Genomic Analysis of Lumpy Skin Disease Virus from Western and Central Africa Suggests a Distinct Sub-Lineage within the 1.2 LSDV Cluster

Lumpy Skin Disease Virus (LSDV) is a highly contagious, transboundary pathogen that affects cattle, causing sig-nificant economic losses, particularly in Africa and Asia. While the virus was originally endemic to sub-Saharan Africa, it has rapidly spread to Europe, the Middle East, and Asia, necessitating comprehensive genomic surveil-lance. Despite LSDV’s African origins, genomic data from West and Central Africa remain scarce, limiting insights into regional viral evolution and vaccine compatibility. In this study, we used molecular detection, sequencing, and comparative genomic analysis to characterise LSDV strains circulating in Nigeria, Cameroon, and the Republic of Benin. Phylogenetic evaluation revealed that LSDV strains from Nigeria and Cameroon cluster within the classical 1.2 lineage, but do not align with known sub-lineages, suggesting the presence of a novel West/Central African sub-lineage. Functional genomic analysis identified mutations in genes encoding ankyrin repeat kelch-like proteins, and envelope proteins known for immune evasion, as well as virulence-associated genes, raising concerns about vaccine effectiveness. Furthermore, the detection of LSDV in flesh flies (Sarcophaga spp.) underlines their potential role in virus transmission. These findings highlight the importance of genomic monitoring and targeted surveil-lance or polyvalent vaccines to address emerging variants, and improve disease control strategies.