title: Phylogenetic analysis of avian infectious bronchitis virus S1 glycoprotein regions reveals emergence of a new genotype in Moroccan broiler chicken flocks.
abstract: BACKGROUND
  Infectious bronchitis virus (IBV), a major pathogen of commercial poultry flocks, circulates in the form of several serotypes/genotypes. Only a few amino-acid changes in the S1 subunit of wild-type IBVS proteins may result in mutants unaffected by current vaccines.
  
  
  METHODS
  Partial S1 gene sequences of 3 IBV isolates of the Moroccan Italy 02 genotype from vaccinated and unvaccinated broiler chicken flocks, located in southern and central regions of Morocco, were amplified by RT-PCR, sequenced, and aligned for phylogenetic and amino-acid similarity analyses.
  
  
  RESULTS
  The three isolates were found genetically highly distant from known avian IBV based on partial sequences of their S1 genes: gammaCoV/chicken/Morocco/I01/2011(IBV/Morocco/01), gammaCoV/chicken/Morocco/I30/2010 (IBV/Morocco/30), and gammaCoV/chicken/Morocco/I38/2013 (IBV/Morocco/38), nucleotide sequence identities reached 89.5 % to 90.9 % among the three isolates. The deduced protein sequence identities ranged from 29.7 % (between IBV/Morocco/38 and Egypt SCU-14/2013-1) to 78.2 % (between IBV/Morocco/01 and Spain/05/866). Amino acid sequence comparison and phylogenetic analysis indicated the emergence of a new Moroccan genotype, clustering with regionally related isolates from Spain (Spain/05/866) and belonging to a new sub-genotype.
  
  
  CONCLUSIONS
  Our sequencing results demonstrate a co-circulation of wild-type infectious bronchitis viruses in broiler chickens. These results justify permanent monitoring of circulating strains in order to rationally modify vaccination strategies to make them appropriate to the evolving field situation.
authors.affiliation: Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaire, Institut Agronomique et Vétérinaire Hassan II, Rabat, 10000, Morocco. fellahisiham2015@gmail.com.
authors.forename: Siham
authors.initials: S
authors.lastname: Fellahi
authors.affiliation: Société de Produits Biologiques et Pharmaceutiques Vétérinaires, Rabat, 10000, Morocco. elharrak_m@hotmail.com.
authors.forename: Mehdi
authors.initials: M
authors.lastname: El Harrak
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1225 Interaction hôtes-agents pathogènes, F-31076, Toulouse, France. m.ducatez@envt.fr.|Université de Toulouse, Institut National Polytechnique, Ecole Nationale Vétérinaire de Toulouse, Unité Mixte de Recherche 1225 Interaction hôtes-agents pathogènes, F-31076, Toulouse, France. m.ducatez@envt.fr.
authors.forename: Mariette
authors.initials: M
authors.lastname: Ducatez
authors.affiliation: Société de Produits Biologiques et Pharmaceutiques Vétérinaires, Rabat, 10000, Morocco. chafiqal@hotmail.com.
authors.forename: Chafiqa
authors.initials: C
authors.lastname: Loutfi
authors.affiliation: Laboratoire de Biotechnologie Microbienne, Université Sidi Mohamed Ben Abdellah, Fez, 30000, Morocco. ibnsouda@hotmail.com.
authors.forename: Saad Ibn Souda
authors.initials: SI
authors.lastname: Koraichi
authors.affiliation: Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA. kuhnjens@mail.nih.gov.
authors.forename: Jens H
authors.initials: JH
authors.lastname: Kuhn
authors.affiliation: Genomique Cellulaire et Techniques Moléculaire Investigations, Université Moulay Ismail, Meknès, 50000, Morocco. slimane.khayi@gmail.com.
authors.forename: Slimane
authors.initials: S
authors.lastname: Khayi
authors.affiliation: Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaire, Institut Agronomique et Vétérinaire Hassan II, Rabat, 10000, Morocco. elhouadfimohammed@yahoo.fr.
authors.forename: Mohammed
authors.initials: M
authors.lastname: El Houadfi
authors.affiliation: Laboratoirede Virologie, Microbiologie et Qualité/ETB- Faculté des Sciences et Techniques, Mohammedia, Université Hassan II- Casablanca, Mohammedia, 20650, Morocco. m.ennaji@yahoo.fr.
authors.forename: My Mustapha
authors.initials: MM
authors.lastname: Ennaji
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002645:Chickens; D005838:Genotype; D006023:Glycoproteins / Q000737:chemistry / Q000235:genetics*; D001351:Infectious bronchitis virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics*
chemical_list: D006023:Glycoproteins; D014764:Viral Proteins