only transient for most children, around 40% are still diagnosed with recurrent wheezing or asthma after the age of six years2,4. Wheezing is often induced by various respiratory tract infections, which include respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), influenza viruses, parainfluenza viruses (PIV), and coronavirus 2. While RSV is the leading cause of hospitalization for lower respiratory tract infection (LRTI) and first wheezing episode in infants3,5, recent improvements in virus detection through methods such as real-time reverse transcriptase polymerase chain reaction (qRT-PCR) have allowed investigators to better elucidate the important role of HRV in LRTIs, wheezing and asthma development. HRV is now known to be the most common virus associated with wheezing at ages 6-12 months and is the second most common virus detected among wheezing infants during the first six months of life, after RSV6,7.Developments in molecular diagnostics have also contributed to the discovery of HMPV and its role in respiratory illnesses8. Because studies show that virus-associated wheezing and LRTI during infancy are associated with the subsequent development of childhood asthma, it is important to determine which viruses are most strongly associated with wheezing and to assess other risk factors that contribute to wheezing, in order to develop interventions when possible6. Few viral epidemiological studies in the Middle East focus on the association between wheezing and respiratory viruses9,10. Our study aimed to determine the association of wheezing with respiratory viruses, demographic and clinical characteristics in young children.