Asymmetric structural transitions in the icosahedral organization of Eastern equine encephalitis virus

Delivery of the viral genome into host cells is a critical step in successful viral infection. Alphaviruses achieve this step by fusing the viral and endosomal membranes under acidic conditions. This process requires significant structural changes in the alphavirus glycoprotein organization. Structural characterization of acidic pH-induced conformational changes in alphavirus virions has remained elusive due to the rapid, transient nature of these states, conformational heterogeneity, and particle aggregation. Antibody binding studies conducted at elevated temperatures or under acidic pH conditions have further revealed the presence of transitional epitopes that are inaccessible on alphaviruses at room temperature or neutral pH. In this report, we present structural snapshots of the conformational changes in the glycoproteins and nucleocapsid core of a prototypical alphavirus, Eastern equine encephalitis virus, caused by exposure to 40 °C or pH 5.6. These findings provide insights into the structural transitions that occur prior to viral fusion with the endosomal membrane. This approach has also allowed us to define the molecular basis for recognition of a pan-alphavirus epitope by a patient-derived human antibody.