Infectious bronchitis viruses with naturally occurring genomic rearrangement and gene deletion
Faculty of Veterinary Science, Veterinary Clinical Centre, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia.Archives of Virology (Impact Factor: 2.39). 11/2010; 156(2):245-52. DOI: 10.1007/s00705-010-0850-6
Infectious bronchitis viruses (IBVs) are group III coronaviruses that infect poultry worldwide. Genetic variations, including whole-gene deletions, are key to IBV evolution. Australian subgroup 2 IBVs contain sequence insertions and multiple gene deletions that have resulted in a substantial genomic divergence from international IBVs. The genomic variations present in Australian IBVs were investigated and compared to those of another group III coronavirus, turkey coronavirus (TCoV). Open reading frames (ORFs) found throughout the genome of Australian IBVs were analogous in sequence and position to TCoV ORFs, except for ORF 4b, which appeared to be translocated to a different position in the subgroup 2 strains. Subgroup 2 strains were previously reported to lack genes 3a, 3b and 5a, with some also lacking 5b. Of these, however, genes 3b and 5b were found to be present but contained various mutations that may affect transcription. In this study, it was found that subgroup 2 IBVs have undergone a more substantial genomic rearrangements than previously thought.
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- "IBV has a positive sense, single-stranded RNA genome approximately 27.6 kb in length (Tannock, 1973; Watkins et al., 1975; Schochetman et al., 1977; Jackwood & de Witt, 2013) with the general organization 5′ untranslated region (UTR) -1 a, ab (or polymerase genes) -S -3 a, b, c (E) -M -4 b, c -5 a, b -N -6b -3′ UTR (Cavanagh, 2007; Ammayappan et al., 2008). The genes encoding the structural proteins are S (spike glycoprotein), E (envelope glycoprotein), M (membrane glycoprotein) and N (nucleocapsid protein) (Ignjatovic et al., 1997; Cavanagh, 2007), while the 3a, 3b, 4b, 4c, 5a, 5b and 6b genes encode accessory proteins (Liu et al., 1991; Liu & Inglis, 1992a, b; Cao et al., 2008; Hewson et al., 2011; Bentley et al., 2013), the functions of which are still unknown (Liu et al., 2008). The S glycoprotein is a virion surface, rod-shaped protein that is post-translationally cleaved into two subunits, S1 and S2 (Cavanagh, 1981; Stern & Sefton, 1982; Cavanagh, 2007). "
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 nsp6, a transmembrane (TM) domain that may participate in autocatalytic release of the 3CL protease; a polymorphic difference at the end of the S2 gene, which coincided with the B-TRS of mRNA 3 and a truncated ORF 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 ovo. 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' UTR 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.
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- "Genes 3 and 5 are polycistronic and encode proteins 3a, 3b and E, and 5a and 5b respectively  . There was previously reported to be an 'intergenic' region located between the genes M and 5 in the group 3 coronaviruses, IBV and TCoV, however recent reports have demonstrated the presence of two ORFs, 4b and 4c, in this region   . Another ORF, 6b, was also detected in these studies immediately downstream of the N gene. "
ABSTRACT: There are currently four commercially available vaccines in Australia to protect chickens against infectious bronchitis virus (IBV). Predominantly, IBV causes clinical signs associated with respiratory or kidney disease, which subsequently cause an increase in mortality rate. Three of the current vaccines belong to the same subgroup (subgroup 1), however, the VicS vaccine has been reported to cause an increased vaccinal reaction compared to the other subgroup 1 vaccines. Molecular anomalies detected in VicS suggested the presence of two major subspecies, VicS-v and VicS-del, present in the commercial preparation of VicS. The most notable anomaly is the absence of a 40 bp sequence in the 3'UTR of VicS-del. In this investigation, the two subspecies were isolated and shown to grow independently and to similar titres in embryonated chicken eggs. An in vivo investigation involved 5 groups of 20 chickens each and found that VicS-del grew to a significantly lesser extent in the chicken tissues collected than did VicS-v. The group inoculated with an even ratio of the isolated subspecies scored the most severe clinical signs, with the longest duration. These results indicate the potential for a cooperative, instead of an expected competitive, relationship between VicS-v and VicS-del to infect a host, which is reminiscent of RNA viral quasi-species.
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ABSTRACT: Phylogenetic analysis of complete genomes of the avian coronaviruses avian infectious bronchitis (AIBV) and turkey coronavirus (TCoV) supported the hypothesis that numerous recombination events have occurred between these viruses. Although the two groups of viruses differed markedly in the sequence of the spike protein, the gene (S) encoding this protein showed no evidence of positive selection or of an elevated mutation rate. Rather, the data suggested that recombination events have homogenized the portions of the genome other than the S gene between the two groups of viruses, while continuing to maintain the two distinct, anciently diverged versions of the S gene. The latter hypothesis was supported by a phylogeny of S proteins from representative coronaviruses, in which S proteins of AIBV and TCoV fell in the same clade.
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