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. 2014 Jul;95(Pt 7):1444-1463.
doi: 10.1099/vir.0.063495-0. Epub 2014 Apr 10.

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

Rabeh El-Shesheny  1 , Ahmed Kandeil  1 , Ola Bagato  1 , Asmaa M Maatouq  1 , Yassmin Moatasim  1 , Adam Rubrum  2 , Min-Suk Song  2 , Richard J Webby  2 , Mohamed Ahmed Ali  1 , Ghazi Kayali  2
Affiliations

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

Rabeh El-Shesheny et al. J Gen Virol. 2014 Jul.

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.

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Figures

Fig. 1.
Fig. 1.
Phylogenetic tree of the HA gene. Phylogenetic analysis was done using the neighbour-joining algorithm with the Kimura two-parameter model. The reliability of phylogenetic inference at each branch node was estimated by the bootstrap method with 1000 replications; evolutionary analysis was conducted in mega5. Viruses sequenced for this study are marked in bold.
Fig. 2.
Fig. 2.
Phylogenetic tree of the NA gene. Phylogenetic analysis was done using the neighbour-joining algorithm with the Kimura two-parameter model. The reliability of phylogenetic inference at each branch node was estimated by the bootstrap method with 1000 replications; evolutionary analysis was conducted in mega5. Viruses sequenced for this study are marked in bold.
Fig. 3.
Fig. 3.
Phylogenetic trees of the (a) PB2, (b) PB1, (c) PA, (d) NP, (e) M and (f) NS genes. Phylogenetic analysis was done using the neighbour-joining algorithm with the Kimura two-parameter model. The reliability of phylogenetic inference at each branch node was estimated by the bootstrap method with 1000 replications; evolutionary analyses were conducted in mega5. Viruses sequenced for this study are marked in bold.
Fig. 3.
Fig. 3.
Phylogenetic trees of the (a) PB2, (b) PB1, (c) PA, (d) NP, (e) M and (f) NS genes. Phylogenetic analysis was done using the neighbour-joining algorithm with the Kimura two-parameter model. The reliability of phylogenetic inference at each branch node was estimated by the bootstrap method with 1000 replications; evolutionary analyses were conducted in mega5. Viruses sequenced for this study are marked in bold.
Fig. 3.
Fig. 3.
Phylogenetic trees of the (a) PB2, (b) PB1, (c) PA, (d) NP, (e) M and (f) NS genes. Phylogenetic analysis was done using the neighbour-joining algorithm with the Kimura two-parameter model. The reliability of phylogenetic inference at each branch node was estimated by the bootstrap method with 1000 replications; evolutionary analyses were conducted in mega5. Viruses sequenced for this study are marked in bold.
Fig. 3.
Fig. 3.
Phylogenetic trees of the (a) PB2, (b) PB1, (c) PA, (d) NP, (e) M and (f) NS genes. Phylogenetic analysis was done using the neighbour-joining algorithm with the Kimura two-parameter model. The reliability of phylogenetic inference at each branch node was estimated by the bootstrap method with 1000 replications; evolutionary analyses were conducted in mega5. Viruses sequenced for this study are marked in bold.
Fig. 3.
Fig. 3.
Phylogenetic trees of the (a) PB2, (b) PB1, (c) PA, (d) NP, (e) M and (f) NS genes. Phylogenetic analysis was done using the neighbour-joining algorithm with the Kimura two-parameter model. The reliability of phylogenetic inference at each branch node was estimated by the bootstrap method with 1000 replications; evolutionary analyses were conducted in mega5. Viruses sequenced for this study are marked in bold.
Fig. 3.
Fig. 3.
Phylogenetic trees of the (a) PB2, (b) PB1, (c) PA, (d) NP, (e) M and (f) NS genes. Phylogenetic analysis was done using the neighbour-joining algorithm with the Kimura two-parameter model. The reliability of phylogenetic inference at each branch node was estimated by the bootstrap method with 1000 replications; evolutionary analyses were conducted in mega5. Viruses sequenced for this study are marked in bold.
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