title: S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification.
abstract: 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.
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy; University of Padova, Padova, Italy. Electronic address: viviana.valastro@gmail.com.
authors.forename: Viviana
authors.initials: V
authors.lastname: Valastro
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.affiliation: Pirbright Institute, Compton Laboratory, Compton, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Britton
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy.
authors.forename: Alice
authors.initials: A
authors.lastname: Fusaro
authors.affiliation: Department of Population Health, College of Veterinary Medicine, Poultry Diagnostic and Research Center, University of Georgia, Athens, GA 30602, USA.
authors.forename: Mark W
authors.initials: MW
authors.lastname: Jackwood
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Cattoli
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy.
authors.forename: Isabella
authors.initials: I
authors.lastname: Monne
mesh_terms: D000818:Animals; D002645:Chickens; D019295:Computational Biology / Q000379:methods; D018352:Coronavirus Infections / Q000821:virology*; D005838:Genotype; D001351:Infectious bronchitis virus / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014759:Viral Envelope Proteins / Q000235:genetics*
chemical_list: D014759:Viral Envelope Proteins
keywords: Classification; Evolution; IBV; Phylogeny