Literature detail

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.

PMID 24722680 2014 J Gen Virol eng ppublish

PubMed DOI Browse context

Article

Publication summary

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.

Poultry Animals Cluster Analysis Egypt Genotype Influenza A Virus, H5N1 Subtype Influenza in Birds Molecular Sequence Data Phylogeny RNA, Viral Sequence Analysis, DNA

Structured evidence records

Evidence records

4 total

Genomic Evolution 1 records

Genomic Evolution Extraction confidence 0.95

Key finding

Phylogenetic analysis of full-genome sequences of Egyptian H5N1 poultry isolates revealed ongoing evolution and the emergence of a novel subclade.

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 ... Results indicated that H5N1 viruses in Egypt continue to evolve and a new distinct cluster has emerged.

Genes or proteins: whole genome
Analysis methods: full-genome sequencing; phylogenetic analysis

Molecular Adaptation 1 records

Molecular Adaptation Extraction confidence 0.90

Key finding

H5N1 viruses circulating in Egypt accumulated mutations associated with changes in virulence, pathogenicity, transmission, receptor binding, and drug resistance, demonstrating ongoing molecular adaptation.

Virus

Host

Location

Supporting text

Mutations affecting viral virulence, pathogenicity, transmission, receptor-binding preference and drug resistance were studied.

Mechanism types: virulence; pathogenicity; transmission_fitness; receptor_binding; drug_resistance

Receptor Usage 1 records

Receptor Usage Extraction confidence 0.75

Key finding

H5N1 influenza viruses circulating in Egyptian poultry exhibit mutations linked to changes in receptor-binding preference.

Virus

Host

Location

Supporting text

Mutations affecting viral virulence, pathogenicity, transmission, receptor-binding preference and drug resistance were studied.

Method: sequence analysis; phylogenetic analysis

Zoonotic Surveillance 1 records

Zoonotic Surveillance Extraction confidence 0.90

Key finding

Systematic surveillance of Egyptian poultry detected ongoing evolution of H5N1 viruses, including emergence of new subclades.

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.

Method: full-genome sequence analysis; phylogenetic analysis
Geographic raw: Egypt
Country inferred: Egypt

Citation context

References

69 references

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Evidence overview

Evidence 4

Types 4

Virus 1

Host 1

Evidence types

Genomic Evolution 1 Molecular Adaptation 1 Receptor Usage 1 Zoonotic Surveillance 1

Linked entities

Viruses

Hosts

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