Potential link of single nucleotide polymorphisms to virulence of vaccine-associated field strains of lumpy skin disease virus in South Africa.

South Africa is endemic for lumpy skin disease and is therefore reliant on various live attenuated vaccines for the control and prevention of the disease. In recent years, widespread outbreaks of vaccine-like strains of lumpy skin disease virus (LSDV) were reported internationally, leading to an increase in the generation of full genome sequences from field isolates. In this study, the complete genomes of six LSDVs submitted during active outbreaks in the 1990s in South Africa were generated. Based on phylogenetic analysis, the six viruses clustered with vaccine strains in LSDV Subgroup 1.1 and are subsequently referred to as vaccine-associated. The genetic differences between the phenotypically distinct vaccine and vaccine-associated strains were 67 single nucleotide polymorphisms (SNPs). This study characterized the location and possible importance of each of these SNPs in their role during virulence and host specificity.

Sequence analysis and evaluation of the NS3/A gene region of bluetongue virus isolates from South Africa.

Phylogenetic networks and sequence analysis allow a more accurate understanding of the serotypes, genetic relationships and epidemiology of viruses. Based on gene sequences of the conserved segment 10 (NS3), bluetongue virus (BTV) can be divided into five topotypes. In this molecular epidemiology study, segment 10 sequence data of 11 isolates obtained from the Virology Section of the Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, were analyzed and compared to sequence data of worldwide BTV strains available in the GenBank database. The consensus nucleotide sequences of NS3/A showed intermediate levels of variation, with the nucleotide sequence identity ranging from 79.72 % to 100 %. All 11 strains demonstrated conserved amino acid characteristics. Phylogenetic networks were used to identify BTV topotypes. The phylogeny obtained from the nucleotide sequence data of the NS3/A-encoding gene presented three major and two minor topotypes. The clustering of strains from different geographical areas into the same group indicated spatial spread of the segment 10 genes, either through gene reassortment or through the introduction of new strains from other geographical areas via trade. The effect of reassortment and genetic drift on BTV and the importance of correct serotyping to identify viral strains are highlighted.