Phenotypic diversity in viral evolution

National Institute Of Allergy And Infectious Diseases

Investigators

Abstract

Research in SVBBU has pioneered a range of methods for quantitative measurements in virology. For example, our single-virion analyses of influenza A virus (IAV) membrane fusion have revealed the functional advantage of the larger, filamentous virions over the smaller, spherical ones in the presence of cell-entry pressures including antibodies. This led to our proposal that the diversity of shapes in pleomorphic (mixed shape) populations is a viral mechanism of evasion of both natural and treatment-induced pressures. In a study published in FY2025, we established a rapid and sensitive flow virometry method for virion counting and shape measurements and revealed that assembly of filaments is actively tuned to the infection environment rather than being a fixed genetic property. IAV shape responds to the host-cell permissiveness and can rapidly shift in the presence of attenuating external factors, such as replication inhibitors or neutralizing antibodies. By analyzing shape as a function of replication efficiency of four different IAV strains (representing two subtypes and 80 years of antigenic evolution) in four different cell lines, we discovered that shape is a conserved rather than a distinguishing genetic feature of these IAV strains. In other words, the distribution of shapes produced in an infection is a measure of the host permissiveness or the viral adaptive status in each host environment. Building upon these insights, we aim to probe whether shape tuning is a universal feature of all IAV biology. Toward this aim, in FY2025 we developed a range of tools enabling high-throughput shape assays and infection profiling. One innovation was the development of a universal antibody binder enabling flow virometry across practically all IAV strains, including isolates from the recent H5N1 IAV outbreak. The goal of this large-scale effort will be to both uncover shared biological rules and to identify naturally occurring exceptions to those rules, together informing the mechanism of shape tuning and revealing universal targets for combatting infections by circulating and emerging IAV.