Global evolutionary dynamics of peste des petits ruminants virus reveals geographic lineage structuring and clade-defining mutational signatures

Peste des petits ruminants virus (PPRV) is recognized as one of the most economically significant transboundary pathogens affecting small ruminants. However, despite the increasing availability of whole-genome sequences, comprehensive global analyses integrating evolutionary history, phylogeography, and genome-wide lineage-defining molecular markers remain limited. This study investigated the global genomic diversity, evolutionary history, and molecular characteristics of PPRV using whole-genome sequences. A total of 212 temporally informative whole-genome sequences, retrieved from GenBank (between 1969 and 2025) representing all four recognized PPRV lineages, were analyzed using comparative genomics, Bayesian time-scaled phylogenetic reconstruction, and genome-wide candidate phylogenetic marker; single nucleotide polymorphism (SNP) analysis and codon-based selective-pressure analyses. The results demonstrated high genomic conservation across all genomes despite their broad geographic distribution. Bayesian analysis estimated a mean evolutionary rate of 5.07 × 10 −4 substitutions per site per year (95% HPD: 4.79 × 10 −4 to 5.35 × 10 −4 ) and dated the most recent common ancestor of PPRV to 1839 (95% HPD: 1829 to 1848) which likely reflects the ancestry of currently sampled viral diversity rather than the historical emergence of PPRV. Lineage IV, the predominant contemporary lineage, was further subdivided into four geographically structured subclades: A, B.1, B.2a, and B.2b. A total of 125 subclade-associated fixed SNP signatures were identified, primarily within the L gene, with most variants resulting in nonsynonymous substitutions. The overlapping P, V, and C coding regions underscored the complex functional consequences of lineage-defining mutations. Gene-wide dN/dS values were below 1 for all six genes, indicating predominant purifying selection, while functional mapping identified several SNP related amino acid substitutions within experimentally characterized antigenic regions; however, these substitutions were not supported as positively selected in the present analyses. These results provide a comprehensive genomic framework for understanding PPRV evolution and identify candidate phylogenetic markers for lineage discrimination to support genomic surveillance, molecular epidemiology, and the Food and Agriculture Organization (FAO)-World Organisation for Animal Health (WOAH) Global PPR Eradication Programme.