Phylogenetic comparison of the genus Lyssavirus using distal coding sequences of the glycoprotein and nucleoprotein genes

Abstract

The phylogenetic relationships between all seven genotypes within the genus Lyssavirus were compared at the nucleotide level utilising two distal regions of the viral genome. The resulting analysis of each region produced similar, although not identical, phylogenetic results, suggesting that the evolutionary pressures on individual proteins within the genome vary. These differences are in part due to the increased variability observed within the glycoprotein sequence over the nucleoprotein sequence. Pair-wise comparison using the glycoprotein partial sequence between different isolates demonstrate that within genotypes, viruses show between 80 and 100% sequence identity, whilst between genotypes, viruses show between 50 and 75% identity. This provides a consistent guide to assigning new viruses to existing genotypes. Alignment of the amino acid sequence for the truncated glycoprotein sequence to the Pasteur Virus vaccine strain show significant residue variation between positions 139 and 170. However, residue variation tends to vary with genotype implying that these changes have not evolved due to immunological pressure from the host but have occurred following the separation of viruses into discrete groups. Comparison of the phylogenetic analysis for this partial region of the glycoprotein suggest that it gives comparable results to studies that have used larger regions of the Lyssavirus genome.