Variant mutation G215C in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation

The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations outside of spike are not well studied, the entire viral genome is undergoing evolutionary selection, with several variants containing mutations in the central disordered linker region of the nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic of the Delta variant, that introduces a novel cysteine into this linker domain, which results in the formation of a more stable N-N dimer. Using reverse genetics, we determined that this cysteine residue is necessary and sufficient for stable dimer formation in a WA1 SARS-CoV-2 background, where it results in significantly increased viral growth both in vitro and in vivo. Mechanistically, we show that the N:G215C mutant has more encapsidation as measured by increased RNA binding to N, N incorporation into virions, and electron microscopy showing that individual virions are larger, with elongated morphologies.

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Publication Details

Journal
PLoS Biology
Published
2025-04-29
DOI
https://doi.org/10.1371/journal.pbio.3003115
Citations
4
Primary Topic
SARS-CoV-2 and COVID-19 Research
Type
article
Field-Weighted Citation Impact
5.58

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article

Variant mutation G215C in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation

Bryan A. Ballif, Hannah C. Kubinski, Caroline M. Dumas, Keith R. Jerome et al.
4 citations
PLoS Biology
SARS-CoV-2 and COVID-19 Research
5.58
article

Variant mutation G215C in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation

Bryan A. Ballif, Hannah C. Kubinski, Caroline M. Dumas, Keith R. Jerome, Mark S. Ladinsky, Jessica W. Crothers, Kumari G. Lokugamage, Allyson H Turner, Pavitra Roychoudhury, Emily A. Bruce, Madaline M. Schmidt, David J. Shirley, Vineet D. Menachery, David H. Walker, Alexander L. Greninger, Andrew Pekosz, Pamela J. Björkman, Hannah W. Despres, Bruno Martorelli Di Genova, Bryan A. Johnson, Margaret G. Mills, Sara A Jaffrani, Leah K. Estes
article en
4 citations

Abstract

The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations outside of spike are not well studied, the entire viral genome is undergoing evolutionary selection, with several variants containing mutations in the central disordered linker region of the nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic of the Delta variant, that introduces a novel cysteine into this linker domain, which results in the formation of a more stable N-N dimer. Using reverse genetics, we determined that this cysteine residue is necessary and sufficient for stable dimer formation in a WA1 SARS-CoV-2 background, where it results in significantly increased viral growth both in vitro and in vivo. Mechanistically, we show that the N:G215C mutant has more encapsidation as measured by increased RNA binding to N, N incorporation into virions, and electron microscopy showing that individual virions are larger, with elongated morphologies.

PLoS BiologyVol. 23(4)
University of Vermont (US), California Institute of Technology (US), Infectious Disease Research Institute (US), Johns Hopkins University (US), Emory University (US), University of Washington (US), Emory University Orthopaedics and Spine Hospital (US), Fred Hutch Cancer Center (US), Faraday Technology (United States) (US), Atlanta VA Medical Center (US), The University of Texas Medical Branch at Galveston (US)
Burroughs Wellcome Fund, American Lung Association, George Mason University, University of Vermont, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases
Good health and well-being
Openalex Percentile: Top 4%
SARS-CoV-2 and COVID-19 Research
5.58
DOIOpen Access PDFOpenAlex
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