Statistical analysis of the envelope gene and the prM region of Japanese encephalitis virus: Evidence suggestive of positive selection

Abstract

The variation in nucleotide sequence observed in the envelope (E) gene and the prM (precursor of M protein) region of different strains of Japanese encephalitis virus (JEV) was analysed. Presence of selective forces acting on these regions was investigated by computing the relative rates of synonymous (Ks) and nonsynonymous (Ka) substitutions. The ratioKs/Ka was used as an indicator of the overall selective constraints on the amino acid sequence of JEV proteins. The possibility that different regions of the gene may be subject to varying selective pressures was tested by dividing the gene into three regions and estimating theKs/Ka ratio for each region. On the basis of analysis of a limited number (17) of strains of JEV, evidence suggestive of positive selection acting on certain regions of the E gene of the virus, and in some cases on the entire gene, was obtained. Analysis ofKa diversity in the prM region of 46 JEV strains grouped into three genotypes revealed that strains included in genotype II were more heterogeneous than strains belonging to genotype I, while the differences between meanKa values for genotypes I and III and genotypes II and III were not statistically significant. Analysis of host-specific heterogeneity in the prM region revealed that pig isolates were more Xa-diverse than human isolates.