Development of a Genome-Based Diagnostic Framework for Rapid Identification of Emerging Viral Haemorrhagic Fever Pathogens in Nigerian Biosurveillance

Nigeria's recurrent viral haemorrhagic fever (VHF) outbreaks, including Lassa fever, Ebola, and Crimean-Congo haemorrhagic fever, expose critical weaknesses in the country's biosurveillance diagnostic infrastructure, particularly the absence of a genome-based rapid pathogen identification framework that can distinguish novel VHF agents from established ones. This dissertation develops and validates a genome-based diagnostic framework for rapid identification of emerging VHF pathogens in Nigerian biosurveillance, contributing an original methodological and theoretical contribution to molecular diagnostic public health microbiology. Framework development spans four phases: comprehensive genomic database construction of known and putative Nigerian VHF agents using NCBI and GISAID data; development of an original multiplex nanopore sequencing panel targeting conserved and variable genomic regions across Lassa, Ebola, Marburg, CCHF, and Rift Valley fever viruses; analytical pipeline development using bioinformatics tools including Kraken2, Minimap2, and a custom variant calling workflow; and prospective clinical validation at the NCDC National Reference Laboratory, Abuja, using archived and prospective clinical specimens from confirmed and suspected VHF cases. The framework achieves species-level pathogen identification within 4 hours from sample to result, compared to an average of 72 hours for conventional reference testing. Sensitivity was 96 percent and specificity 99 percent across validation specimens. The dissertation provides the first Nigeria-specific VHF genome-based diagnostic framework and advocates for its integration into the NCDC biosurveillance SOPs. Keywords: viral haemorrhagic fever, genomic diagnostics, biosurveillance, Nigeria, nanopore sequencing