title: Isolation and genetic characterization of a novel 2.2.1.2a H5N1 virus from a vaccinated meat-turkeys flock in Egypt.
abstract: Vaccination of poultry to control highly pathogenic avian influenza virus (HPAIV) H5N1 is used in several countries. HPAIV H5N1 of clade 2.2.1 which is endemic in Egypt has diversified into two genetic clades. Clade 2.2.1.1 represents antigenic drift variants in vaccinated commercial poultry while clade 2.2.1.2 variants are detected in humans and backyard poultry. Little is known about H5N1 infection in vaccinated turkeys under field conditions.
  
  
  
  Here, we describe an HPAI H5N1 outbreak in a vaccinated meat-turkey flock in Egypt. Birds were vaccinated with inactivated H5N2 and H5N1 vaccines at 8 and 34 days of age, respectively. At 72ndday of age (38 days post last vaccination), turkeys exhibited mild respiratory signs, cyanosis of snood and severe congestion of the internal organs. Survivors had a reduction in feed consumption and body gain. A mortality of ~29% cumulated within 10 days after the onset of clinical signs. Laboratory diagnosis using RT-qPCRs revealed presence of H5N1 but was negative for H7 and H9 subtypes. A substantial antigenic drift against different serum samples from clade 2.2.1.1 and clade 2.3.4.4 was observed. Based on full genome sequence analysis the virus belonged to clade 2.2.1.2 but clustered with recent H5N1 viruses from 2015 in poultry in Israel, Gaza and Egypt in a novel subclade designated here 2.2.1.2a which is distinct from 2014/2015 2.2.1.2 viruses. These viruses possess 2.2.1.2 clade-specific genetic signatures and also mutations in the HA similar to those in clade 2.2.1.1 that enabled evasion from humoral immune response. Taken together, this manuscript describes a recent HPAI H5N1 outbreak in vaccinated meat-turkeys in Egypt after infection with a virus representing novel distinct 2.2.1.2a subclade.
  
  
  
  Infection with HPAIV H5N1 in commercial turkeys resulted in significant morbidity and mortality despite of vaccination using H5 vaccines. The isolated virus showed antigenic drift and clustered in a novel cluster designated here 2.2.1.2a related to viruses in poultry in Israel, Gaza and Egypt. Enforcement of biosecurity and constant update of vaccine virus strains may be helpful to protect vaccinated birds and prevent spillover infection to neighbouring countries.
authors.affiliation: Institute of Poultry Diseases, Free University of Berlin, Königsweg 63, 14163, Berlin, Germany.|Department of Poultry Diseases, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt.
authors.forename: Ahmed H
authors.initials: AH
authors.lastname: Salaheldin
authors.affiliation: Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493, Insel Riems-Greifswald, Germany.
authors.forename: Jutta
authors.initials: J
authors.lastname: Veits
authors.affiliation: Faculty of Veterinary Medicine, Damanhur University, Damanhur, Egypt.
authors.forename: Hatem S
authors.initials: HS
authors.lastname: Abd El-Hamid
authors.affiliation: Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493, Insel Riems-Greifswald, Germany.
authors.forename: Timm C
authors.initials: TC
authors.lastname: Harder
authors.affiliation: Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia.
authors.forename: Davud
authors.initials: D
authors.lastname: Devrishov
authors.affiliation: Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493, Insel Riems-Greifswald, Germany.
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Mettenleiter
authors.affiliation: Institute of Poultry Diseases, Free University of Berlin, Königsweg 63, 14163, Berlin, Germany. hafez@vetmed.fu-berlin.de.
authors.forename: Hafez M
authors.initials: HM
authors.lastname: Hafez
authors.affiliation: Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493, Insel Riems-Greifswald, Germany.
authors.forename: Elsayed M
authors.initials: EM
authors.lastname: Abdelwhab
mesh_terms: D000818:Animals; D000956:Antigens, Viral / Q000235:genetics / Q000276:immunology; D016000:Cluster Analysis; D004196:Disease Outbreaks; D004534:Egypt / Q000453:epidemiology; D040961:Genetic Drift; D016679:Genome, Viral; D005838:Genotype; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000401:mortality / Q000473:pathology / Q000821:virology*; D010802:Phylogeny; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D016019:Survival Analysis; D014422:Turkeys
chemical_list: D000956:Antigens, Viral
keywords: Avian influenza; Clade 2.2.1.2; Egypt; H5N1; Vaccinated turkeys; Vaccination failure