Whole Genome Characterization of Lumpy Skin Disease Virus and Bovine Papular Stomatitis Virus Detected in Cattle During the 2024–2025 Outbreaks in Tunisia

Lumpy Skin Disease (LSD) is an economically significant viral disease of cattle, widely prevalent across Africa, particularly in sub-Saharan regions. In 2024, Tunisia reported its first outbreak. Understanding the genetic characteristics of lumpy skin disease virus (LSDV) and related poxviruses is critical for surveillance and control. Twenty-nine samples from 26 suspected cases were screened for LSDV using qPCR, followed by a High-Resolution Multiplex Melting (HRM) assay. Three representative samples, two LSDV-positive and one bovine papular stomatitis virus (BPSV)-positive, were subjected to whole-genome sequencing using Pacific Biosciences (PacBio) HiFi long-read technology. Phylogenetic analyses of the LSDV-marker gene RPO30 and complete genomes were performed alongside SNP and InDel profiling. The Tunisian LSDV isolates clustered with Clade 1.2.2 field strains and were 100% identical to each other and to the Italian isolate LSDV_Italy_Sardinia_2025, sharing 99.99% nucleotide identity with LSDV_V281_Nigeria. Although only two LSDV isolates were sequenced which showed no genetic differences, these findings suggest genomic stability within Clade 1.2.2. The Tunisian BPSV isolate showed high similarity (98.15–98.59%) to strains reported in Germany and Switzerland. This study presents the first genetic characterization of LSDV and BPSV in Tunisia, highlighting the importance of accurate differential diagnosis among poxviruses and continuous genomic surveillance to inform control strategies.