Infectious bronchitis viruses with naturally occurring genomic rearrangement and gene deletion
ABSTRACT 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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- "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.Vaccine 04/2012; 30(28):4190-9. DOI:10.1016/j.vaccine.2012.04.054 · 3.62 Impact Factor
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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.Archives of Virology 07/2011; 156(10):1823-9. DOI:10.1007/s00705-011-1061-5 · 2.39 Impact Factor
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ABSTRACT: Coronavirus subgenomic (sg) mRNA synthesis occurs via a process of discontinuous transcription involving transcription regulatory sequences (TRSs) located in the 5' leader sequence (TRS-L) and upstream of each structural and group-specific gene (TRS-B). Several gammacoronaviruses including infectious bronchitis virus (IBV) contain a putative open reading frame (ORF), localised between the M gene and Gene 5, which is controversial due to the perceived absence of a TRS. We have studied the transcription of a novel sg mRNA associated with this potential ORF and found it to be transcribed via a previously unidentified non-canonical TRS-B. Using an IBV reverse genetics system we demonstrated that the template-switching event during IR sg mRNA synthesis occurs at the 5' end of the non-canonical TRS-B and recombines between nucleotides 5 and 6 of the 8-nucleotide consensus TRS-L. Introduction of a complete TRS-B showed higher transcription levels are achieved by increasing the number of nucleotide matches between TRS-L and TRS-B. Translation of a protein from the sg mRNA was demonstrated using enhanced green fluorescent protein, suggesting the translation of a 5(th) novel group-specific protein for IBV. This study has resolved an issue concerning the number of ORFs expressed by members of the gammacoronavirus genus and proposes the existence of a 5(th) IBV accessory protein. We confirmed previous reports that coronaviruses can produce sg mRNAs from non-canonical TRS-Bs, which may expand their repertoire of proteins. We also demonstrated that non-canonical TRS-Bs may provide a mechanism by which coronaviruses can control protein expression levels by reducing sg mRNA synthesis.Journal of Virology 12/2012; 87(4). DOI:10.1128/JVI.02967-12 · 4.44 Impact Factor