Genomic Surveillance

The study generated 338 high-quality MPXV genomes from Sierra Leone cases sampled between 10 January and 3 August 2025. The analysis included 340 high-quality genomes after adding two external genomes. Sampling coverage and spatial heterogeneity limited the study's inference. Air travel contributes to the global dispersal of variants of concern. Mpox-positive samples with Ct values of 30 or lower were prioritized for sequencing. Sampling bias is an important limitation for genomic surveillance and phylogeographic inference. Public genomes used in the analysis came from Pathoplexus. Metagenomic surveillance enables pathogen-agnostic detection from clinical or environmental samples. Phylogenetic and phylodynamic methods are central tools for understanding and responding to SARS-CoV-2. These genomic methods can reconstruct transmission histories, estimate epidemic parameters, and identify variant emergence events. Standardized dynamic lineage naming is necessary for global genomic epidemiology.