A Capsid Tyrosine Residue Governs the Proteolytic Inactivation of Echovirus 11 in Lakewater

Abstract Enteroviruses are environmentally transmissible human pathogens whose stability in natural waters varies widely, yet the molecular determinants underlying this variability remain largely unknown. Echovirus 11 (E11), a reemerging cause of severe neonatal infections, is efficiently transmitted via contaminated water, making its environmental stability a critical factor in infection risk. Here, we identify a viral capsid residue as one of the drivers of E11 susceptibility to inactivation by extracellular microbial proteases in freshwater. By combining virus decay measurements in lakewater with proteolytic-cleavage profiling, viral capsid structural analyses, and reverse genetics, we show that the presence of VP2.Y97 renders E11 highly sensitive to microbially mediated proteolytic decay. Strikingly, this residue is absent from multiple enteroviruses with greater environmental stability, indicating that substitution at a single capsid position is sufficient to shift virus fate in natural waters. These findings reveal that fine-scale capsid architecture controls virus–microbe interactions in aquatic environments and establish a molecular mechanism linking capsid variation to environmental transmission potential among enteroviruses.