| Literature DB >> 23185975 |
Elham F El-Zoghby1, Abdel-Satar Arafa, Walid H Kilany, Mona M Aly, Elsayed M Abdelwhab, Hafez M Hafez.
Abstract
BACKGROUND: Uninterrupted transmission of highly pathogenic avian influenza virus (HPAIV) H5N1 of clade 2.2.1 in Egypt since 2006 resulted in establishment of two main genetic clusters. The 2.2.1/C group where all recent human and majority of backyard origin viruses clustered together, meanwhile the majority of viruses derived from vaccinated poultry in commercial farms grouped in 2.2.1.1 clade.Entities:
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Year: 2012 PMID: 23185975 PMCID: PMC3546856 DOI: 10.1186/1743-422X-9-294
Source DB: PubMed Journal: Virol J ISSN: 1743-422X Impact factor: 4.099
Figure 1Phylogenetic trees of H5 (A) and N1 (B) genes of A/chicken /Egypt/0987-NLQP/2009 virus with other H5N1 viruses currently circulating in poultry and human in Egypt. The evolutionary history of the HA and NA was inferred using the Neighbor-Joining method with 1000 bootstrap replicates and the evolutionary distances were computed using the Maximum Composite Likelihood method implemented in MEGA5. The bootstrap values are shown next to the branches. Trees were edited for publication using Inkscape software. Virus obtained from this study is highlighted in yellow while other related viruses are written in bold. The virus clustered with H5N1 viruses isolated from poultry in backyards, live bird market and confirmed human infections. Two major H5N1 genetic clusters are currently co-circulating in Egypt: newly designated 2.2.1.1 clade (depicted in red) representing variant viruses isolated exclusively from vaccinated poultry in commercial farms and group C of 2.2.1 clade (blue) denoted 2.2.1/C group that mainly isolated from human and backyard birds according to the recent classification of WHO/OIE/FAO Evolution Working Group. The 2.2.1 index virus introduced into 2006 (black) was no longer isolated and was denoted as 2.2.1 clade.
Percentage identity of the hemagglutinin and neuraminidase sequences of A/chicken/Egypt/0987-NLQP/2009 in relation to other Egyptian H5N1 viruses and vaccine strain
| | 99.77 | 99.83 | 99.77 | 98.90 | 96.19 | 94.28 | |
| 99.65 | | 99.94 | 99.88 | 98.96 | 96.19 | 94.46 | |
| 99.65 | 100.00 | | 99.94 | 99.02 | 96.13 | 94.52 | |
| 99.47 | 99.82 | 99.82 | | 98.96 | 96.25 | 94.46 | |
| 98.94 | 99.29 | 99.29 | 99.12 | | 96.88 | 96.02 | |
| 94.89 | 95.24 | 95.24 | 95.06 | 95.59 | | 92.96 | |
| 94.53 | 93.47 | 94.71 | 94.53 | 95.41 | 91.71 | | |
| | 99.85 | 99.64 | 99.55 | 98.58 | 97.30 | 93.01 | |
| 99.78 | | 99.75 | 99.78 | 98.73 | 97.43 | 91.54 | |
| 99.49 | 99.58 | | 99.49 | 98.56 | 97.20 | 90.59 | |
| 99.55 | 99.70 | 99.41 | | 98.74 | 97.43 | 91.63 | |
| 98.88 | 99.10 | 98.98 | 98.89 | | 98.49 | 92.62 | |
| 97.96 | 98.19 | 97.96 | 97.96 | 99.09 | | 91.76 | |
| 92.04 | 92.26 | 91.35 | 92.04 | 93.18 | 92.19 |
Percentage identity of nucleotide (above the diagonal) and amino acid (below the diagonal).
1 The virus isolated in this study was designated as A/chicken/Egypt/0987-NLQP/2009 under GenBank accession numbers GU366078 and HQ908461 for the HA and NA genes, respectively.
2 A/goose/Egypt/09324sm-NLQP/2009 [GenBank: GU811737 and HM352793] isolated from geese in live bird market (LBM) in the same region.
3 A/duck/Egypt/0918-NLQP/2009 [GenBank: GU002674 and HQ908452] isolated from backyard birds.
4 A/Egypt/N02039/2009 [GenBank: CY041918 and CY041919] isolated from 32 months old boy from the same village.
5 A/chicken/Egypt/06207-NLQP/2006 [GenBank: EU372943 and GQ184251] was isolated in February 2006 and represents the index 2.2.1 Egyptian viruses.
6A/chicken/Egypt/1055/2010 [GenBank: HQ198268 and HQ908478] variant 2.2.1.1 virus isolated from vaccinated chickens in a commercial farm.
7 A/Goose/Guangdong/1/96 [GenBank: AF144305 and AF144304] vaccine strain used in vaccination of the current commercial layer flock.
Figure 2Predicted location of amino acid substitutions found in the isolated virus on the tertiary structure of HA H5 (A) and N1 NA (B) monomers. Shown are the substitutions in D43N, S120N, I151T and S320G in the HA and A46D, N200D, L224M, S339V and S450G in the NA proteins. Substitutions have been imposed upon the tertiary structure of A/chicken/Egypt/06207-NLQP/2006(H5N1) (index virus of clade 2.2.1 introduced into Egypt in early 2006). Protein modeling was generated by JIGSAW [28] and edited by RasTop version 2.7.1 and further edited by Inkscape.