title: 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.
authors.affiliation: Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia. Electronic address: jose.quinteros@unimelb.edu.au.
authors.forename: José A
authors.initials: JA
authors.lastname: Quinteros
authors.affiliation: Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia; College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 143-701, Republic of Korea, Republic of Korea.
authors.forename: Sang-Won
authors.initials: SW
authors.lastname: Lee
authors.affiliation: Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
authors.forename: Philip F
authors.initials: PF
authors.lastname: Markham
authors.affiliation: Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, 3030, Victoria, Australia.
authors.forename: Amir H
authors.initials: AH
authors.lastname: Noormohammadi
authors.affiliation: Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
authors.forename: Carol A
authors.initials: CA
authors.lastname: Hartley
authors.affiliation: Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
authors.forename: Alistair R
authors.initials: AR
authors.lastname: Legione
authors.affiliation: Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
authors.forename: Mauricio J C
authors.initials: MJC
authors.lastname: Coppo
authors.affiliation: Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
authors.forename: Paola K
authors.initials: PK
authors.lastname: Vaz
authors.affiliation: Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
authors.forename: Glenn F
authors.initials: GF
authors.lastname: Browning
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001315:Australia / Q000453:epidemiology; D002645:Chickens; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D016679:Genome, Viral; D001351:Infectious bronchitis virus / Q000235:genetics*; D010802:Phylogeny; D011201:Poultry Diseases / Q000453:epidemiology / Q000821:virology; D016865:Reassortant Viruses; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism; D014765:Viral Vaccines
chemical_list: D014764:Viral Proteins; D014765:Viral Vaccines
keywords: Full genome sequences; Infectious bronchitis virus; Recombinants; Recombination; Unknown avian coronaviruses; Vaccine recombinants