Defining Viral Co-Infection Patterns and Their Impact on Clinical Outcomes in Paediatric Pneumonia in South West Nigeria Using Comprehensive Multiplex Diagnostics

Paediatric pneumonia remains the leading cause of child death in Nigeria, yet the virological aetiology of severe childhood pneumonia in South West Nigeria is poorly characterised beyond single-pathogen studies. Viral co-infections involving RSV, influenza, rhinovirus, metapneumovirus, adenovirus, and SARS-CoV-2 may worsen pneumonia severity through immune interference mechanisms that are not captured by standard clinical diagnostics. This study defines viral co-infection patterns and their impact on clinical outcomes in paediatric pneumonia at three tertiary children's hospitals in Lagos, Ibadan, and Ilesha, Osun State, South West Nigeria. Children aged 1 month to 12 years hospitalised for radiologically confirmed pneumonia will be enrolled over 24 months (n=600). Nasopharyngeal specimens will undergo comprehensive multiplex real-time RT-PCR testing for 18 respiratory viruses using the Fast Track Diagnostics Respiratory Pathogen 21 kit. Disease severity will be scored using the Paediatric Respiratory Severity Score, and clinical outcomes including intensive care unit admission, mechanical ventilation, and 28-day mortality will be recorded. Multivariable regression and survival analysis will quantify the independent and interaction effects of specific co-infection combinations on clinical outcomes. Metagenomic characterisation of a subset of samples will capture unanticipated viral agents. This study produces an original dataset defining respiratory virome complexity in South West Nigerian paediatric pneumonia, providing a theoretically grounded assessment of viral co-infection pathogenesis with direct clinical and public health implications. Keywords: paediatric pneumonia, viral co-infections, respiratory virome, South West Nigeria, clinical outcomes