A single residue in the yellow fever virus envelope protein modulates virion architecture and antigenicity

Summa Bibby, James Jung, Yu Shang Low, Alberto A. Amarilla, Natalee D. Newton, Connor A. P. Scott, Jessica Balk, Yi Tian Ting, Morgan E. Freney, Benjamin Liang, Timothy Grant, Fasséli Coulibaly, Paul Young, Roy A. Hall, Jody Hobson-Peters, Naphak Modhiran () and Daniel Watterson ()
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Summa Bibby: The University of Queensland
James Jung: The University of Queensland
Yu Shang Low: The University of Queensland
Alberto A. Amarilla: The University of Queensland
Natalee D. Newton: The University of Queensland
Connor A. P. Scott: The University of Queensland
Jessica Balk: Monash University
Yi Tian Ting: Monash University
Morgan E. Freney: The University of Queensland
Benjamin Liang: The University of Queensland
Timothy Grant: Morgridge Institute for Research
Fasséli Coulibaly: Monash University
Paul Young: The University of Queensland
Roy A. Hall: The University of Queensland
Jody Hobson-Peters: The University of Queensland
Naphak Modhiran: The University of Queensland
Daniel Watterson: The University of Queensland

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Yellow fever virus (YFV) is a re-emerging flavivirus that causes severe hepatic disease and mortality in humans. Despite being researched for over a century, the structure of YFV has remained elusive. Here we use a chimeric virus platform to resolve the first high resolution cryo-EM structures of YFV. Stark differences in particle morphology and homogeneity are observed between vaccine and virulent strains of YFV, and these are found to have significant implications on antibody recognition and neutralisation. We identify a single residue (R380) in the YFV17D envelope protein that stabilises the virion surface, and leads to reduced exposure of the cross-reactive fusion loop epitope. The differences in virion morphology between YFV strains also contribute to the reduced sensitivity of the virulent YFV virions to vaccine-induced antibodies. These findings have significant implications for YFV biology, vaccinology and structure-based flavivirus antigen design.

Date: 2025
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DOI: 10.1038/s41467-025-63038-5

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