Naturally occurring recombination between distant strains of infectious bronchitis virus

Abstract

New variants of infectious bronchitis virus (IBV) have emerged in Australia despite its geographical isolation and intensive vaccination programs. In the present study, the 3' terminal 7.2 kb of the genome of a recently isolated variant of IBV (N1/03) was sequenced and compared with the sequences of classical and novel strains of IBV, the two main groups of these viruses in Australia. The comparison revealed that recombination between classical and novel IBVs was responsible for the emergence of the new variant. It was concluded that novel IBVs, which have not been detected since 1993, and which are phylogenically more distant from classical IBVs than turkey coronaviruses, might still be circulating and contributing to the evolution of IBV in Australia.

Fig. 1

Evolutionary relationships between S genes of Australian IBV strains inferred using the neighbour-joining method. The evolutionary distances were computed using the Maximum Composite Likelihood method and are given in the number of base substitutions per site

Fig. 2

Evolutionary relationships between E genes of Australian IBV strains inferred using the neighbour-joining method. The evolutionary distances were computed using the Maximum Composite Likelihood method and are given in the number of base substitutions per site

Fig. 3

Evolutionary relationships between M genes of Australian IBV strains inferred using the neighbour-joining method. The evolutionary distances were computed using the Maximum Composite Likelihood method and are given in the number of base substitutions per site

Fig. 4

Evolutionary relationships between N genes of Australian IBV strains inferred using the neighbour-joining method. The evolutionary distances were computed using the Maximum Composite Likelihood method and are given in the number of base substitutions per site

Fig. 5

Similarity plot analysis of Australian IBVs. The y-axis shows the percentage similarity within a sliding window of 200 bp centered on the position plotted, with a step size between plots of 20 bp. IBV strains VicS and N1/88 were compared to N1/03, and Armidale was used as the query strain. The genomic map is shown at the top of the plot

Fig. 6

Bootscanning analysis of the 3′ terminal 7.2-kb of the genomes of Australian IBVs. The y-axis shows the percentage of permutated trees using a sliding window of 200 bp wide centered on the position plotted, with a step size between plots of 20 bp. IBV strains VicS and N1/88 were compared to N1/03, with Armidale used as the query strain. The genomic map is shown at the top of the plot. The vertical lines are the breakpoints and the numbers at the bottom of these lines are their positions in the sequence