title: Predominance and geo-mapping of avian influenza H5N1 in poultry sectors in Egypt.
abstract: Highly pathogenic avian influenza (HPAI) virus of the H5N1 subtype has been enzootic in the Egyptian poultry with significant human infections since 2008. This work evaluates the epidemiological and virological information from February 2006 to May 2015 in spatial and temporal terms. Only data with confirmed HPAI H5N1 sub-type were collected, and matched with the epidemiological data from various spatially and temporally-dispersed surveillances implemented between 2006 and 2015. Spatio-temporal analysis was conducted on a total of 3338 confirmed H5N1 HPAI poultry disease outbreaks and outputs described based on transmission patterns, poultry species, production types affected, trade, geographic and temporal distributions in Egypt. The H5N1 virus persists in the Egyptian poultry displaying a seasonal pattern with peak prevalence between January and March. There was no specific geographic pattern, but chickens and ducks were more affected. However, relatively higher disease incidences were recorded in the Nile Delta. Phylogenetic studies of the haemagglutinin gene sequences of H5N1 viruses indicated that multiple clusters circulated between 2006 and 2015, with significant deviations in circulation. Epidemiological dynamics of HPAI has changed with the origins of majority of outbreaks shifted to household poultry. The persistence of HPAI H5N1 in poultry with recurrent and sporadic infections in humans can influence virus evolution spatio-temporally. Household poultry plays significant roles in the H5N1 virus transmission to poultry and humans, but the role of commercial poultry needs further clarifications. While poultry trading supports the persistence and transmission of H5N1, the role of individual species may warrant further investigation. Surveillance activities, applying a multi-sectoral approach, are recommended.
authors.affiliation: Emergency Center of Transboundary Animal Diseases, Food and Agriculture Organization of the United Nations, Giza; National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza. Abdelsatar.Arafa@fao.org.
authors.forename: Abdelsatar
authors.initials: A
authors.lastname: Arafa
authors.forename: Ihab
authors.initials: I
authors.lastname: El-Masry
authors.forename: Shereen
authors.initials: S
authors.lastname: Khoulosy
authors.forename: Mohammed K
authors.initials: MK
authors.lastname: Hassan
authors.forename: Moussa
authors.initials: M
authors.lastname: Soliman
authors.forename: Olubunmi G
authors.initials: OG
authors.lastname: Fasanmi
authors.forename: Folorunso O
authors.initials: FO
authors.lastname: Fasina
authors.forename: Gwenaelle
authors.initials: G
authors.lastname: Dauphin
authors.forename: Juan
authors.initials: J
authors.lastname: Lubroth
authors.forename: Yilma M
authors.initials: YM
authors.lastname: Jobre
mesh_terms: D000818:Animals; D002645:Chickens; D004196:Disease Outbreaks; D004534:Egypt / Q000453:epidemiology; D006801:Humans; D053124:Influenza A Virus, H5N1 Subtype / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000453:epidemiology*; D010802:Phylogeny; D011200:Poultry; D011201:Poultry Diseases / Q000453:epidemiology* / Q000821:virology