This work package (WP) will apply cutting-edge phylogenetic analyses to a database of African swine fever virus (ASFV) and lumpy skin disease virus (LSDV) full genome sequences in order to understand the evolution and spread of these viruses and develop tools for disease control.
Very few strains of ASFV or LSDV have been fully sequenced. Most previous phylogenetic studies have therefore relied on analysis of a limited number (usually two-three) of open reading frames (ORFs). This WP will use complete viral genomes (150-170 ORFs) to carry out phylogenetic analyses. This will be possible due to a large-scale full genome sequencing project of LSDV and ASFV genomes currently underway at The Pirbright Institute, funded by the British Biotechnology and Science Research Council (BBSRC).
Data from this project, plus additional strains with well documented metadata donated by consortium partners, will be studied. Historical and real-time phylodynamics will be researched in order to investigate the source and pathways of spread of ASFV and LSDV, supporting the development of strategies to prevent virus introduction. In addition, attenuated and virulent strains will be compared to identify putative viral virulence factors. Finally, the resulting sequence information and strain and DNA collections will be valorised to develop or validate new qPCR-based LSD diagnostic tests with strain specificity.