title: Genome analysis linking recent European and African influenza (H5N1) viruses.
abstract: To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted.
authors.affiliation: University of Maryland Center for Bioinformatics and Computational Biology, College Park, Maryland 20742, USA. salzberg@umd.edu
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Carl
authors.initials: C
authors.lastname: Kingsford
authors.forename: Giovanni
authors.initials: G
authors.lastname: Cattoli
authors.forename: David J
authors.initials: DJ
authors.lastname: Spiro
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Janies
authors.forename: Mona Mehrez
authors.initials: MM
authors.lastname: Aly
authors.forename: Ian H
authors.initials: IH
authors.lastname: Brown
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Couacy-Hymann
authors.forename: Gian Mario
authors.initials: GM
authors.lastname: De Mia
authors.forename: Do Huu
authors.initials: do H
authors.lastname: Dung
authors.forename: Annalisa
authors.initials: A
authors.lastname: Guercio
authors.forename: Tony
authors.initials: T
authors.lastname: Joannis
authors.forename: Ali Safar
authors.initials: AS
authors.lastname: Maken Ali
authors.forename: Azizullah
authors.initials: A
authors.lastname: Osmani
authors.forename: Iolanda
authors.initials: I
authors.lastname: Padalino
authors.forename: Magdi D
authors.initials: MD
authors.lastname: Saad
authors.forename: Vladimir
authors.initials: V
authors.lastname: Savić
authors.forename: Naomi A
authors.initials: NA
authors.lastname: Sengamalay
authors.forename: Samuel
authors.initials: S
authors.lastname: Yingst
authors.forename: Jennifer
authors.initials: J
authors.lastname: Zaborsky
authors.forename: Olga
authors.initials: O
authors.lastname: Zorman-Rojs
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
authors.forename: Ilaria
authors.initials: I
authors.lastname: Capua
mesh_terms: D000352:Africa, Northern / Q000453:epidemiology; D000818:Animals; D001717:Birds / Q000821:virology*; D005060:Europe / Q000453:epidemiology; D019143:Evolution, Molecular; D005814:Genes, Viral / Q000235:genetics*; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification / Q000235:genetics*; D005585:Influenza in Birds / Q000145:classification / Q000235:genetics*; D008877:Middle East / Q000453:epidemiology; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny