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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 - J. Gen. Virol. (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK.

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.

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Time-resolved phylogenetic tree of influenza A H1N1 2009 sequences. Time-resolved phylogeny produced in beast for seven-segment sequences from Scotland, RUK and global sequences listed in Table 2. See Fig. S3 for strain labels. Global sequences are not shown for clarity. Branch colours: cyan, global clade 2 (Nelson et al., 2011b); red, global clade 3; blue, global clade 5; green, global clade 6; black, global clade 7. Bar, 0.5 years.
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f2: Time-resolved phylogenetic tree of influenza A H1N1 2009 sequences. Time-resolved phylogeny produced in beast for seven-segment sequences from Scotland, RUK and global sequences listed in Table 2. See Fig. S3 for strain labels. Global sequences are not shown for clarity. Branch colours: cyan, global clade 2 (Nelson et al., 2011b); red, global clade 3; blue, global clade 5; green, global clade 6; black, global clade 7. Bar, 0.5 years.

Mentions: The global sequence diversity exhibited by pandemic H1N1/2009 has been divided into seven major clades (Nelson et al., 2011b). Initial phylogenetic analysis by maximum likelihood (ML) revealed that influenza virus sequences from Scotland were distributed across the global tree, indicating a series of introductions from which the virus spread locally, rather than a single point source introduction in each phase (Fig. S1, available in JGV Online). The overall total evolutionary change was restricted as revealed by a root-to-tip plot (Fig. 1), but even with a divergence of as little as 0.3 % occurring over the 1 year observation period, there was a very strong molecular-clock effect. Comparison of early and late sequences for three regional categories, Scotland, rest of UK (RUK) and North America, showed clear and significant divergence between sequences from the summer and winter phases of the epidemic (Fig. S2). Despite the small amount of evolution that occurred even globally within the summer phase, there was clear clustering of Scottish sequences into a series of clades that were not split by global sequences. As all samples analysed have accurate date information, the 492 strain dataset was analysed using time-resolved phylogenetic methodology implemented in the beast package (Drummond & Rambaut, 2007) to enhance resolution (Figs 2 and S3). The results were highly concordant with the ML tree overall, with minor differences such as might be expected given the low level of support for many individual clades.


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 - J. Gen. Virol. (2012)

Time-resolved phylogenetic tree of influenza A H1N1 2009 sequences. Time-resolved phylogeny produced in beast for seven-segment sequences from Scotland, RUK and global sequences listed in Table 2. See Fig. S3 for strain labels. Global sequences are not shown for clarity. Branch colours: cyan, global clade 2 (Nelson et al., 2011b); red, global clade 3; blue, global clade 5; green, global clade 6; black, global clade 7. Bar, 0.5 years.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3755513&req=5

f2: Time-resolved phylogenetic tree of influenza A H1N1 2009 sequences. Time-resolved phylogeny produced in beast for seven-segment sequences from Scotland, RUK and global sequences listed in Table 2. See Fig. S3 for strain labels. Global sequences are not shown for clarity. Branch colours: cyan, global clade 2 (Nelson et al., 2011b); red, global clade 3; blue, global clade 5; green, global clade 6; black, global clade 7. Bar, 0.5 years.
Mentions: The global sequence diversity exhibited by pandemic H1N1/2009 has been divided into seven major clades (Nelson et al., 2011b). Initial phylogenetic analysis by maximum likelihood (ML) revealed that influenza virus sequences from Scotland were distributed across the global tree, indicating a series of introductions from which the virus spread locally, rather than a single point source introduction in each phase (Fig. S1, available in JGV Online). The overall total evolutionary change was restricted as revealed by a root-to-tip plot (Fig. 1), but even with a divergence of as little as 0.3 % occurring over the 1 year observation period, there was a very strong molecular-clock effect. Comparison of early and late sequences for three regional categories, Scotland, rest of UK (RUK) and North America, showed clear and significant divergence between sequences from the summer and winter phases of the epidemic (Fig. S2). Despite the small amount of evolution that occurred even globally within the summer phase, there was clear clustering of Scottish sequences into a series of clades that were not split by global sequences. As all samples analysed have accurate date information, the 492 strain dataset was analysed using time-resolved phylogenetic methodology implemented in the beast package (Drummond & Rambaut, 2007) to enhance resolution (Figs 2 and S3). The results were highly concordant with the ML tree overall, with minor differences such as might be expected given the low level of support for many individual clades.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK.

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.

Show MeSH
Related in: MedlinePlus