Network Analysis of Global Influenza Spread

Abstract

Although vaccines pose the best means of preventing influenza infection, strain selection and optimal implementation remain difficult due to antigenic drift and a lack of understanding global spread. Detecting viral movement by sequence analysis is complicated by skewed geographic and seasonal distributions in viral isolates. We propose a probabilistic method that accounts for sampling bias through spatiotemporal clustering and modeling regional and seasonal transmission as a binomial process. Analysis of H3N2 not only confirmed East-Southeast Asia as a source of new seasonal variants, but also increased the resolution of observed transmission to a country level. H1N1 data revealed similar viral spread from the tropics. Network analysis suggested China and Hong Kong as the origins of new seasonal H3N2 strains and the United States as a region where increased vaccination would maximally disrupt global spread of the virus. These techniques provide a promising methodology for the analysis of any seasonal virus, as well as for the continued surveillance of influenza.

Phylodynamics of influenza A(H3N2) in South America, 1999–2012

“…AU, HK, NY and the UK were the locations chosen as representative of Oceania, Asia, North America and Europe, respectively, based upon the extensive sampling density over the study period and owing to the fact that these places were shown to be important hubs of influenza A(H3N2) dissemination and airport traffic at global scale (ACI, 2012;Chan et al, 2010). To reduce potential biases in the global phylogeographic reconstructions due to sampling heterogeneity between locations Lemey et al, 2014) we generate a "non-redundant" global balanced subset by removing very closely related sequences from the same geographic region.…”

Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission

“…It is clear that a complete understanding of influenza metapopulation dynamics will require deeper sampling from understudied tropical and subtropical regions, notably in Africa, India and Latin America, and from seasonal influenza A/H1N1 and influenza B virus, for which there is limited information (figure 1). Overall, the debate over the existence and location of a global source population highlights the dangers of drawing strong conclusions from limited sampling [27].…”

Blurred line between chemotactic chase and phagocytic consumption: an immunophysical single-cell perspective

“…Immunophysics is not limited to the study of cells but encompasses a wide range of subjects and scales: from structure-function relationships of individual molecules (Somers et al, 2000;Kim et al, 2006) and the dynamic strengths of receptor-ligand interactions (Williams et al, 2000;Marshall et al, 2003;Evans and Calderwood, 2007) to population dynamics of pathogens (McQueen, 2010;Vynnycky and White, 2010) and mathematical models of pandemics (Lemey et al, 2009;Chan et al, 2010). At the cellular scale, processes such as phagocytosis and chemotaxis exemplify both the necessity and benefits of an interdisciplinary analysis (Box 1).…”