The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation

Abstract

The S:A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-CoV-2 variant identified in Spain in early summer 2020. This mutation has since reappeared in the Delta subvariant AY.4.2, raising questions about its specific effect on viral infection. We report combined serological, functional, structural and computational studies characterizing the impact of this mutation. Our results reveal that S:A222V promotes an increased RBD opening and slightly increases ACE2 binding as compared to the parent S:D614G clade. Finally, S:A222V does not reduce sera neutralization capacity, suggesting it does not affect vaccine effectiveness.

SciScore for 10.1101/2021.12.05.471263: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Antibodies
Sentences	Resources
The absence of the polyhistidine tag in the purified protein was verified by western blot using antihistidine antibodies.	antihistidine suggested: None
Experimental Models: Cell Lines
Sentences	Resources
After 96-hr culturing (27°C, orbital shaking at 125 rpm) and centrifugation, the high-titre baculovirus supernatant produced was collected and used to infect Sf9 cells at a density of 3 × 106 Sf9 cells/ml by 1:8 dilution of the supernatant virus stock.	Sf9 suggested: None
Experimental Models: Organisms/Strains
Sentences	Resources
The [S:A222V + S:D614G]-1-up, [S:A222V + S:D614G]-2-up, [S:A222V + S:D614G]-3-down, …

SciScore for 10.1101/2021.12.05.471263: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Antibodies
Sentences	Resources
The absence of the polyhistidine tag in the purified protein was verified by western blot using antihistidine antibodies.	antihistidine suggested: None
Experimental Models: Cell Lines
Sentences	Resources
After 96-hr culturing (27°C, orbital shaking at 125 rpm) and centrifugation, the high-titre baculovirus supernatant produced was collected and used to infect Sf9 cells at a density of 3 × 106 Sf9 cells/ml by 1:8 dilution of the supernatant virus stock.	Sf9 suggested: None
Experimental Models: Organisms/Strains
Sentences	Resources
The [S:A222V + S:D614G]-1-up, [S:A222V + S:D614G]-2-up, [S:A222V + S:D614G]-3-down, S:D614G-1-up and S:D614G-2-up cryo-EM density maps were deposited in the EM Data Bank with codes EMD-13916, EMD-13917, EMD-13918, EMD-13919 and EMD-13920, respectively.	S:A222V + S:D614G]-1-up, [S:A222V + S:D614G]-2-up suggested: None
Recombinant DNA
Sentences	Resources
Plasmid pSPIKE (a generous gift from Cesar Santiago, CNB-CSIC) was designed to include the region encoding the SARS-CoV-2 protein S ectodomain (residues 15-1213) with substitutions to proline at residues 986 and 987 and of 668RRAR671 furin cleavage site to alanine, with a N-terminal gp67 signal peptide for secretion, and C-terminal foldon trimerization motif, a thrombin protease recognition site and 9x His and Myc tags, into the insect expression plasmid pFastBac.	pSPIKE suggested: None pFastBac suggested: RRID:Addgene_1925)
Plasmid pACE2TEV was prepared from that previously used to express the N-terminal peptidase domain of human ACE2 (Lan et al. 2020), by including a cleavage site for TEV protease, to allow removing the C-terminal 6×His tag in an additional purification step.	pACE2TEV suggested: None
Software and Algorithms
Sentences	Resources
Plots, curve fittings and numerical calculations were performed with the program GraphPad Prism 5 (GraphPad Software, San Diego, CA, USA).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
2D classification was performed in cryoSPARC (Punjani et al. 2017) and 310,162 and 165,304 particles were selected.	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
After several rounds of refinement in Refmac and model building in Coot, acceptable refinement metrics were obtained.	Coot suggested: (Coot, RRID:SCR_014222)
Point mutations at position 222 (A-->V) of the S1-NTD domain (residues 13-305) and 614 (D-->G) of the S1/S2 furin cleavage site were introduced by using the mutagenesis tool of PyMol 2.0 (glycan-free) or an in-house topology editing tool (glycosylated; see gitlab.com/KomBioMol/gromologist).	PyMol suggested: (PyMOL, RRID:SCR_000305)

Results from OddPub: Thank you for sharing your data.

Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
Thank you for including a protocol registration statement.

Results from scite Reference Check: We found no unreliable references.

Read the original source

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation

This article has been Reviewed by the following groups

Listed in

Abstract

Article activity feed