Genomic analysis of closely related astroviruses

Abstract

To understand astrovirus biology, it is essential to understand factors associated with its evolution. The current study reports the genomic sequences of nine novel turkey astrovirus (TAstV) type 2-like clinical isolates. This represents, to our knowledge, the largest genomic-length data set available for any one astrovirus type. The comparison of these TAstV sequences suggests that the TAstV species contains multiple subtypes and that recombination events have occurred across the astrovirus genome. In addition, the analysis of the capsid gene demonstrated evidence for both site-specific positive selection and purifying selection.

FIG. 1.

Phylogenetic relationship of TAstV-2-like viruses. (A) A Bayesian phylogenetic tree describing evolutionary relationships among predicted amino acid sequences for human (HAstV), pig (PAstV), sheep (OAstV), mink (MAstV), avian (ANV), and turkey (TAstV) astrovirus capsids. (B to E) Bayesian phylogenetic trees describing the nucleotide relationships among the newly reported TAstV-2-like isolates and the TAstV-2/NC/99 reference sequence. Alignments were constructed using whole genomes (B), ORF1a (C), ORF1b (D), and ORF2 (E). Branch lengths represent the expected number of amino acid substitutions (A) and the expected number of nucleotide substitutions per site (B to E). Posterior support values are shown only for nodes with values less than 0.95. Estimates of phylogeny were made by using the MrBayes program (6).

FIG. 2.

Phylogenetic evidence for recombination across TAstV-2-like virus genomes. (A) All pairwise comparisons of the TAstV-2-like genomic sequences were tested by using GENECONV to identify the sites of recombination between isolates (P < 0.05). Gray rectangles represent the TAstV-2 genome and individual ORFs. The start and end of each black line correspond to the relative locations within the genome of the start and end of the recombination breakpoint as identified by GENECONV. (B) The analysis of recombination in the multiple alignments of TAstV-2-like isolates was also performed by using the TOPALi program. On the x axis, the nucleotide position within the genome is shown, while the likelihood ratio (LRT) score indicating support for recombination is shown on the y axis. The LRT score corresponds to the difference in likelihood between models that restrict recombination and models that allow for recombination at a particular nucleotide position. LRT scores above the dashed horizontal line are significant at a P of 0.05.