Escape from serum antibody neutralization

Interactive plot of mutation effects

The plot below shows how mutations affect neutralization by polyclonal serum from mice or ferrets vaccinated or infected with a clade 2.3.4.4b H5 HA. The plot is interactive, and allows you to zoom and mouseover sites and mutations. Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or click here to open the plot in a stand-alone window. For a larger version of the plot that shows escape from each animal's sera in a separate plot, click here. Note that the two different shades of gray in the heatmaps have differing meanings: light gray means a mutation was missing (not measured) in the library, whereas dark gray means a mutation was measured but was so deleterious for cell entry it is not possible to reliably estimate its effect on other phenotypes (the threshold for how deleterious a mutation must be for cell entry to be shown in dark gray is controlled by the cell entry slider at the bottom of the plot).

Interactive plot showing effects of mutations on escape from serum neutralization

Here is an explanation of the key plot elements:

• The zoom bar at the top of the plot shows different regions of HA, and can be used to zoom in on specific sites.
• The line plot summarizes the neutralization escape caused by mutations at each site (larger values indicate more escape) first for mouse sera and then for ferret sera. The black lines show the average across sera for different animals, and the gray lines show escape for individual animals. The escape at a site is quantified using the site summary statistic specified by the interactive option at the bottom of the plot (eg, sum or mean effect of mutations at a site).
• The heatmaps then show how each individual mutation affects each measured phenotype. The x's indicate the amino-acid identity in the parental HA strain, light gray indicates mutations that were not measured, and dark gray indicates mutations that are filtered out by one of the interactive sliders at the by one of the interactive sliders at the bottom of the plot (eg, they have a very negative effect on cell entry). You can mouse over any of the points. You can mouse over any of the heatmap cells for details.
• The options at the bottom of the plot allow you to interactively adjust what is displayed. For instance, the minimum mutation entry in 293T cells only shows mutations with at least some minimal cell entry function (and grays out mutations that are more deleterious). You can also select to only show mutations accessible by some number of mutations to the codon in the parental sequence (eg, only accessible by single -nucleotide mutations), or floor the escape at zero to show / not show "negative" escape values.

Numerical values of escape

For per-serum escape values, see this CSV file.

Detailed plots for each sera

See the more detailed results for escape from each individual serum, look here under the Antibody/serum escape section.