Defining the Virome of Paediatric Febrile Illness in Rural North East Nigeria Using Metagenomic Sequencing: Discovery of Novel and Known Viral Pathogens

Paediatric febrile illness in rural northern Nigeria is predominantly attributed to malaria by default clinical diagnosis, yet substantial proportions of fever episodes are likely viral in aetiology and remain completely uncharacterised. North East Nigeria, with its fragile health infrastructure and post-conflict population displacement, represents a context where undiscovered viral pathogens may circulate undetected. This study characterises the complete virome of paediatric febrile illness in rural Yobe and Borno states using unbiased metagenomic next-generation sequencing. Children aged 6 months to 12 years presenting with acute undifferentiated fever at 10 primary healthcare centres will be enrolled over 24 months. Malaria-negative febrile cases (n=400) and matched asymptomatic controls (n=200) will provide nasopharyngeal swabs, blood, and stool for metagenomic analysis using the Illumina NextSeq platform. Bioinformatics pipelines (Kraken2, DIAMOND, VIBRANT) will classify viral reads against comprehensive reference databases. Novel viral contigs will be assembled and characterised phylogenetically. Known viral pathogens detected will be clinically correlated with severity indices and laboratory parameters. This study makes a landmark contribution to West African paediatric virology by generating the first comprehensive febrile illness virome dataset from rural North East Nigeria, establishing which known viral pathogens are responsible for malaria-negative fevers and potentially discovering novel viruses with public health significance in this vulnerable population. Keywords: paediatric virome, metagenomics, febrile illness, North East Nigeria, novel viruses