title: First full-length sequences of the S gene of European isolates reveal further diversity among turkey coronaviruses.
abstract: An increasing incidence of enteric disorders clinically suggestive of the poult enteritis complex has been observed in turkeys in France since 2003. Using a newly designed real-time reverse transcriptase-polymerase chain reaction assay specific for the nucleocapsid (N) gene of infectious bronchitis virus (IBV) and turkey coronaviruses (TCoV), coronaviruses were identified in 37% of the intestinal samples collected from diseased turkey flocks. The full-length spike (S) gene of these viruses was amplified, cloned and sequenced from three samples. The French S sequences shared 98% identity at both the nucleotide and amino acid levels, whereas they were at most 65% and 60% identical with North American (NA) TCoV and at most 50% and 37% identical with IBV at the nucleotide and amino acid levels, respectively. Higher divergence with NA TCoV was observed in the S1-encoding domain. Phylogenetic analysis based on the S gene revealed that the newly detected viruses form a sublineage genetically related with, but significantly different from, NA TCoV. Additionally, the RNA-dependent RNA polymerase gene and the N gene, located on the 5' and 3' sides of the S gene in the coronavirus genome, were partially sequenced. Phylogenetic analysis revealed that both the NA TCoV and French TCoV (Fr TCoV) lineages included some IBV relatives, which were however different in the two lineages. This suggested that different recombination events could have played a role in the evolution of the NA and Fr TCoV. The present results provide the first S sequence for a European TCoV. They reveal extensive genetic variation in TCoV and suggest different evolutionary pathways in North America and Europe.
authors.affiliation: Anses-French Agency for Food, Environmental and Occupational Health Safety, Ploufragan-Plouzané Laboratory, Avian and Rabbit Virology, Immunology, and Parasitology Unit, Ploufragan, France.
authors.forename: S
authors.initials: S
authors.lastname: Maurel
authors.forename: D
authors.initials: D
authors.lastname: Toquin
authors.forename: F X
authors.initials: FX
authors.lastname: Briand
authors.forename: M
authors.initials: M
authors.lastname: Queguiner
authors.forename: C
authors.initials: C
authors.lastname: Allee
authors.forename: J
authors.initials: J
authors.lastname: Bertin
authors.forename: L
authors.initials: L
authors.lastname: Ravillion
authors.forename: C
authors.initials: C
authors.lastname: Retaux
authors.forename: V
authors.initials: V
authors.lastname: Turblin
authors.forename: H
authors.initials: H
authors.lastname: Morvan
authors.forename: N
authors.initials: N
authors.lastname: Eterradossi
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D004752:Coronavirus, Turkey / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D004753:Enteritis, Transmissible, of Turkeys / Q000453:epidemiology / Q000821:virology*; D005602:France / Q000453:epidemiology; D014644:Genetic Variation; D008562:Membrane Glycoproteins / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D019590:Nucleocapsid Proteins / Q000235:genetics; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods / Q000662:veterinary; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D064370:Spike Glycoprotein, Coronavirus; D014422:Turkeys; D014759:Viral Envelope Proteins / Q000737:chemistry / Q000235:genetics*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D008562:Membrane Glycoproteins; D019590:Nucleocapsid Proteins; D012367:RNA, Viral; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins; D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase