Cell entry
Effects of mutations on cell entry
Deep mutational scanning of H3 influenza HA
A collection of data, figures, and analysis for exploring pleiotropic constraints on the antigenic evolution of human H3N2 influenza virus.
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Overview
This site hosts interactive visualizations from deep mutational scanning experiments that measure the effects of mutations to the HA of A/Massachusetts/18/2022 (H3N2) influenza virus. Clicking on the links in the boxes above will take you to pages that access the visualizations.
This work was performed in the Bloom lab. To read the paper that describes the results, see Yu et al (2025).
Note that the experiments were performed using pseudovirus deep mutational scanning. These pseudoviruses encode no viral genes other than HA, and so can only undergo a single round of cell entry. These pseudoviruses are therefore not infectious agents and are not disease-causing pathogens, and so provide a safe way to study HA mutations at biosafety-level 2.
All of the plots and files here use the widely adopted H3 numbering scheme. This numbering starts with one at the first amino-acid of the ectodomain, not the N-terminal methionine. Click here for the site numbering map.
The GitHub repository with the full analysis and code is at https://github.com/dms-vep/Flu_H3_Massachusetts2022_DMS and the full output of the analysis pipeline is in the Appendix.