title: Origin and fate of A/H1N1 influenza in Scotland during 2009.
abstract: The spread of influenza has usually been described by a 'density' model, where the largest centres of population drive the epidemic within a country. An alternative model emphasizing the role of air travel has recently been developed. We have examined the relative importance of the two in the context of the 2009 H1N1 influenza epidemic in Scotland. We obtained genome sequences of 70 strains representative of the geographical and temporal distribution of H1N1 influenza during the summer and winter phases of the pandemic in 2009. We analysed these strains, together with another 128 from the rest of the UK and 292 globally distributed strains, using maximum-likelihood phylogenetic and bayesian phylogeographical methods. This revealed strikingly different epidemic patterns within Scotland in the early and late parts of 2009. The summer epidemic in Scotland was characterized by multiple independent introductions from both international and other UK sources, followed by major local expansion of a single clade that probably originated in Birmingham. The winter phase, in contrast, was more diverse genetically, with several clades of similar size in different locations, some of which had no particularly close phylogenetic affinity to strains sampled from either Scotland or England. Overall there was evidence to support both models, with significant links demonstrated between North American sequences and those from England, and between England and East Asia, indicating that major air-travel routes played an important role in the pattern of spread of the pandemic, both within the UK and globally.
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK.
authors.forename: Samantha
authors.initials: S
authors.lastname: Lycett
authors.affiliation: Centre for Immunity, Infection and Evolution, Ashworth Laboratories, West Mains Rd, Edinburgh EH9 3JT, UK.
authors.forename: Nigel J
authors.initials: NJ
authors.lastname: McLeish
authors.affiliation: Health Protection Scotland (HPS), 3 Clifton Place, Glasgow G3 7LN, UK.|Department of Mathematics and Statistics, University of Strathclyde, 26 Richmond Street, Glasgow G1 1XH, UK.
authors.forename: Christopher
authors.initials: C
authors.lastname: Robertson
authors.affiliation: West of Scotland Specialist Virology Centre, Gartnavel General Hospital, Glasgow, UK.
authors.forename: William
authors.initials: W
authors.lastname: Carman
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Gregory
authors.initials: G
authors.lastname: Baillie
authors.affiliation: Health Protection Scotland (HPS), 3 Clifton Place, Glasgow G3 7LN, UK.
authors.forename: James
authors.initials: J
authors.lastname: McMenamin
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.affiliation: Centre for Immunity, Infection and Evolution, Ashworth Laboratories, West Mains Rd, Edinburgh EH9 3JT, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Simmonds
authors.affiliation: Centre for Immunity, Infection and Evolution, Ashworth Laboratories, West Mains Rd, Edinburgh EH9 3JT, UK.
authors.forename: Mark
authors.initials: M
authors.lastname: Woolhouse
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Leigh Brown
mesh_terms: D058872:Epidemics; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D007251:Influenza, Human / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012606:Scotland / Q000453:epidemiology; D012621:Seasons; D014195:Travel; D006113:United Kingdom / Q000453:epidemiology