A high-quality telomere-to-telomere lumpy skin disease virus genome assembly

Lumpy skin disease virus (LSDV) is an emerging livestock capripoxvirus (CaPV) that continues to cause substantial economic losses across Africa, Asia and Europe. However, important uncertainties remain regarding LSDV genome structure, particularly at the telomeric inverted terminal repeats (ITRs) that are central to host interaction, replication and adaptive evolution. Structural variation at the ITRs is driven by recombination during virus replication. Previous assemblies have relied primarily on short-read sequencing, which provides limited resolution of repeat-rich telomeric regions and propagates structural ambiguities into downstream annotation and comparative analyses. Here, we present a high-quality telomere-to-telomere assembly of the LSDV Oman 2009 isolate, generated using a hybrid approach that integrates short Illumina reads with higher-accuracy long Nanopore reads. The resulting 151,091 bp genome contains 157 annotated ORFs and fully resolves complex repeat-rich structures at both ITRs. This new reference corrects misassemblies present in earlier LSDV genomes and confirms clade-specific gene truncations. This genome provides a robust foundation for improved genomic surveillance, accurate read mapping, mutation detection and evolutionary inference of LSDV and demonstrates the value of long-read approaches for resolving complex CaPV genome structures.