Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea

Abstract

Background: Astroviruses infect a variety of mammals and birds and are causative agents of diarrhea in humans and other animal hosts. We have previously described the identification of several sequence fragments with limited sequence identity to known astroviruses in a stool specimen obtained from a child with acute diarrhea, suggesting that a novel virus was present.

Results: In this study, the complete genome of this novel virus isolate was sequenced and analyzed. The overall genome organization of this virus paralleled that of known astroviruses, with 3 open reading frames identified. Phylogenetic analysis of the ORFs indicated that this virus is highly divergent from all previously described animal and human astroviruses. Molecular features that are highly conserved in human serotypes 1-8, such as a 3'NTR stem-loop structure and conserved nucleotide motifs present in the 5'NTR and ORF1b/2 junction, were either absent or only partially conserved in this novel virus.

Conclusion: Based on the analyses described herein, we propose that this newly discovered virus represents a novel species in the family Astroviridae. It has tentatively been named Astrovirus MLB1.

Figure 1

Multiple sequence alignments of putative astrovirus regulatory regions. A.) Alignment of the 20 nucleotides at the very 5' end of the Astrovirus MLB1 genome with those of fully sequenced astroviruses. MLB1 only shares 13 of the 20 conserved nucleotides present in human strains 1–8. B.) Alignment of the 52 nt highly conserved nucleotide motif (shown in box) present immediately upstream of the ORF1b/ORF2 junction of Astrovirus MLB1 and other astroviruses. (Note: there is no overlap in the Turkey Astroviruses). MLB1 lacks the high degree of sequence identity seen between the human astroviruses. The start codon of ORF2 is shown underlined and the stop codon of ORF1b is shown italicized in bold for each virus.

Figure 2

Phylogenetic analysis of AstV-MLB1 open reading frames. Phylogenetic trees are based on amino acid sequences and were generated using the maximum parsimony method with 1,000 bootstrap replicates. Significant bootstrap values are shown. (A) ORF1a; (B) ORF1b; (C) ORF2. HAstV = Human astrovirus; CAstV = Chicken astrovirus; MAstV = Mink astrovirus; TAstV = Turkey astrovirus; OAstV = Ovine astrovirus.