Determination of the full length sequence of a chicken astrovirus suggests a different replication mechanism

The genomic RNA of a novel chicken astrovirus was determined. The full length sequence is 7520 nucleotides and encodes three open reading frames (1a, 1b, 2) for three proteins. The genomic organization was similar to other astroviruses with two exceptions. The open reading frame of the RNA-dependent RNA polymerase contains its own start codon which is different from other astroviruses described to date, providing evidence for a replication mechanism different than what has previously been described for astroviruses. Furthermore, the stem-loop structure located at the potential ribosomal frameshift signal described for other astroviruses has been shown to be a hairpin structure for the novel chicken astrovirus. Phylogenic analysis of the full length sequence revealed that this chicken astrovirus formed a branch independent from other astroviruses, indicating that this astrovirus is significantly different from astroviruses described to date.