Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function

Background: Complete genome sequences of the Astroviridae include human, non- human mammalian and avian species. A consensus topology of astroviruses has been derived from nucleotide substitutions in the full- length genomes and from non- synonymous nucleotide substitutions in each of the three ORFs. Analyses of synonymous substitutions displayed a loss of tree structure, suggesting either saturation of the substitution model or a deviant pattern of synonymous substitutions in certain virus species. Results: We analyzed the complete Astroviridae family for the inference of adaptive molecular evolution at sites and in branches. High rates of synonymous mutations are observed among the non- human virus species. Deviant patterns of synonymous substitutions are found in the capsid structural genes. Purifying selection is a dominant force among all astrovirus genes and only few codon sites showed values for the dN/ dS ratio that may indicate site- specific molecular adaptation during virus evolution. One of these sites is the glycine residue of a RGD motif in ORF2 of human astrovirus serotype 1. RGD or similar integrin recognition motifs are present in nearly all astrovirus species. Conclusion: Phylogenetic analysis directed by maximum likelihood approximation allows the inclusion of significantly more evolutionary history and thereby, improves the estimation of dN and dS. Sites with enhanced values for dN/ dS are prominent at domains in charge of environmental communication ( f.i. VP27 and domain 4 in ORFIa) more than at domains dedicated to intrinsic virus functions ( f.i. VP34 and ORFIb ( the virus polymerase)). Integrin recognition may play a key role in astrovirus to target cell attachment.