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.