title: Evolutionary dynamics of multiple sublineages of H5N1 influenza viruses in Nigeria from 2006 to 2008.
abstract: Highly pathogenic A/H5N1 avian influenza (HPAI H5N1) viruses have seriously affected the Nigerian poultry industry since early 2006. Previous studies have identified multiple introductions of the virus into Nigeria and several reassortment events between cocirculating lineages. To determine the spatial, evolutionary, and population dynamics of the multiple H5N1 lineages cocirculating in Nigeria, we conducted a phylogenetic analysis of whole-genome sequences from 106 HPAI H5N1 viruses isolated between 2006 and 2008 and representing all 25 Nigerian states and the Federal Capital Territory (FCT) reporting outbreaks. We identified a major new subclade in Nigeria that is phylogenetically distinguishable from all previously identified sublineages, as well as two novel reassortment events. A detailed analysis of viral phylogeography identified two major source populations for the HPAI H5N1 virus in Nigeria, one in a major commercial poultry area (southwest region) and one in northern Nigeria, where contact between wild birds and backyard poultry is frequent. These findings suggested that migratory birds from Eastern Europe or Russia may serve an important role in the introduction of HPAI H5N1 viruses into Nigeria, although virus spread through the movement of poultry and poultry products cannot be excluded. Our study provides new insight into the genesis and evolution of H5N1 influenza viruses in Nigeria and has important implications for targeting surveillance efforts to rapidly identify the spread of the virus into and within Nigeria.
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, Research & Development Department, OIE/FAO, and National Reference Laboratory for Newcastle Disease and Avian Influenza, OIE Collaborating Centre for Epidemiology, Training and Control of Emerging Avian Diseases, Viale dell'Università 10, 35020, Legnaro, Padua, Italy. afusaro@izsvenezie.it
authors.forename: Alice
authors.initials: A
authors.lastname: Fusaro
authors.forename: Martha I
authors.initials: MI
authors.lastname: Nelson
authors.forename: Tony
authors.initials: T
authors.lastname: Joannis
authors.forename: Luigi
authors.initials: L
authors.lastname: Bertolotti
authors.forename: Isabella
authors.initials: I
authors.lastname: Monne
authors.forename: Annalisa
authors.initials: A
authors.lastname: Salviato
authors.forename: Olufemi
authors.initials: O
authors.lastname: Olaleye
authors.forename: Ismaila
authors.initials: I
authors.lastname: Shittu
authors.forename: Lanre
authors.initials: L
authors.lastname: Sulaiman
authors.forename: Lami H
authors.initials: LH
authors.lastname: Lombin
authors.forename: Ilaria
authors.initials: I
authors.lastname: Capua
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.forename: Giovanni
authors.initials: G
authors.lastname: Cattoli
mesh_terms: D000818:Animals; D001483:Base Sequence; D001717:Birds / Q000821:virology; D019143:Evolution, Molecular; D014644:Genetic Variation; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification* / Q000235:genetics; D008969:Molecular Sequence Data; D009549:Nigeria; D010802:Phylogeny; D016865:Reassortant Viruses / Q000235:genetics; D013997:Time Factors