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