title: Capsid protein sequence diversity of chicken astrovirus.
abstract: The complete capsid gene sequences of 24 chicken astroviruses (CAstVs), collected in the UK, Germany, the Netherlands and South Africa from the 1980s to 2008, were determined and compared with that of a US CAstV (UGA-2006). Pairwise comparisons and phylogenetic analysis demonstrated the existence of two major capsid groups, designated A and B, which shared 38 to 40% amino acid identity. CAstVs from groups A and B shared capsid protein identities ranging from 26 to 38% with other avian astroviruses. The group A CAstVs comprised three subgroups, which displayed inter-subgroup identities ranging from 77 to 82%, while group B comprised two clearly separated subgroups, Bi and Bii, which displayed intra-subgroup identities of 97 to 99% and 94 to 99%, respectively, and shared inter-subgroup identities of 84 to 85%. Phylogenetic analyses performed with contiguous open reading frame 1b (polymerase) and open reading frame 2 (capsid) CAstV sequences showed that CAstVs from capsid subgroup Bi had polymerase genes that differed from those possessed by CAstVs belonging to group A and subgroup Bii. The N-terminal capsid regions (residues 1 to 415) were more conserved than the C-terminal regions, with the C-terminal regions of the subgroup Bi and Bii CAstVs sharing 76 to 78% amino acid identity, while the C-terminal regions of the A subgroups displayed identities less than 75%. CAstVs representative of both capsid groups and more than one subgroup were detected within the same broiler flock. The high level of capsid sequence diversity observed in this study has important implications for both the control and diagnosis of CAstV infections.
authors.affiliation: Agri-Food & Biosciences Institute, Stoney Road, Stormont, Belfast, UK. victoria.smyth@afbini.gov.uk
authors.forename: V J
authors.initials: VJ
authors.lastname: Smyth
authors.forename: D
authors.initials: D
authors.lastname: Todd
authors.forename: J
authors.initials: J
authors.lastname: Trudgett
authors.forename: A
authors.initials: A
authors.lastname: Lee
authors.forename: M D
authors.initials: MD
authors.lastname: Welsh
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D052676:Avastrovirus / Q000145:classification / Q000235:genetics*; D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics*; D002645:Chickens / Q000821:virology*; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D005060:Europe; D014644:Genetic Variation; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013019:South Africa; D013045:Species Specificity; D014481:United States
chemical_list: D036022:Capsid Proteins; D017931:DNA Primers