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Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.

Leonid Yurkovetskiy1 Xue Wang2 Kristen E Pascal3 Christopher Tomkins-Tinch4,5 Thomas P Nyalile1 Yetao Wang1 Alina Baum3 William E Diehl1 Ann Dauphin1 Claudia Carbone1 Kristen Veinotte1 Shawn B Egri1 Stephen F Schaffner4,5 Jacob E Lemieux4,6 James B Munro7,8 Ashique Rafique3 Abhi Barve2 Pardis C Sabeti4,9,10,11,12 Christos A Kyratsous13 Natalya V Dudkina14 Kuang Shen15 Jeremy Luban16,4,17,18
Affiliations 18 institutions
  1. Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
  2. Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands.
  3. Regeneron Pharmaceutical, Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA.
  4. Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
  5. Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
  6. Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA.
  7. Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue, Worcester, MA 01605, USA
  8. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA.
  9. Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
  10. Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, 02115 Boston, MA, USA
  11. Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
  12. Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA. Electronic address: [email protected].
  13. Regeneron Pharmaceutical, Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA. Electronic address: [email protected].
  14. Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands. Electronic address: [email protected].
  15. Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA. Electronic address: [email protected].
  16. Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
  17. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA
  18. Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA. Electronic address: [email protected].
PMID 32991842 2020 Cell eng ppublish
PubMed DOI Browse context

Article

Publication summary

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.

ACE2 coronavirus COVID-19 cryo-electron microscopy infectivity neutralizing antibody pandemic SARS-CoV-2 Spike protein Angiotensin-Converting Enzyme 2 Animals Antibodies, Monoclonal Antibodies, Viral Betacoronavirus Cells, Cultured Coronavirus Infections COVID-19 Female

Structured evidence records

Evidence records

5 total
Host Range Experiment 3 records
Host Range Experiment Extraction confidence 0.88
Key finding

The SARS-CoV-2 D614G spike variant increased infectivity in human lung and colon cells and in cells expressing ACE2 from Chinese rufous horseshoe bat and Malayan pangolin.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

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.

Method
infectivity assay; cell-entry assay
Sample type
lung cells; colon cells
Experimental system
in vitro cell culture
Host Range Experiment Extraction confidence 0.88
Key finding

Cells expressing ACE2 from Chinese rufous horseshoe bat and Malayan pangolin supported infection by SARS-CoV-2 D614G, indicating cross-species host range potential.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

Here we show that D614G was more infectious than the ancestral form on cells rendered permissive by ectopic expression of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin.

Method
infectivity assay; cell-entry assay
Experimental system
in vitro cell culture
Host Range Experiment Extraction confidence 0.88
Key finding

Cells expressing ACE2 from Malayan pangolin supported infection by SARS-CoV-2 D614G, demonstrating susceptibility across mammalian ACE2 orthologs.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

Here we show that D614G was more infectious than the ancestral form on cells rendered permissive by ectopic expression of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin.

Method
infectivity assay; cell-entry assay
Experimental system
in vitro cell culture
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.95
Key finding

The D614G mutation in the SARS-CoV-2 spike protein enhances infectivity and promotes an ACE2 binding–competent conformation, representing molecular adaptation that modulates receptor interaction and viral fitness.

Virus
SARS-CoV-2
Host
Not specified
Location
Not specified
Supporting text

The SARS-CoV-2 spike (S) protein variant 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 affinity for ACE2 was reduced due to a faster dissociation rate, and cryo-electron microscopy showed that D614G disrupts an interprotomer contact shifting conformation toward an ACE2 binding-competent state.

Genes or proteins
spike
Receptors
ACE2
Mutations
D614G
Mechanism types
receptor_binding; cell_entry; replication_efficiency; pathogenicity
Receptor Usage 1 records
Receptor Usage Extraction confidence 0.92
Key finding

The SARS-CoV-2 spike D614G mutation decreased affinity for ACE2 but promoted a conformation more competent for ACE2-mediated binding, maintaining receptor usage across human and selected mammalian ACE2 orthologs.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

D614G was more infectious 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 affinity for ACE2 was reduced due to a faster dissociation rate.

Method
infectivity assay; cryo-electron microscopy; structural modeling
Receptors
ACE2