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

• Published in: Veterinary microbiology Vol. 197; pp. 27 - 38
• Main Authors: Quinteros, José A., Lee, Sang-Won, Markham, Philip F., Noormohammadi, Amir H., Hartley, Carol A., Legione, Alistair R., Coppo, Mauricio J.C., Vaz, Paola K., Browning, Glenn F.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 25.12.2016; Elsevier BV
• Subjects: Amino Acid Sequence; Animals; Australia - epidemiology; Bronchitis; Chickens; Coronaviridae; Coronavirus Infections - epidemiology; Coronavirus Infections - veterinary; Coronavirus Infections - virology; Coronaviruses; Event-related potentials; Full genome sequences; Genome, Viral; Genomes; Immunization; Infectious bronchitis virus; Infectious bronchitis virus - genetics; Phylogeny; Poultry Diseases - epidemiology; Poultry Diseases - virology; Reassortant Viruses; Recombinants; Recombination; S1 gene; Strain; Strains (organisms); Studies; Unknown avian coronaviruses; Vaccine recombinants; Vaccines; Viral infections; Viral Proteins - genetics; Viral Proteins - metabolism; Viral Vaccines; Viruses; Full genome sequences; Unknown avian coronaviruses; Vaccine recombinants; Recombination; Recombinants; Infectious bronchitis virus
• ISSN: 0378-1135; 1873-2542; 1873-2542
• DOI: 10.1016/j.vetmic.2016.11.003

•Vaccines contributed to emergence of recombinant IBV strains.•Exotic avian coronaviruses have played a decisive role in recombination events.•Recombination breakpoints have been in genes for nsp 2, 3 and 16 and the S protein.•Avian coronavirus of unknown origin have been recombining with IBV for 20 years. 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.