Classical swine fever virus (CSFV) contains a specific motif within the E2 glycoprotein that varies between strains of different virulence. In the highly virulent CSFV Koslov, this motif comprises residues S763/L764 in the polyprotein. However, L763/P764 represent the predominant alleles in published CSFV genomes. In this study, changes were introduced into the CSFV Koslov (here called vKos_SL), to generate modified CSFVs with substitutions at residues 763/764 (vKos_LL, vKos_SP and vKos_LP). The properties of these mutant viruses, in comparison to vKos_SL, were determined in pigs. Each of the viruses was virulent and induced typical clinical signs of CSF but the vKos_LP produced them significantly earlier. Full-length CSFV cDNA amplicons (12.3kb) derived from sera of infected pigs were deep sequenced and cloned to reveal the individual haplotypes that contributed to the single nucleotide polymorphism (SNP) profiles observed in the virus population. The SNP profiles for vKos_SL and vKos_LL displayed low-level heterogeneity across the entire genome, whereas vKos_SP and vKos_LP displayed limited diversity with a few high frequency SNPs. This indicated that vKos_SL and vKos_LL exhibited a higher level of fitness in the host and more stability at the consensus level, whereas several consensus changes were observed in the vKos_SP and vKos_LP sequences, pointing to adaptation. For each virus, only a subset of the variants present within the virus inoculums were maintained in the infected pigs. No clear tissue dependent quasispecies differentiation occurred within inoculated pigs, however, clear evidence for transmission bottle-necks to contact animals was observed, with subsequent loss of sequence diversity.IMPORTANCE The surface exposed E2 protein of classical swine fever virus is required for its interaction with host cells. A short motif within this protein varies between strains of different virulence. The importance of two particular amino acid residues in determining the properties of a highly virulent strain of the virus has been analyzed. Each of the different viruses tested proved highly virulent but one of them produced earlier, but not more severe, disease. By analyzing the virus genomes present within infected pigs, it was found that the viruses which replicated within inoculated animals were only a subset of those within the virus inoculum. Furthermore, following contact transmission, it was shown that a very restricted set of viruses had transferred between animals. There were no significant differences in the virus populations present in various tissues of the infected animals. These results indicate mechanisms of virus population change during transmission between animals.