Sequencing approach to analyze the role of quasispecies for classical swine fever

Classical swine fever virus (CSFV) is a positive-sense RNA virus with a high degree of genetic variability among isolates. High diversity is also found in virulence, with strains covering the complete spectrum from avirulent to highly virulent. The underlying genetic determinants are far from being understood. Since RNA polymerases of RNA viruses lack any proof-reading activity, different genome variations called haplotypes, occur during replication. A set of haplotypes is referred to as a viral quasispecies. Genetic variability can be a fitness advantage through facilitating of a more effective escape from the host immune response. In order to investigate the correlation of quasispecies composition and virulence in vivo, we analyzed next-generation sequencing data of CSFV isolates of varying virulence. Viral samples from pigs infected with the highly virulent isolates “Koslov” and “Brescia” showed higher quasispecies diversity and more nucleotide variability, compared to samples of pigs infected with low and moderately virulent isolates.

► Quasispecies analysis of ex vivo CSFV samples was applied using next generation sequencing.
► QuRe, QuasiRecomb, and ShoRAH software were used for quasispecies analysis.
► Highly virulent CSFV isolates showed the highest genome variability and quasispecies diversity.