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

Abstract

Phylogenetic networks and sequence analyses allow for a more accurate understanding of the serotype, genetic relationships and the epidemiology of viruses. Based on gene sequences of the conserved segment 10 (NS3), bluetongue virus 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 on GenBank. The consensus nucleotide sequences of NS3/A showed intermediate levels of nucleotide variation with a nucleotide 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.