Genomic plasticity and phylogeny of sheeppox and goatpox viruses reveal progressive host and terrestrial adaptation

Sheeppox virus (SPPV) and Goatpox virus (GTPV), members of the genus Capripoxvirus, cause transboundary pox diseases in sheep and goats. Although disease is mostly host-specific, uncertainty of cross-infection always exists under mixed farming practices. A comprehensive genome-wide plasticity and phylogenetic analysis was performed by comparing 17 SPPV and 11 GTPV field strains with host-specific native SPPV-SP3-Nur and GTPV-GP5-Indora strains. Compared to the reference strains, SPPV TU-V02127 (NC_004002.1) and GTPV Pellor (NC_004003.1), both native strains showed genetically conserved core genes with variations concentrated in terminal regions genes linked to virulence and host interaction (B22R-like protein, kelch- like protein, serpins, ankyrin repeat proteins). The majority of studied SPPV and GTPV strains maintained strong genomic stability, except for a GTPV Yemen strain, for which cross-species (host) infection was reported, and a few strains showed evidence of frequent involvement as minor parents in interspecies recombination within highly plastic regions containing genes for immune evasion and host determinants. Phylogenetic analysis of 28 complete genomes showed host-specific, territory-definite clades and subclades with SP3-Nur and GP5-Indora clustering within the Asian subclade S2.3 and G1.1, respectively, representing Indian regional subclades. This study highlights the progressive host as well as terrestrial adaptation of SPPV and GTPV in general. Though the existence of strains with high genomic plasticity may be a localised and evolving high-risk phenomenon at present, it poses a larger threat of transboundary and cross-species spread. These findings underscore the need for wider genomic surveillance to monitor viral transmission and tracking transboundary spread for effective disease management.