Integrating influenza antigenic dynamics with molecular evolution

By Trevor Bedford, Marc A. Suchard, Philippe Lemey, G. Dudas, V. Gregory, A. Hay, J. McCauley, C. Russell, Derek J. Smith, Andrew Rambaut. eLife, 2013

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Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001

Subfields: Agronomy and Crop Science, Ecology, Epidemiology

View Paper: https://www.semanticscholar.org/paper/e672796ab12fa51ed3efa992f17d21ed67bf809e

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Citations in the corpus

Predicting evolution (2017, background): “This problem is difficult in general, but at least the response of pathogen population size to immune or vaccination pressure can be computed using fitness models of immune interactions 13,120,121 .”
Global circulation patterns of seasonal influenza viruses vary with antigenic drift (2015, neutral): “We hypothesized a relationship between rates of global movement and rates of antigenic drift: though rates of genetic evolution were similar for H3N2 and H1N1 viruses, both H1N1 and B viruses evolved antigenically more slowly than H3N2 viruses 13 (Extended Data Table 1).”
Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin (2016, background): “Perhaps in part because of the high mutational tolerance of the antigenic sites in its globular head, HA is adept at escaping antibody-mediated immunity [1,40].”
SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes. (2016, background): “However, SpreaD3 can project trees in any arbitrary space, which allows for example producing two-dimensional plots of influenza antigenic evolution based on Bayesian multidimensional scaling estimates (Bedford et al. 2014) (fig.”
A human coronavirus evolves antigenically to escape antibody immunity (2020, background): “The rate at which 229E escapes neutralization by human sera is several fold slower than the rate at which influenza A/H3N2 escapes HAI by ferret sera, but comparable to the rate of such escape by influenza B [19,64].”
Predicting evolution from the shape of genealogical trees (2014, background): “…predictions for seasonal influenza virus evolution could likely be improved by combining the shape of genealogical tree with antigenic information (Bedford et al., 2014), biophysical and biochemical knowledge (Koel et al., 2013), patterns of past evolution (Łuksza and Lässig, 2014), and…”
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 (2018, background): “…other spaces, and integration of antibody binding assay data have extended ‘antigenic cartography’ (Smith et al. 2004) approaches to model simultaneous antigenic and genetic evolution and infer the viral trajectories in the immunological space generated by the host population (Bedford et al. 2014).”
Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin (2019, background): “Unfortunately, the effectiveness of this immunity against future strains is rapidly degraded by viral antigenic evolution (Bedford et al., 2014; Smith et al., 2004), such that the typical human is infected by influenza virus roughly every 5 years (Couch and Kasel, 1983; Kucharski et al.”