title: Evolutionary features of influenza A/H5N1 virus populations in Egypt: poultry and human health implications.
abstract: Since 2006, in Egypt, highly pathogenic avian influenza virus (HPAIV) H5N1 has established endemic status in poultry. Bayesian evolutionary analysis sampling trees suggested an introduction date in the third quarter of 2005. Evolutionary dynamics using Bayesian analysis showed that H5N1 viruses of clade 2.2.1.1 evolved at higher rates than those of clade 2.2.1.2. Bayesian skyline plot analysis of the HA gene of 840 and NA gene of 401 Egyptian H5N1 viruses from 2006-2015 identified two waves of viral population expansion correlating with the stepwise emergence of the 2.2.1.1 variant lineage in 2008 and with the newly emerging 2.2.1.2 cluster in late 2014. H5N1 infections in human hosts in 2014-2015 were statistically linked to a contemporary poultry outbreak.
authors.affiliation: The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany.|National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, P.O. Box 246, Giza, 12618, Egypt.
authors.forename: Mahmoud M
authors.initials: MM
authors.lastname: Naguib
authors.affiliation: The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany.
authors.forename: E M
authors.initials: EM
authors.lastname: Abdelwhab
authors.affiliation: The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany. timm.harder@fli.bund.de.
authors.forename: Timm C
authors.initials: TC
authors.lastname: Harder
mesh_terms: D000818:Animals; D004196:Disease Outbreaks; D004534:Egypt / Q000453:epidemiology; D019143:Evolution, Molecular; D006801:Humans; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D005585:Influenza in Birds / Q000453:epidemiology / Q000821:virology*; D007251:Influenza, Human / Q000453:epidemiology / Q000821:virology*; D010802:Phylogeny; D011200:Poultry; D011201:Poultry Diseases / Q000453:epidemiology / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins