Prevalence of respiratory viral pathogens in nasopharyngeal and oropharyngeal specimens and clinical outcomes in young children presenting with severe acute respiratory infections at Kenyatta National Hospital

Abstract

Background Acute respiratory infections are one of the leading causes of under-5 mortality worldwide with the majority of these deaths occurring in the developing countries. Viruses have been shown to contribute significantly to the burden of respiratory infections (1). Improved diagnostic tests have improved viral yield but remain costly and as such, there is limited data on respiratory virus burden in resource poor settings such as Kenya. Objectives To determine the prevalence and spectrum of respiratory viral pathogens from nasopharyngeal and oropharyngeal specimens among children aged 2-59 months hospitalized with severe acute respiratory illness (SARI) at Kenyatta National Hospital To describe and compare the clinical outcomes of children with SARI with and without respiratory viral pathogens isolated. Design, Setting and Participants This hospital based short longitudinal survey was conducted at Kenyatta National Hospital (KNH), the main referral hospital in Kenya. Participants were children aged 2 months to 59 months hospitalized in the general pediatric wards with severe acute respiratory illness (SARI) as defined by an adapted WHO SARI case definition. Methods Patients were enrolled consecutively and nasopharyngeal and oropharyngeal swabs tested using polymerase chain reaction for adenovirus(AdV), respiratory syncytial virus (RSV), human metapneumovirus (HMPV), influenza A and B (FluA and FluB) and parainfluenza viruses (PIV) 1 to 3. Good outcomes was discharge ≤5days while poor outcomes included prolonged hospital stay> 5 days, admission in the intensive care unit or death. Results We enrolled 281 patients with a median age of 10 months (IQR, 6-13), 54.8% were male. Respiratory viruses were detected in 177 of the 281 participants giving a prevalence of 63.0% [95% CI,57.1-68.6]. Adenovirus (AdV) was the most commonly detected (37.7%) followed by respiratory syncytial virus (RSV) (19.2%) and parainfluenza 3 (PIV 3) (13.5%). Co-infections with more than one virus were present in 50 (17.8%) cases. Poor outcomes were similar in children with viral isolates and without viral infection (Odds Ratio (OR): 1.139, 95%CI: 0.694-1.871) p=0.606. Conclusion The majority of SARI cases had a virus detected, mainly adenovirus . Viral coinfections were not unusual most of which were co- infections with adenovirus. More than half of the patients with SARI had a prolonged hospital stay but ICU admission and death were rare outcomes of hospitalization.