Phylodynamics of avian influenza clade 2.2.1 H5N1 viruses in Egypt

[tetano]

Virol J. 2016 Mar 22;13(1):49. doi: 10.1186/s12985-016-0477-7.
Phylodynamics of avian influenza clade 2.2.1 H5N1 viruses in Egypt.

Arafa A^1,2, El-Masry I³, Kholosy S⁴, Hassan MK⁴, Dauphin G⁵, Lubroth J⁵, Makonnen YJ⁶.
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Abstract

BACKGROUND:

Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are widely distributed within poultry populations in Egypt and have caused multiple human infections. Linking the epidemiological and sequence data is important to understand the transmission, persistence and evolution of the virus. This work describes the phylogenetic dynamics of H5N1 based on molecular characterization of the hemagglutinin (HA) gene of isolates collected from February 2006 to May 2014.
METHODS:

Full-length HA sequences of 368 H5N1 viruses were generated and were genetically analysed to study their genetic evolution. They were collected from different poultry species, production sectors, and geographic locations in Egypt. The Bayesian Markov Chain Monte Carlo (BMCMC) method was applied to estimate the evolutionary rates among different virus clusters; additionally, an analysis of selection pressures in the HA gene was performed using the Single Likelihood Ancestor Counting (SLAC) method.
RESULTS:

The phylogenetic analysis of the H5 gene from 2006-14 indicated the presence of one virus introduction of the classic clade (2.2.1) from which two main subgroups were originated, the variant subgroup which was further subdivided into 2 sub-divisions (2.2.1.1 and 2.2.1.1a) and the endemic subgroup (2.2.1.2). The clade 2.2.1.2 showed a high evolution rate over a period of 6 years (6.9 ? 10(-3) sub/site/year) in comparison to the 2.2.1.1a variant cluster (7.2 ? 10(-3) over a period of 4 years). Those two clusters are under positive selection as they possess 5 distinct positively selected sites in the HA gene. The mutations at 120, 154, and 162 HA antigenic sites and the other two mutations (129∆, I151T) that occurred from 2009-14 were found to be stable in the 2.2.1.2 clade. Additionally, 13 groups of H5N1 HPAI viruses were identified based on their amino acid sequences at the cleavage site and "EKRRKKR" became the dominant pattern beginning in 2013.
CONCLUSIONS:

Continuous evolution of H5N1 HPAI viruses in Egypt has been observed in all poultry farming and production systems in almost all regions of the country. The wide circulation of the 2.2.1.2 clade carrying triple mutations (120, 129∆, I151T) associated with increased binding affinity to human receptors is an alarming finding of public health importance.


KEYWORDS:

Clade 2.2.1; Egypt; H5N1 HPAI; Phylodynamic; Poultry; Sequence and phylogenetic analysis; Virus evolution

PMID: 27000533 [PubMed - in process] PMCID: PMC4802640 Free PMC Article

[bertrand789]

merci,

quand on se repr?sente la g?ographie de ce pays et la r?partition des animaux sauvages et domestiques , vu ce qui est en oeuvre, en terme de ma?trise des pathog?nes, ce n'est pas mieux de ne leur envoyer que de la viande ?


je dis cela, car ce qui est produit, en un lieu, circule, certes plus ou moins vite mais circule

[bertrand789]

compl?ment,

les pays ou pour des raisons x ou y ( la guerre est une raison ), la gestion des influenzas n'est pas effective ne devraient plus ?tre autoris?s ? recevoir de la g?n?tique de lign?e certes plus productive mais aussi plus sensible .

je pense que c'est ? la F.A.O, d'enfin dire, un certain nombre de choses importantes, bien s?r si le d?sir partag? est un mieux pour tous .