Transmission Dynamics and Genomic Evolution of Monkeypox Virus in Nigeria Across Pre- and Post-COVID-19 Periods

Abstract The COVID-19 pandemic altered human civilization, healthcare systems, and disease surveillance, potentially influencing the transmission and evolution of zoonotic pathogens such as monkeypox virus (MPXV). However, changes in MPXV transmission dynamics and genomic evolution in Nigeria across pre- and post-COVID-19 periods remain poorly understood. To infer the transmission dynamics of the virus as influenced by the COVID-19 pandemic, we analyzed whole genomic sequences, and their associated metadata to reveal host range, circulating clades, and seasonal factors that could be implicated in its transmission. From the NCBI, MPXV sequences were retrieved together with their metadata. The whole genome sequences were categorized into pre, during, and post-COVID-19 periods. Neighbour joining trees were used infer the relationships between circulating clades during both periods. Principal component analysis (PCA) was used to evaluate how genome size, season, State of origin, and sample type influenced MPXV transmission dynamics across Nigeria. A total of 172 MPXV sequences from Nigeria (1971 to 2023) were retrieved, with outbreak peaks observed in 2017 to 2019 and 2022. Most cases were recorded in the months of September and October, followed by January to March, with southern States such as Bayelsa and Rivers reporting the highest numbers. Sample data lacked standardization, and seasonal analysis showed a weak correlation between outbreaks and seasons. PCA revealed the year of isolation as the most influential variable in transmission patterns. Phylogenetic analysis confirmed Clade IIb persistence across all periods, with links to exported cases in Singapore (2019), the UK, and the USA (2020 and 2022). There is a need to strengthen routine surveillance, standardize reporting, and targeted interventions.