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United States Department of Agriculture

Agricultural Research Service

Research Project: APPLICATION OF BIOLOGICAL AND MOLECULAR TECHNIQUES TO THE DIAGNOSIS AND CONTROL OF AVIAN INFLUENZA AND OTHER EMERGING POULTRY PATHOGENS

Location: Exotic and Emerging Avian Viral Diseases Research Unit

Title: Phylogenetic analysis of hemagglutinin and neuraminidase genes of highly pathogenic avian influenza H5N1 Egyptian strains isolated from 2006 to 2008 indicates heterogeneity with multiple distinct sublineages

Authors
item Arafa, A -
item Suarez, David
item Aly, M -
item Hassan, M -

Submitted to: Avian Diseases
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 4, 2009
Publication Date: March 1, 2010
Citation: Arafa, A., Suarez, D.L., Aly, M.M., Hassan, M.K. 2010. Phylogenetic analysis of hemagglutinin and neuraminidase genes of highly pathogenic avian influenza H5N1 Egyptian strains isolated from 2006 to 2008 indicates heterogeneity with multiple distinct sublineages. Avian Diseases. 54:345-349.

Interpretive Summary: Highly pathogenic avian influenza is a serious disease of poultry because it is easily transmitted and causes high mortality. The H5N1 Asian lineage highly pathogenic avian influenza has spread farther, 3 continents and over 40 countries, and killed more birds, more than 200 million, than any other form of the virus. It continues to be both a veterinary and public health threat because humans can be infected with this lineage of viruses. This lineage of virus was first detected in Egypt in 2006, and has since become widespread throughout the country. This study examined the genetic sequence of two of the viral gene from viruses isolated in 2006 through 2008 to determine how the virus was changing in the country. It appears that there was a single source of introduction of virus into the country, and the viruses have changed into 5 distinct clusters. It is unusual to see this many unique clusters of virus in a country, and further work is needed to understand why there are these differences in the country.

Technical Abstract: The Eurasian lineage H5N1 Highly pathogenic avian influenza (HPAI) virus caused widespread outbreaks in Egypt in 2006 and eventually become enzootic in poultry. Although outbreaks have a seasonal pattern with most occurring during the cooler winter months, it remains unclear if this seasonality reflects virus maintenance within Egypt or yearly introductions of the virus into the country. To evaluate the epidemiology of H5N1 HPAI in Egypt, sequence analysis of the Hemagglutinin (HA) and Neuraminidase (NA) genes of selected Egyptian isolates from early 2006 to 2008 was conducted. The data from this study identifies distinct genetic markers in both HA and NA genes and suggests grouping of Egyptian isolates into 2 main HA sublineages of isolates from 2006 to 2008, but with 3 smaller emergent groups. The NA phylogenetic and sequence analysis showed a similar pattern except that two of the emergent groups on the HA phylogenetic tree were clustered together, evidence of likely reassortment. No observable pattern of why isolates clustered with a specific lineage was observed by date of isolation, species of isolation, or geographic location of the viruses, which creates uncertainity about the most appropriate control measures needed to eradicate the virus.

Last Modified: 7/30/2014
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