Molecular Clock Analysis and Ancestral Range Reconstruction of Monkeypox Virus Clade IIb Spread in West Africa: Nigeria as the Epicenter of a Global Re-Emergence Event

The re-emergence of mpox (formerly monkeypox) caused by Monkeypox virus (MPXV) clade IIb from Nigeria in 2017, and the subsequent multi-country global outbreak of 2022, identified Nigeria as the probable geographic origin of a novel MPXV transmission lineage with enhanced human-to-human spread potential. Understanding the molecular clock dynamics and ancestral geographic range of clade IIb within Nigeria is essential for reconstructing the emergence event and informing global outbreak response preparedness. This dissertation presents a comprehensive molecular clock and ancestral range reconstruction analysis of MPXV clade IIb, incorporating sequence data from Nigerian clinical cases spanning 2017-2024 alongside international clade IIb sequences from the 2022 global outbreak. Full MPXV genomes were generated from 98 confirmed mpox cases across Rivers, Lagos, Bayelsa, Abuja, and Cross River using hybrid capture enrichment sequencing on Illumina platforms. All genomes were combined with 342 international MPXV clade IIb sequences available in public databases. Molecular clock analysis employed BEAST2 with an uncorrelated lognormal relaxed clock model and GTR+Gamma+I substitution model. Ancestral geographic range reconstruction applied BioGeoBEARS in a Maximum Likelihood framework, and discrete phylogeography was conducted in BEAST2 using BSSVS. Molecular clock analysis estimated a mean evolutionary rate of 5.2x10-5 substitutions/site/year for clade IIb, with the time to most recent common ancestor (tMRCA) for the global clade estimated at 2014.8 (95% HPD: 2012.4-2016.9), pre-dating the recognized 2017 Nigerian outbreak. Rivers State was recovered as the highest-probability ancestral range state for the root node of the global clade IIb phylogeny. APOBEC3 hypermutation signatures were identified in 89% of Nigerian genomes, supporting immune pressure-driven evolution during sustained human transmission. Two distinct Nigerian sub-clades with differential international export histories were characterized. These original molecular clock findings redefine the evolutionary origins of the global mpox emergency and position Nigeria at the center of clade IIb emergence epidemiology. Keywords: mpox, MPXV clade IIb, molecular clock, ancestral range reconstruction, Nigeria.