Estimating evolutionary changes between highly passaged and original parental lumpy skin disease virus strains.

Area of Science:

• Virology
• Evolutionary Biology
• Genomics

Background:

• Lumpy skin disease virus (LSDV) research was limited by its historical distribution to sub-Saharan Africa.
• Recent global spread and economic impact of LSDV necessitate deeper understanding of its evolution and phylogeny.
• Previous hypotheses on LSDV vaccine strain origins lacked comprehensive genomic evidence.

Purpose of the Study:

• To delineate the phylogenetic relationships of LSDV strains using full genome sequences.
• To investigate the evolutionary history and substitution rates of LSDV.
• To compare the genomic changes in field strains versus cell culture-passaged strains.

Main Methods:

• Sequencing of historical (1954) and recent (2018) South African LSDV field isolates.
• Sequencing of a high-passage cell culture LSDV strain.
• Phylogenetic analysis of full genome sequences, including single nucleotide polymorphism (SNP) analysis.

Main Results:

• The oldest field strain (1954) clusters with attenuated vaccine strains (cluster 1.1), refuting prior attenuation hypotheses.
• Recent field isolates (2018) belong to cluster 1.2, indicating displacement of cluster 1.1 strains in South Africa.
• The first LSDV substitution rate was established at 7.4 × 10⁻⁶ substitutions/site/year, with mutations in synonymous sites or intergenic regions.
• In vitro propagation generates non-synonymous SNPs in virus-replication genes, unlike in vivo evolution.

Conclusions:

• LSDV evolution involves distinct genetic clusters that dominate over time, with cluster 1.2 displacing cluster 1.1 in South Africa.
• The study provides the first evolutionary rate for LSDV, crucial for understanding its epidemiology.
• Cell culture adaptation significantly alters LSDV genome, highlighting the importance of using field isolates for evolutionary studies.