Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission

Abstract

One contribution of 18 to a Discussion Meeting Issue 'Next-generation molecular and evolutionary epidemiology of infectious disease'. In the past decade, rapid increases in the availability of high-resolution molecular and epidemiological data, combined with developments in statistical and computational methods to simulate and infer migration patterns, have provided key insights into the spatial dynamics of influenza A viruses in humans. In this review, we contrast findings from epidemiological and molecular studies of influenza virus transmission at different spatial scales. We show that findings are broadly consistent in large-scale studies of interregional or inter-hemispheric spread in temperate regions, revealing intense epidemics associated with multiple viral introductions, followed by deep troughs driven by seasonal bottlenecks. However, aspects of the global transmission dynamics of influenza viruses are still debated, especially with respect to the existence of tropical source populations experiencing high levels of genetic diversity and the extent of prolonged viral persistence between epidemics. At the scale of a country or community, epidemiological studies have revealed spatially structured diffusion patterns in seasonal and pandemic outbreaks, which were not identified in molecular studies. We discuss the role of sampling issues in generating these conflicting results, and suggest strategies for future research that may help to fully integrate the epidemiological and evolutionary dynamics of influenza virus over space and time.

Viral Epidemiology

“…Phylodynamic and phylogeographic models also have been useful in reconstructing the spatial spread of viruses to reveal hidden patterns of transmission. For example, epidemiological and molecular studies of influenza virus transmission were compared at different spatial scales to highlight the similarities and differences between these data sources (Viboud, 2013). The findings were broadly consistent with large-scale studies of interregional or inter-hemispheric spread in temperate regions with multiple viral introductions resulting in epidemics followed by interepidemic periods driven by seasonal bottlenecks.…”

Influenza seasonality in Madagascar: the mysterious African free‐runner

“…Early research has put forward the concept of a sink–source model for A(H3N2) that favors the emergence of new virus variants in tropical South‐East Asia . This model is still debated, in part due to the paucity of influenza epidemiological and virological information from Africa and South America . A further issue is the seemingly lack of persistence and low diversity of influenza viruses in tropical locations such as Hong Kong, which is inconsistent with the role of “source population” .…”

Molecular Evidence of Transmission of Influenza A/H1N1 2009 on a University Campus

“…Although there are available data on the spatial and temporal transmission dynamics of influenza at global and national levels [5–10], transmission dynamics have not been thoroughly explored at the level of individual communities, especially in semi-closed settings such as universities or military camps. A better understanding of transmission dynamics in localized communities helps to identify foci of influenza transmission for more targeted interventions, such as school closure or household prophylaxis [11]. An examination of the spatial diffusion of pH1N1/09 virus in a localized community of the University of California found that although there was intra-campus transmission, there was no significant association of on-campus residence with clustering of similar viral strains [12].…”