Influenza Evolution: New Insights into an Old Foe

Identifying viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution. We describe a high-throughput approach to quantify the selection that monoclonal antibodies exert on all single amino-acid mutations to a viral protein. This approach, mutational antigenic profiling, involves creating all replication-competent protein variants of a virus, selecting with antibody, and using deep sequencing to identify enriched mutations. We use mutational antigenic profiling to comprehensively identify mutations that enable influenza virus to escape four monoclonal antibodies targeting hemagglutinin, and validate key findings with neutralization assays. We find remarkable mutation-level idiosyncrasy in antibody escape: for instance, at a single residue targeted by two antibodies, some mutations escape both antibodies while other mutations escape only one or the other. Because mutational antigenic profiling rapidly maps all mutations selected by an antibody, it is useful for elucidating immune specificities and interpreting the antigenic consequences of viral genetic variation.
Author summary Many viruses evolve rapidly, and this evolution sometimes enables them to escape antibodies that would otherwise neutralize their infectivity. An important aspect of studying this evolution is determining which viral mutations can mediate antibody escape. The classic way of identifying such mutations is to select or test them one by one. However, a vast number of possible mutations can be made to a virus. For instance, there are over 10,000 single amino-acid mutations that can be made to the most abundant surface protein of influenza virus, hemagglutinin. This is too many to test one by one, and so all previous studies of antibody escape have examined just a fraction of the possible amino-acid mutations to any given viral protein. Here we describe a new approach to quantify the selection that an antibody exerts on all these mutations in a single experiment. This approach enables us to reproducibly and sensitively identify mutations that affect antibody neutralization—for instance, at individual sites in hemagglutinin, we can distinguish which of several different mutations have the largest effect on antibody escape. The ability to completely map viral escape from antibodies opens the door to much more detailed characterization of viral antigenic evolution.