Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
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Abstract
The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin. D614G did not alter S protein synthesis, processing, or incorporation into SARS-CoV-2 particles, but D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts an interprotomer contact and that the conformation is shifted toward an ACE2 binding-competent state, which is modeled to be on pathway for virion membrane fusion with target cells. Consistent with this more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated.
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The D614G mutation enhances viral infectivity and shifts S protein conformation toward an ACE2-binding fusion-competent state without significantly modifying sensitivity to antibody neutralization.
“One of the first identified variants includes the D614G mutation in the gene encoding the spike (S) protein, which enhances viral infectivity and shifts S protein conformation toward an angiotensin-converting enzyme 2 (ACE2)-binding fusion-competent state, without significantly modifying sensitivity to antibody neutralization 1,[6][7][8] .”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [1]
A222V does not cause the same large titer increases of spike-pseudotyped lentivirus as D614G.
“Therefore, A222V does not lead to the same large increases in the titers of spike-pseudotyped lentivirus that has been observed for the D614G mutation 7,10”
From Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 (2021) · cites this paper as [10]
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Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Hodcroft, E. B., Zuber, M., Nadeau, S., Vaughan, T. G., Crawford, K. H. D., Althaus, C. L., Reichmuth, M. L., Bowen, J. E., Walls, A. C., Corti, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03677-y · Cited by 425 · see citing works
BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants
Liu, J., Liu, Y., Xia, H., Zou, J., Weaver, S. C., Swanson, K. A., Cai, H., Cutler, M., Cooper, D., Muik, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03693-y · Cited by 342 · see citing works
D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization
Weissman, D., Alameh, M.-G., de Silva, T., Collini, P., Hornsby, H., Brown, R., LaBranche, C. C., Edwards, R. J., Sutherland, L., Santra, S., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2020.11.012 · Cited by 324 · see citing works
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Self-citationRecurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
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The SARS-CoV-2 Spike variant D614G favors an open conformational state
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“The SARS-CoV-2 S D614G mutation has become globally dominant and is associated with enhanced viral transmission and replication but does not significantly affect Abmediated neutralization (Hou et al., 2020; Korber et al., 2020; Plante et al., 2020; Yurkovetskiy et al., 2020).”
N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
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A self-amplifying RNA vaccine against COVID-19 with long-term room-temperature stability
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Shooting at a Moving Target—Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development
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Structural Analysis of Spike Protein Mutations in the SARS-CoV-2 P.3 Variant
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- Authors
- Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., Baum, A., Diehl, W. E., Dauphin, A., Carbone, C., Veinotte, K., Egri, S. B., Schaffner, S. F., Lemieux, J. E., Munro, J. B., Rafique, A., Barve, A., Sabeti, P. C., Kyratsous, C. A., Dudkina, N. V., Shen, K., & Luban, J.
- Affiliations
- University of Massachusetts Chan Medical School (US)
- Thermo Fisher Scientific (Netherlands) (NL)
- Regeneron (United States) (US)
- Broad Institute (US)
- Corresponding author
- Sabeti, Pardis C.
- Kyratsous, Christos A.
- Dudkina, Natalya V.
- Shen, Kuang
- Luban, Jeremy
- ORCID
- Yurkovetskiy, Leonid
- Wang, Xue
- Pascal, Kristen E.
- Tomkins-Tinch, Christopher
- Wang, Yetao
- Baum, Alina
- Diehl, William E.
- Dauphin, Ann
- Carbone, Claudia
- Egri, Shawn B.
- Schaffner, Stephen F.
- Lemieux, Jacob E.
- Munro, James B.
- Rafique, Ashique
- Sabeti, Pardis C.
- Kyratsous, Christos A.
- Dudkina, Natalya V.
- Shen, Kuang
- Luban, Jeremy
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2020-10
- Volume
- 183
- Issue
- 3
- Pages
- 739-751.e8
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7492024
- OpenAlex
- W3084653951
- Cited by
- 1,025
- References
- 63
- Citations by year
- 2026: 30 · 2025: 51 · 2024: 67 · 2023: 128 · 2022: 268 · 2021: 400 · 2020: 79
- FWCI
- 28.74
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- SSRN Electronic Journal (acceptedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion, cc-by-nc-nd)
- The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion)
- Funders
- National Science Foundation
- Biomedical Advanced Research and Development Authority
- National Cancer Institute
- National Institute of Allergy and Infectious Diseases
- Charles A. King Trust
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Keywords
- SARS-CoV-2, spike protein, D614G mutation, ACE2 receptor, receptor binding affinity, viral infectivity, antibody neutralization, receptor binding domain, membrane fusion, viral evolution
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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