title: Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS.
abstract: Although sequencing of the 3' end of the genome of Australian infectious bronchitis viruses (IBVs) has shown that their structural genes are distinct from those of IBVs found in other countries, their replicase genes have not been analysed. To examine this, the complete genomic sequences of the two subpopulations of the VicS vaccine, VicS-v and VicS-del, were determined. Compared with VicS-v, the more attenuated VicS-del strain had two non-synonymous changes in the non-structural protein 6 (nsp6), a transmembrane (TM) domain that may participate in autocatalytic release of the 3-chymotrypsin-like protease, a polymorphic difference at the end of the S2 gene, which coincided with the body transcription-regulating sequence (B-TRS) of mRNA 3 and a truncated open reading frame for a peptide encoded by gene 4 (4b). These genetic differences could be responsible for the differences between these variants in pathogenicity in vivo, and replication in vitro. Phylogenetic analysis of the whole genome showed that VicS-v and VicS-del did not cluster with strains from other countries, supporting the hypothesis that Australian IBV strains have been evolving independently for some time, and analyses of individual polymerase peptide and S glycoprotein genes suggested a distant common ancestor with no recent recombination. This study suggests the potential role of the TM domain in nsp6, the integrity of the S2 protein and the B-TRS 3, and the putative accessory protein 4b, as well as the 3' untranslated region, in the virulence and replication of IBV and has provided a better understanding of relationships between the Australian vaccine strain of IBV and those used elsewhere.
authors.affiliation: a Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences , The University of Melbourne , Parkville , Victoria , Australia.
authors.forename: José A
authors.initials: JA
authors.lastname: Quinteros
authors.forename: Philip F
authors.initials: PF
authors.lastname: Markham
authors.forename: Sang-Won
authors.initials: SW
authors.lastname: Lee
authors.forename: Kylie A
authors.initials: KA
authors.lastname: Hewson
authors.forename: Carol A
authors.initials: CA
authors.lastname: Hartley
authors.forename: Alistair R
authors.initials: AR
authors.lastname: Legione
authors.forename: Mauricio J C
authors.initials: MJ
authors.lastname: Coppo
authors.forename: Paola K
authors.initials: PK
authors.lastname: Vaz
authors.forename: Glenn F
authors.initials: GF
authors.lastname: Browning
mesh_terms: D001315:Australia; D001483:Base Sequence; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D001351:Infectious bronchitis virus / Q000235:genetics* / Q000472:pathogenicity; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D014765:Viral Vaccines / Q000235:genetics; D014779:Virus Replication / Q000235:genetics
chemical_list: D017361:Viral Nonstructural Proteins; D014765:Viral Vaccines