Studies on avian infectious bronchitis virus in New Zealand. I. Serotypes

S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification

Infectious bronchitis virus (IBV) is the causative agent of a highly contagious disease that results in severe economic losses to the global poultry industry. The virus exists in a wide variety of genetically distinct viral types, and both phylogenetic analysis and measures of pairwise similarity among nucleotide or amino acid sequences have been used to classify IBV strains. However, there is currently no consensus on the method by which IBV sequences should be compared, and heterogeneous genetic group designations that are inconsistent with phylogenetic history have been adopted, leading to the confusing coexistence of multiple genotyping schemes. Herein, we propose a simple and repeatable phylogeny-based classification system combined with an unambiguous and rationale lineage nomenclature for the assignment of IBV strains. By using complete nucleotide sequences of the S1 gene we determined the phylogenetic structure of IBV, which in turn allowed us to define 6 genotypes that together comprise 32 distinct viral lineages and a number of inter-lineage recombinants. Because of extensive rate variation among IBVs, we suggest that the inference of phylogenetic relationships alone represents a more appropriate criterion for sequence classification than pairwise sequence comparisons. The adoption of an internationally accepted viral nomenclature is crucial for future studies of IBV epidemiology and evolution, and the classification scheme presented here can be updated and revised novel S1 sequences should become available.

Infectious bronchitis virus variants: a review of the history, current situation and control measures

The history, current situation and control measures for infectious bronchitis virus (IBV) variants are reviewed. A large number of IBV variants exist worldwide; some being unique to a particular area, others having a more general distribution. The possible reasons why some strains spread readily over major parts of the world, whereas other strains stay more localized are discussed. The advantages and disadvantages of strain classification by protectotyping, serotyping and genotyping are discussed in relation to in vivo protection. The different vaccination strategies are also considered.

Infectious bronchitis virus variants: a review of the history, current situation and control measures

The history, current situation and control measures for infectious bronchitis virus (IBV) variants are reviewed. A large number of IBV variants exist worldwide; some being unique to a particular area, others having a more general distribution. The possible reasons why some strains spread readily over major parts of the world, whereas other strains stay more localized are discussed. The advantages and disadvantages of strain classification by protectotyping, serotyping and genotyping are discussed in relation to in vivo protection. The different vaccination strategies are also considered.

Rapid detection and characterisation of infectious bronchitis virus (IBV) from New Zealand using RT-PCR and sequence analysis

AIMS

To develop a reverse transcriptase-polymerase chain reaction (RT-PCR) assay to detect infectious bronchitis virus (IBV) from commercially-raised poultry in New Zealand and compare results with those from virus isolation. To characterise the IBV isolates using sequence analysis.

METHODS

Pooled tissue samples (trachea, kidney, caecal tonsils and cloacal swabs) from 164 broiler and 53 layer flocks located throughout New Zealand were collected in transport medium containing antibiotics. Tissues were homogenised and the resultant supernatant used directly in a RT-PCR assay, and also inoculated into the allantoic cavity of 10-day-old embryonated eggs for virus isolation. Primers for the RT-PCR were selected from an area close to the N-terminus of the S1 (spike) gene and bracketed the hypervariable region 1 (HVR 1). The RT-PCR amplimers were sequenced from both termini, and alignment was constructed and analysed.

RESULTS

From the 217 field samples that were subjected to RT-PCR, 42 (19%) were positive. Twenty-nine (69%) of these RT-PCR-positive, and none of the RT-PCR-negative, samples yielded virus by isolation in chicken embryos. A phylogenetic tree constructed from these amplimers, that spanned the HVR of the S1 gene, revealed the IBV isolates clustered into two demarcated groups which had <60% homology. It is likely that the isolates of one group were derived from the live attenuated vaccine commonly used in New Zealand.

CONCLUSIONS

The RT-PCR assay exhibited higher sensitivity than virus isolation and could be used for rapid diagnosis of IBV in the field. The prevalence of IBV appears to be surprisingly high in New Zealand although the use of pooled samples in the study did not allow accurate calculation of the prevalence in birds. Sequence analysis of a hypervariable region from the S1 gene was informative for the differentiation of closely-related strains.

Australian infectious bronchitis viruses: identification of nine subtypes by a neutralisation test

The antigenic relationships between 17 Australian infectious bronchitis viruses, including six vaccine viruses, were studied by a neutralisation test using a plaque reduction method in chick embryo kidney cell monolayers. The 17 viruses formed nine distinct subtypes. Antiserum to each subtype had a high titre to viruses of the same subtype and a lower titre to viruses of different subtypes. The heterologous titres of sera varied widely.