title: A high diversity of Eurasian lineage low pathogenicity avian influenza A viruses circulate among wild birds sampled in Egypt.
abstract: Surveillance for influenza A viruses in wild birds has increased substantially as part of efforts to control the global movement of highly pathogenic avian influenza A (H5N1) virus. Studies conducted in Egypt from 2003 to 2007 to monitor birds for H5N1 identified multiple subtypes of low pathogenicity avian influenza A viruses isolated primarily from migratory waterfowl collected in the Nile Delta. Phylogenetic analysis of 28 viral genomes was performed to estimate their nearest ancestors and identify possible reassortants. Migratory flyway patterns were included in the analysis to assess gene flow between overlapping flyways. Overall, the viruses were most closely related to Eurasian, African and/or Central Asian lineage low pathogenicity viruses and belonged to 15 different subtypes. A subset of the internal genes seemed to originate from specific flyways (Black Sea-Mediterranean, East African-West Asian). The remaining genes were derived from a mixture of viruses broadly distributed across as many as 4 different flyways suggesting the importance of the Nile Delta for virus dispersal. Molecular clock date estimates suggested that the time to the nearest common ancestor of all viruses analyzed ranged from 5 to 10 years, indicating frequent genetic exchange with viruses sampled elsewhere. The intersection of multiple migratory bird flyways and the resulting diversity of influenza virus gene lineages in the Nile Delta create conditions favoring reassortment, as evident from the gene constellations identified by this study. In conclusion, we present for the first time a comprehensive phylogenetic analysis of full genome sequences from low pathogenic avian influenza viruses circulating in Egypt, underscoring the significance of the region for viral reassortment and the potential emergence of novel avian influenza A viruses, as well as representing a highly diverse influenza A virus gene pool that merits continued monitoring.
authors.affiliation: Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Nancy A
authors.initials: NA
authors.lastname: Gerloff
authors.forename: Joyce
authors.initials: J
authors.lastname: Jones
authors.forename: Natosha
authors.initials: N
authors.lastname: Simpson
authors.forename: Amanda
authors.initials: A
authors.lastname: Balish
authors.forename: Maha Adel
authors.initials: MA
authors.lastname: Elbadry
authors.forename: Verina
authors.initials: V
authors.lastname: Baghat
authors.forename: Ivan
authors.initials: I
authors.lastname: Rusev
authors.forename: Cecilia C
authors.initials: CC
authors.lastname: de Mattos
authors.forename: Carlos A
authors.initials: CA
authors.lastname: de Mattos
authors.forename: Luay Elsayed Ahmed
authors.initials: LE
authors.lastname: Zonkle
authors.forename: Zoltan
authors.initials: Z
authors.lastname: Kis
authors.forename: C Todd
authors.initials: CT
authors.lastname: Davis
authors.forename: Sam
authors.initials: S
authors.lastname: Yingst
authors.forename: Claire
authors.initials: C
authors.lastname: Cornelius
authors.forename: Atef
authors.initials: A
authors.lastname: Soliman
authors.forename: Emad
authors.initials: E
authors.lastname: Mohareb
authors.forename: Alexander
authors.initials: A
authors.lastname: Klimov
authors.forename: Ruben O
authors.initials: RO
authors.lastname: Donis
mesh_terms: D000595:Amino Acid Sequence; D025041:Animal Migration; D000818:Animals; D000835:Animals, Wild / Q000821:virology*; D001499:Bayes Theorem; D001717:Birds / Q000821:virology*; D002645:Chickens; D004534:Egypt / Q000453:epidemiology; D005814:Genes, Viral / Q000235:genetics; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000737:chemistry / Q000235:genetics; D009980:Influenza A virus / Q000235:genetics / Q000472:pathogenicity*; D005585:Influenza in Birds / Q000453:epidemiology / Q000821:virology*; D009439:Neuraminidase / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011159:Population Surveillance
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; D009439:Neuraminidase