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01.12.2017 | Case report | Ausgabe 1/2017 Open Access

Virology Journal 1/2017

Isolation and genetic characterization of a novel H5N1 virus from a vaccinated meat-turkeys flock in Egypt

Virology Journal > Ausgabe 1/2017
Ahmed H. Salaheldin, Jutta Veits, Hatem S. Abd El-Hamid, Timm C. Harder, Davud Devrishov, Thomas C. Mettenleiter, Hafez M. Hafez, Elsayed M. Abdelwhab
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Electronic supplementary material

The online version of this article (doi:10.​1186/​s12985-017-0697-5) contains supplementary material, which is available to authorized users.



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 represents antigenic drift variants in vaccinated commercial poultry while clade variants are detected in humans and backyard poultry. Little is known about H5N1 infection in vaccinated turkeys under field conditions.

Case presentation

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 72nd day 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 and clade was observed. Based on full genome sequence analysis the virus belonged to clade but clustered with recent H5N1 viruses from 2015 in poultry in Israel, Gaza and Egypt in a novel subclade designated here which is distinct from 2014/2015 viruses. These viruses possess clade-specific genetic signatures and also mutations in the HA similar to those in clade 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 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 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.
Additional file 1: Table S1. Amino acids differences from A/turkey/Egypt/AR1507/2016 and ancestral 2006 virus, vaccine strain and closest human isolate (DOC 36 kb)
Additional file 2: Figure S1. Phylogenetic analysis of internal protein coding gene segments of A/turkey/Egypt/AR1507/2016 to other related H5N1 viruses in poultry and humans. Phylogenetic analysis of non HA/NA genes of Egyptian viruses showing different genetic clades. Viruses in 2015 from Egypt including A/turkey/Egypt/AR1507/2016 are clustered in clade The tree was generated by MrBayes under the best-fit model selected by jModelTest. (PDF 701 kb)
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