Molecular characterization of avian influenza H5N1 virus in Egypt and the emergence of a novel endemic subclade.

Rabeh El-Shesheny¹ Ahmed Kandeil¹ Ola Bagato¹ Asmaa M Maatouq¹ Yassmin Moatasim¹ Adam Rubrum² Min-Suk Song² Richard J Webby² Mohamed Ahmed Ali¹ Ghazi Kayali²

Affiliations 2 institutions

National Research Centre, Giza, Egypt.
St Jude Children's Research Hospital, Memphis, TN 38105, USA.

PMID24722680 DOI10.1099/vir.0.063495-0 Year2014 Journal The Journal of general virology J Gen Virol Languageeng Statusppublish

Abstract

Clade 2.2 highly pathogenic H5N1 viruses have been in continuous circulation in Egyptian poultry since 2006. Their persistence caused significant genetic drift that led to the reclassification of these viruses into subclades 2.2.1 and 2.2.1.1. Here, we conducted full-genome sequence and phylogenetic analyses of 45 H5N1 isolated during 2006-2013 through systematic surveillance in Egypt, and 53 viruses that were sequenced previously and available in the public domain. Results indicated that H5N1 viruses in Egypt continue to evolve and a new distinct cluster has emerged. Mutations affecting viral virulence, pathogenicity, transmission, receptor-binding preference and drug resistance were studied. In light of our findings that H5N1 in Egypt continues to evolve, surveillance and molecular studies need to be sustained.

Supporting text Virus Host Location

Poultry 112 Animals 1948 Cluster Analysis 31 Egypt 22 Genotype 137 Influenza A Virus, H5N1 Subtype 300 Influenza in Birds 341 Molecular Sequence Data 160 Phylogeny 805 RNA, Viral 193 Sequence Analysis, DNA 113

Evidence records

2 total

Zoonotic Surveillance

1 records · 1 evidence types

Evidence type Virus Isolation

1 records

OVE1698 Virus Isolation

Key finding

Forty-five H5N1 influenza viruses were isolated in Egypt between 2006 and 2013 through systematic surveillance.

Virus

Host

Location

Supporting text

Here, we conducted full-genome sequence and phylogenetic analyses of 45 H5N1 isolated during 2006-2013 through systematic surveillance in Egypt.

Genomic Evolution

1 records · 1 evidence types

Evidence type Phylogenetic Evolution

1 records

OVE1699 Phylogenetic Evolution

Key finding

Phylogenetic analyses revealed that H5N1 viruses circulating in Egyptian poultry are continuing to evolve, forming a new distinct cluster of lineages.

Virus

Host

Location

Supporting text

Clade 2.2 highly pathogenic H5N1 viruses have been in continuous circulation in Egyptian poultry since 2006. Results indicated that H5N1 viruses in Egypt continue to evolve and a new distinct cluster has emerged.

Genes or proteins: full genome
Analysis methods: phylogenetic analysis | full-genome sequence analysis

References

69 references

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Evidence overview

Evidence 2

Categories 2

Types 2

Virus 1

Host 1

Country 0

Host context

Natural host 1

Evidence categories

Linked entities

Viruses

Hosts

birds Aves

Locations

Publication metadata

Journal: The Journal of general virology
Volume / Issue / Pages: 95 / Pt 7 / 1444-1463
ISSN: 1465-2099
Journal country: England
DOI: 10.1099/vir.0.063495-0