Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein

Abstract

The influenza virus polymerase is central to influenza virus evolution. Adaptive mutations within the polymerase are often a prerequisite for efficient spread of novel animal-derived viruses in human populations. The polymerase also determines fidelity, and therefore the rate at which the virus will acquire mutations that lead to host range expansion, drug resistance, or antigenic drift. Despite its importance to viral replication and evolution, our understanding of the mutational effects and associated constraints on the influenza RNA-dependent RNA polymerase (RdRp) is relatively limited. We performed deep mutational scanning of the A/WSN/1933(H1N1) PB1, generating a library of 95.4% of amino acid substitutions at 757 sites. After accuracy filters, we were able to measure replicative fitness for 13,354 (84%) of all possible amino acid substitutions, and 16 were validated by results from pairwise competition assays. Functional and structural constraints were better revealed by individual sites involved in RNA or protein interactions than by major subdomains defined by sequence conservation. Mutational tolerance, as defined by site entropy, was correlated with evolutionary potential, as captured by diversity in available H1N1 sequences. Of 29 beneficial sites, many have either been identified in the natural evolution of PB1 or shown experimentally to have important impacts on replication and adaptation. Accessibility of amino acid substitutions by single nucleotide mutation was a key factor in determining whether mutations appeared in natural PB1 evolution. Our work provides a comprehensive map of mutational effects on a viral RdRp and a valuable resource for subsequent studies of influenza replication and evolution.