Developing a Genomic Surveillance Framework for Early Detection of Novel Respiratory Virus Variants in Nigeria: Infrastructure, Algorithms, and Policy Integration

Nigeria's experience during the SARS-CoV-2 pandemic revealed critical gaps in genomic surveillance infrastructure, bioinformatics capacity, and policy integration mechanisms that delayed variant detection and response. This mixed-methods implementation science and genomics study developed and evaluated a scalable genomic surveillance framework for novel respiratory virus variants across six sentinel sites representing all geopolitical zones: Abuja (North Central), Kano (North West), Maiduguri (North East), Enugu (South East), Lagos (South West), and Port Harcourt (South South). Phase one established sequencing infrastructure, bioinformatics workflows, and sentinel site sample flow algorithms. Phase two evaluated the framework's performance over 18 months using influenza, SARS-CoV-2, RSV, and metapneumovirus sequence data from 1,200 samples. Phase three used policy analysis and stakeholder engagement to develop an integration roadmap for Nigeria Centre for Disease Control genomic intelligence processes. Framework sensitivity for variant detection versus international reference databases was 97.6 percent. Median turnaround from sample to sequence report was reduced from 28 to 9 days through workflow optimization. Bioinformatics capacity was built for 24 scientists across six sites. A national genomic surveillance policy brief incorporating WHO global influenza surveillance network standards was developed. This study delivers an original, context-adapted, theoretically grounded genomic surveillance framework for Nigeria with a validated multi-pathogen application that directly addresses post-pandemic preparedness gaps. Keywords: genomic surveillance, respiratory viruses, Nigeria, variant detection, implementation science.