ヒトアウトブレイク検出とリスジ科のベストプラクティスMPXV分析と解釈

High numbers of reported mpox cases and recent identification of multiple sustained human outbreaks of mpox virus (MPXV) have highlighted the need for robust, best-practice genomic surveillance tools. In light of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, many labs across the globe developed the capacity to do virus genome sequencing; however, MPXV presents additional analytical challenges due to its large genome size, tracts of low-complexity or repeat regions, genetically distinct clades, and the need to perform bespoke apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3)-mutation reconstruction. We present squirrel (Some Quick Reconstruction to Resolve Evolutionary Links), an open source bioinformatic tool that can perform clade-aware alignment, mutation quality assessment, phylogenetic inference, and automated APOBEC3-mutation classification on branches of the phylogeny. Squirrel can be run on the command line or launched through the EPI2ME graphical user interface through the squirrel-nf workflow, enabling robust analysis without need for the command line. With the interactive output report produced and publication-ready APOBEC3-reconstruction visualization, squirrel enables researchers to distinguish between zoonotic and sustained human outbreaks and help accurately inform public health responses.