Key result
Clustering of classical swine fever virus genomes based on their codon pair bias correlates with the genotype rather than with the virulence of the isolates.
Codon pair bias analysis of CSFV genomes supports phylogeny and clusters isolates by genotype rather than virulence.
Codon pair bias clustering aids CSFV genotyping but not virulence assessment; leaves open functional validation before broader application.
BACKGROUND: The genetic code consists of non-random usage of synonymous codons for the same amino acids, termed codon bias or codon usage. Codon juxtaposition is also non-random, referred to as codon context bias or codon pair bias. The codon and codon pair bias vary among different organisms, as well as with viruses. Reasons for these differences are not completely understood. For classical swine fever virus (CSFV), it was suggested that the synonymous codon usage does not significantly influence virulence, but the relationship between variations in codon pair usage and CSFV virulence is unknown. Virulence can be related to the fitness of a virus: Differences in codon pair usage influence genome translation efficiency, which may in turn relate to the fitness of a virus. Accordingly, the potential of the codon pair bias for clustering CSFV isolates into classes of different virulence was investigated. RESULTS: The complete genomic sequences encoding the viral polyprotein of 52 different CSFV isolates were analyzed. This included 49 sequences from the GenBank database (NCBI) and three newly sequenced genomes. The codon usage did not differ among isolates of different virulence or genotype. In contrast, a clustering of isolates based on their codon pair bias was observed, clearly discriminating highly virulent isolates and vaccine strains on one side from moderately virulent strains on the other side. However, phylogenetic trees based on the codon pair bias and on the primary nucleotide sequence resulted in a very similar genotype distribution. CONCLUSION: Clustering of CSFV genomes based on their codon pair bias correlate with the genotype rather than with the virulence of the isolates.
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Leifer et al. (2011) studied Classical swine fever virus (CSFV) isolates (n=52). Codon pair bias analysis was evaluated on Clustering of CSFV isolates. Clustering of classical swine fever virus genomes based on their codon pair bias correlates with the genotype rather than with the virulence of the isolates.
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