Origin and Fate of A/H1N1 Influenza in Scotland during 2009

Lycett S, McLeish NJ, Robertson C, Carman W, Baillie G, McMenamin J, Rambaut A, Simmonds P, Woolhouse M & Leigh Brown AJ

(2012) J Gen Virol 93, 1253-1260.

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 emphasising 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 71 strains representative of the geographic 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 United Kingdom and 293 globally distributed strains using maximum likelihood phylogenetics and Bayesian phylogeographic methods. This revealed strikingly different epidemic patterns within Scotland in the early and late part of 2009. The summer epidemic in Scotland was characterised by multiple independent introductions from both international and other UK sources, followed by major local expansion of a single clade which 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 N. American sequences and those from England, and between England and East Asia, indicating major air travel routes played an important role in the pattern of spread of the pandemic both within the UK and globally.

Andrew Rambaut, 2007