Sequencing and Analysis of Lumpy Skin Disease Virus Whole Genomes Reveals a New Viral Subgroup in West and Central Africa

Haga, Ismar R. and Shih, Barbara B. and Tore, Gessica and Polo, Noemi and Ribeca, Paolo and Gombo-Ochir, Delgerzul and Shura, Gansukh and Tserenchimed, Tsagaan and Enkhbold, Bazarragchaa and Purevtseren, Dulam and Ulziibat, Gerelmaa and Damdinjav, Batchuluun and Yimer, Lama and Bari, Fufa D. and Gizaw, Daniel and Adedeji, Adeyinka Jeremy and Atai, Rebecca Bitiyong and Adole, Jolly Amoche and Dogonyaro, Banenat Bajehson and Kumarawadu, Pradeep Lakpriya and Batten, Carrie and Corla, Amanda and Freimanis, Graham L. and Tennakoon, Chandana and Law, Andy and Lycett, Samantha and Downing, Tim and Beard, Philippa M. (2024) Sequencing and Analysis of Lumpy Skin Disease Virus Whole Genomes Reveals a New Viral Subgroup in West and Central Africa. Viruses, 16 (4): 557. ISSN 1999-4915

Abstract

Lumpy skin disease virus (LSDV) is a member of the capripoxvirus (CPPV) genus of the Poxviridae family. LSDV is a rapidly emerging, high-consequence pathogen of cattle, recently spreading from Africa and the Middle East into Europe and Asia. We have sequenced the whole genome of historical LSDV isolates from the Pirbright Institute virus archive, and field isolates from recent disease outbreaks in Sri Lanka, Mongolia, Nigeria and Ethiopia. These genome sequences were compared to published genomes and classified into different subgroups. Two subgroups contained vaccine or vaccine-like samples (“Neethling-like” clade 1.1 and “Kenya-like” subgroup, clade 1.2.2). One subgroup was associated with outbreaks of LSD in the Middle East/Europe (clade 1.2.1) and a previously unreported subgroup originated from cases of LSD in west and central Africa (clade 1.2.3). Isolates were also identified that contained a mix of genes from both wildtype and vaccine samples (vaccine-like recombinants, grouped in clade 2). Whole genome sequencing and analysis of LSDV strains isolated from different regions of Africa, Europe and Asia have provided new knowledge of the drivers of LSDV emergence, and will inform future disease control strategies.