Isolation of avian influenza H5N1 virus from vaccinated commercial layer flock in Egypt

Table 1 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

Hemagglutinin	¹Layer/0987	²LBM/Gs	³BY/Dk	⁴Human/N02039	⁵ Index/2006	⁶Variant/1055	⁷GsGd/96
Layer/0987		99.77	99.83	99.77	98.90	96.19	94.28
LBM/Gs	99.65		99.94	99.88	98.96	96.19	94.46
BY/Dk	99.65	100.00		99.94	99.02	96.13	94.52
Human/N02039	99.47	99.82	99.82		98.96	96.25	94.46
Index/2006	98.94	99.29	99.29	99.12		96.88	96.02
Variant/1055	94.89	95.24	95.24	95.06	95.59		92.96
GsGd/96	94.53	93.47	94.71	94.53	95.41	91.71
Neuraminidase	Layer/0987	LBM/Gs	BY/Dk	Human/N02039	Index/2006	Variant/1055	GsGd/96
Layer/0987		99.85	99.64	99.55	98.58	97.30	93.01
LBM/Gs	99.78		99.75	99.78	98.73	97.43	91.54
BY/Dk	99.49	99.58		99.49	98.56	97.20	90.59
Human/N02039	99.55	99.70	99.41		98.74	97.43	91.63
Index/2006	98.88	99.10	98.98	98.89		98.49	92.62
Variant/1055	97.96	98.19	97.96	97.96	99.09		91.76
GsGd/96	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.

ISSN: 1743-422X