Full genome analysis of Australian infectious bronchitis viruses suggests frequent recombination events between vaccine strains and multiple phylogenetically distant avian coronaviruses of unknown origin

Abstract

Australian strains of infectious bronchitis virus (IBV) have been evolving independently for many years, with control achieved by vaccination with local attenuated strains. Previous studies have documented the emergence of recombinants over the last 20 years, with the most recent one, Ck/Aus/N1/08, detected in 2008. These recombinants did not appear to be controlled by the vaccines currently in use. In this study we sequenced the complete genomes of three emergent Australian strains of IBV (IBV/Ck/Aus/N1/88, IBV/Ck/Aus/N1/03 and IBV/Ck/Aus/N1/08) and a previously incompletely characterised vaccine strain, IBV/Ck/Aus/Armidale, and compared them to the genome of the vaccine strain VicS. We detected multiple recombination events throughout the genome between wild type viruses and the vaccine strains in all three emergent isolates. Moreover, we found that strain N1/88 was not entirely exogenous, as was previously hypothesised. Rather, it originated from a recombination event involving the VicS vaccine strain. The S glycoprotein genes of N1/88 and N1/03 were known to be genetically distinct from previously characterised circulating strains and from each other, and the original donors of these genes remains unknown. The S1 glycoprotein gene of N1/88, a subgroup 2 strain, shares a high nucleotide identity with the sequence of the S1 gene of the recent isolate N1/08. As the subgroup 2 strains have not been isolated for at least 20 years, it appears likely that an unknown avian coronavirus that was the donor of the S1 glycoprotein sequence of N1/88 in the 1980s is still recombining with IBV strains in the field.

Characterization of the complete genome, antigenicity, pathogenicity, tissue tropism, and shedding of a recombinant avian infectious bronchitis virus with a ck/CH/LJL/140901-like backbone and an S2 fragment from a 4/91-like virus

“…The exchange of part of a region of the genome allows viruses to rapidly explore areas of sequence space, potentially leading to the emergence of variants with different features in terms of their virulence, cross-protection, and cell and host tropisms (Simon-Loriere and Holmes, 2011). It is considered that the emergence of the Australian N1/88 strain was driven by antigenic differences between the virus and other circulating IBVs, but also by the enhanced capacity of the recombinant virus to replicate in chickens (Quinteros et al, 2016). We found that the recombinant I1101/16 isolate was serologically related to but not the same as strain ck/CH/LHLJ/140901.…”

“…In Australia, three recently isolated novel subgroup IBV strains were shown to be derived from recombination between subgroup 1 and 2 strains (Mardani et al, 2010). More recently, the complete genome analysis of newly emerged strains found multiple recombination events throughout the genome between wild-type viruses and vaccine strains (Quinteros et al, 2016). In the USA, the emergent virulent strain Ark DPI appears to have originated from recombination among four different IBV strains (Ammayappan et al, 2008).…”

Genetic, antigenic, and pathogenic characteristics of avian infectious bronchitis viruses genotypically related to 793/B in China

“…A maximum likelihood tree based on a JTT matrix-based model and 100 bootstrap replicates was built using MEGA4 and the S1 nucleotide sequences of our 21 viruses, 27 793/B reference strains that were isolated in different countries, eight Mass genotype strains, and 22 other IBV strains that were isolated in China (Liu et al, 2013). Meanwhile, a network tree was constructed using SplitsTrees, version 4.1.4.3, using the maximum likelihood (F48) distance model, the NeighborNet network algorithm, 1000 bootstrap replicates and an estimated proportion of invariant sites of 0.37 (Quinteros et al, 2016).…”

“…To detect possible recombination events between our 20 isolates and the other viruses, a sliding window analysis was performed using a nucleotide alignment of the available genome sequences that was generated by ClustalX version 1.83 and edited manually with BioEdit version 7.1.3 (Lasergene Corp, Madison, WI, USA). A network tree was constructed using the aforementioned methods (Quinteros et al, 2016). Furthermore, a SimPlot analysis was performed using SimPlot version 3.5.1 (Liu et al, 2013) (window size, 1000 bp; step, 200 bp) with all 20 isolates and the 4/91 vaccine strain, using the H120 vaccine strain as a query.…”

“…Then, representatives of the individual strains, ck/CH/LSD/110857 and ck/CH/LGD/120723, were further selected based on the aforementioned results and used for the SimPlot analysis again with the 4/91 vaccine strain as a query. To further confirm the recombination events and detect the recombination breakpoints, the representatives of the individual strains were examined using Recombination Detection Program 4 (RDP4, version 4.56) as previously described (Quinteros et al, 2016). In addition, the nucleotide sequences encoding an RNAdependent polymerase and the S protein of the representatives of the individual strains were pairwise compared with those of the 4/ 91 vaccine strain and the identified parental virus strains, respectively, to confirm the recombination breakpoints.…”