Genomic Diversity and Regional Epidemiologic Dynamics of mpox Clade II in Nigeria (2017–2024)

Objectives: The reappearance of monkeypox (mpox) in Nigeria since 2017 presented with significant epidemiological shifts which has raised serious public health concern both in the domestic and international front. To implement effective response strategies against the disease, understanding its genomic diversity and transmission dynamics is essential. This study aimed to investigate the genomic diversity and epidemiological patterns of mpox clade II in Nigeria from 2017 to 2024. Methods: 153 mpox clade II genome sequences obtained from 25 Nigerian states were retrieved from Nextstrain and GenBank. After quality assurance, 96 sequences were selected for further analysis. IQ-TREE and BEAST were used in constructing phylogenetic trees, while Nextclade was used for mutation profiling. Epidemiological data were obtained from NCDC and WHO reports. Results: Lineage A.2.3 of mpox clade II was observed to be the most prevalent during the outbreak of 2022. This coincides with the highest national incidence of mpox. Several non-synonymous mutations were identified, predominantly in the envelope proteins, and DNA polymerase. Regional disparities were observed, with the south-south and south-east regions reporting the highest case burdens. It was also observed that males aged 21–40 years were the prominently mpox infections age group. Conclusion: These findings emphasize the significance of continuous genomic surveillance and region-specific interventions for controlling mpox in Nigeria. Understanding local lineage dynamics and demographic risk factors is crucial for targeted outbreak responses.