Implementation Challenges of Next-Generation Sequencing (NGS) for Pathogen Surveillance in Borno State: A Program Evaluation

Next-generation sequencing (NGS) has emerged as a transformative tool for genomic pathogen surveillance, enabling rapid characterization of emerging variants, outbreak clusters, and drug resistance evolution. Despite investment in NGS platforms at select Nigerian reference laboratories, implementation in fragile or conflict-affected states such as Borno presents unique challenges. This study evaluated NGS implementation for infectious disease pathogen surveillance within the Northeast Zonal Influenza and Pathogen Reference Laboratory framework serving Borno State. A program evaluation design was employed, combining document review, equipment audit, utilization data analysis, and semi-structured interviews with laboratory management, bioinformatics officers, and public health program staff. The analysis covered a 30-month operational period from 2022 to 2024. NGS platform utilization was below 40% of projected capacity, primarily due to reagent supply chain disruptions (mean stockout 11 weeks per year), power instability, and the absence of resident bioinformatics expertise. SARS-CoV-2 and influenza sequencing comprised 89% of NGS use, with limited application for tuberculosis or antimicrobial resistance surveillance as originally planned. Staff turnover in bioinformatics positions was 67% over the evaluation period. These findings identify structural and programmatic barriers to sustainable NGS implementation and propose corrective institutional and funding strategies for conflict-affected surveillance settings. Keywords: NGS, pathogen surveillance, implementation evaluation, bioinformatics, Borno State.