Recurrent gene conversions and subcluster-specific variants are associated with

Background: Long-read sequencing has revealed complex variations, such as gene conversions in immunologically critical PE/PPE gene families, yet their role in Methods: We performed a comparative genomic analysis across a gradient of host-imposed selective pressure: chronic within-host infection, latent household transmission, and a 21-year clonal outbreak in Bern, Switzerland. Results: We observed a constrained accumulation of mutational events across distinct epidemiological settings, with rates ranging from 0.36 to 0.81 events per genome per year. Under minimal host-imposed selection, the pathogen accumulated only small-scale variants (i.e., SNPs and indels). During the outbreak, however, the genetic diversity landscape shifted toward larger-scale variants, including recurrent gene conversions and structural variations. Notably, an early PPE19-to-PPE18 conversion emerged in the ancestral strain and was maintained across the entire lineage. In contrast, 86% of variants were transient singletons, with only a small proportion persisting under selection. Conclusion: These findings suggest a framework in which