Patterns of nucleotide substitutions in influenza A virus genes

Abstract

The pattern of nucleotide substitution among the four nucleotides (A, T, C, and G) was studied for seven different genes of the influenza A virus. The direction of substitution was inferred by examining phylogenetic trees reconstructed (Saitou and Nei 1986), and the relative frequency of nucleotide substitutions was computed by Gojobori et al.′s (1982) method. It is found that the transitional changes (between A and G and between T and C) are much more abundant (about 70%) than expected under random substitution. Among the four types of transitional changes, the G→A change is most frequent. There are negative correlations between the chemical distance of nucleotides and the substitution pattern at the first and second codon positions for all genes examined. This result suggests that the influenza virus genes are subject to the purifying selection even though they show an extraordinary high substitution rate.