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Complete genome sequence of canine astrovirus with molecular and epidemiological characterisation of UK strains.

Caddy SL, Goodfellow I - Vet. Microbiol. (2015)

Bottom Line: These viruses can also cause infection in a range of domestic and wild animal species.Sequencing of the capsid sequences from the four CaAstV strains found significant genetic heterogeneity, with only 80% amino acid identity between strains.The full genome sequence of two UK CaAstV strains was then determined, confirming that CaAstV conforms to the classic genome organisation of other astroviruses with ORF1a and ORF1b separated by a frameshift and ORF2 encoding the capsid protein.

View Article: PubMed Central - PubMed

Affiliation: Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge CB2 2QQ, UK; Section of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1PG, UK. Electronic address: slc50@cam.ac.uk.

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Analysis of ORF1a/1b −1 frameshift site. (A) Predicted structure of the −1 frameshift site, directed by a slippery heptamer sequence and a downstream stem loop structure. (B) Sequence alignment of CaAstV and a range of human astrovirus (HuAstV) isolates shows this region to be highly conserved. The slippery heptamer sequence is highlighted in bold, and the stem loop structure is boxed, with nucleotides in bold representing differences.
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fig0020: Analysis of ORF1a/1b −1 frameshift site. (A) Predicted structure of the −1 frameshift site, directed by a slippery heptamer sequence and a downstream stem loop structure. (B) Sequence alignment of CaAstV and a range of human astrovirus (HuAstV) isolates shows this region to be highly conserved. The slippery heptamer sequence is highlighted in bold, and the stem loop structure is boxed, with nucleotides in bold representing differences.

Mentions: ORF1a also encodes the viral genome-linked protein, VPg (Fuentes et al., 2012) (Fig. 4C). CaAstV VPg is predicted to start at aa 656, at a conserved QK cleavage site and is 90 aa in length. In other astroviruses, it has been proposed that the C-terminal VPg cleavage site is coded by Q(P/A/S/L) (Al-Mutairy et al., 2005), and the presence of a QS dipeptide at the same site in CaAstV is consistent with this prediction. The amino acid motif KGK(N/T)K is conserved at the N-terminal end of VPg sequences from both astroviruses and caliciviruses, and this is also identifiable in the CaAstV genome. Another conserved VPg motif is TEXEY, with mutagenesis studies indicating that the Y (tyrosine) residue covalently links VPg to viral RNA (Fuentes et al., 2012). Analysis of the CaAstV ORF1a sequence also identifies the conserved TEXEY motif at 684–688, thus this tyrosine is predicted to covalently link to the RNA genome. However, the CaAstV sequence diverges slightly from the other mamastroviruses studied, in that X of the motif corresponds to K, whereas this is E/Q in all other mamastroviruses.


Complete genome sequence of canine astrovirus with molecular and epidemiological characterisation of UK strains.

Caddy SL, Goodfellow I - Vet. Microbiol. (2015)

Analysis of ORF1a/1b −1 frameshift site. (A) Predicted structure of the −1 frameshift site, directed by a slippery heptamer sequence and a downstream stem loop structure. (B) Sequence alignment of CaAstV and a range of human astrovirus (HuAstV) isolates shows this region to be highly conserved. The slippery heptamer sequence is highlighted in bold, and the stem loop structure is boxed, with nucleotides in bold representing differences.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401448&req=5

fig0020: Analysis of ORF1a/1b −1 frameshift site. (A) Predicted structure of the −1 frameshift site, directed by a slippery heptamer sequence and a downstream stem loop structure. (B) Sequence alignment of CaAstV and a range of human astrovirus (HuAstV) isolates shows this region to be highly conserved. The slippery heptamer sequence is highlighted in bold, and the stem loop structure is boxed, with nucleotides in bold representing differences.
Mentions: ORF1a also encodes the viral genome-linked protein, VPg (Fuentes et al., 2012) (Fig. 4C). CaAstV VPg is predicted to start at aa 656, at a conserved QK cleavage site and is 90 aa in length. In other astroviruses, it has been proposed that the C-terminal VPg cleavage site is coded by Q(P/A/S/L) (Al-Mutairy et al., 2005), and the presence of a QS dipeptide at the same site in CaAstV is consistent with this prediction. The amino acid motif KGK(N/T)K is conserved at the N-terminal end of VPg sequences from both astroviruses and caliciviruses, and this is also identifiable in the CaAstV genome. Another conserved VPg motif is TEXEY, with mutagenesis studies indicating that the Y (tyrosine) residue covalently links VPg to viral RNA (Fuentes et al., 2012). Analysis of the CaAstV ORF1a sequence also identifies the conserved TEXEY motif at 684–688, thus this tyrosine is predicted to covalently link to the RNA genome. However, the CaAstV sequence diverges slightly from the other mamastroviruses studied, in that X of the motif corresponds to K, whereas this is E/Q in all other mamastroviruses.

Bottom Line: These viruses can also cause infection in a range of domestic and wild animal species.Sequencing of the capsid sequences from the four CaAstV strains found significant genetic heterogeneity, with only 80% amino acid identity between strains.The full genome sequence of two UK CaAstV strains was then determined, confirming that CaAstV conforms to the classic genome organisation of other astroviruses with ORF1a and ORF1b separated by a frameshift and ORF2 encoding the capsid protein.

View Article: PubMed Central - PubMed

Affiliation: Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge CB2 2QQ, UK; Section of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1PG, UK. Electronic address: slc50@cam.ac.uk.

Show MeSH
Related in: MedlinePlus