Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera
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Abstract
We engineered three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses containing key spike mutations from the newly emerged United Kingdom (UK) and South African (SA) variants: N501Y from UK and SA; 69/70-deletion + N501Y + D614G from UK; and E484K + N501Y + D614G from SA. Neutralization geometric mean titers (GMTs) of 20 BTN162b2 vaccine-elicited human sera against the three mutant viruses were 0.81- to 1.46-fold of the GMTs against parental virus, indicating small effects of these mutations on neutralization by sera elicited by two BNT162b2 doses.
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- Findingown data§ Main text
The neutralization GMT of the serum panel against the E484K + N501Y + D614G virus was slightly lower than the GMTs against the N501Y virus or the Δ69/70 + N501Y + D614G virus.
“the neutralization GMT of the serum panel against the virus with three mutations from the SA variant (E484K + N501Y + D614G) was slightly lower than the neutralization GMTs against the N501Y virus or the virus with three mutations from the UK variant (Δ69/70 + N501Y + D614G).”
Quote in the paperNot a substantial claim - Findingown data§ Main text
Six of the 20 sera had neutralization titers against the E484K + N501Y + D614G mutant virus that were half their titers against the wild-type virus.
“whereas six out of the 20 sera had neutralization titers against mutant E484K + N501Y + D614G virus that were half their titers against the WT virus (Fig. 1c).”
Quote in the paperSubstantial claim - Findingown data§ Main text
Ten of the 20 sera had neutralization titers against the Δ69/70 + N501Y + D614G mutant virus that were twice their titers against the wild-type virus.
“Notably, ten out of the 20 sera had neutralization titers against mutant Δ69/70 + N501Y + D614G virus that were twice their titers against the WT virus (Fig. 1b)”
Quote in the paperNot a substantial claim - Findingown data§ Main text
All 20 BNT162b2 vaccinee sera showed equivalent neutralization titers against the wild-type and the three mutant viruses, with differences of four-fold or less.
“All sera showed equivalent neutralization titers between the WT and mutant viruses, with differences of four-fold or less (Fig. 1).”
Quote in the paperSubstantial claim - Interpretationown data§ Serum specimens and neutralization assay.
The small magnitude of the differences in neutralization GMTs indicates that these spike mutations have small effects on neutralization by sera elicited by two BNT162b2 doses.
“Neutralization geometric mean titers (GMTs) of 20 BTN162b2 vaccine-elicited human sera against the three mutant viruses were 0.81-to 1.46-fold of the GMTs against parental virus, indicating small effects of these mutations on neutralization by sera elicited by two BNT162b2 doses.”
Quote in the paperSubstantial claim
- Premisecitation§ Main text
N501Y enables the virus to expand its host range to infect mice.
“and enables the virus to expand its host range to infect mice 5,6 .”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [5] Xie X. et al. An infectious cDNA clone of SARS-CoV-2. Cell Host Microbe 27, 841–848 (2020). source
Not checked in the free run.
- cites [6] Wrapp, D. et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367, 1260–1263 (2020). source
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- Premisecitation§ Main text
In a randomized, placebo-controlled trial of approximately 44,000 participants aged 16 years or older, a two-dose regimen of BNT162b2 conferred 95% protection against COVID-19.
“in a randomized, placebo-controlled trial of approximately 44,000 participants 16 years of age or older, a two-dose regimen of BNT162b2 conferred 95% protection against Coronavirus Disease 2019 (COVID-19) 2 .”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [2] Polack F. P. et al. Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. N. Engl. J. Med. 383, 2603–2615 (2020). source
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- Interpretationcitation§ Main text
Preserved neutralization of the N501Y, Δ69/70 + N501Y + D614G and E484K + N501Y + D614G viruses by BNT162b2 vaccine-elicited human sera is consistent with preserved neutralization of a panel of 15 pseudoviruses bearing spikes with other single mutations found in circulating SARS-CoV-2 strains.
“preserved neutralization of N501Y, Δ69/70 + N501Y + D614G and E484K + N501Y + D614G viruses by BNT162b2 vaccine-elicited human sera is consistent with preserved neutralization of a panel of 15 pseudoviruses bearing spikes with other single mutations found in circulating SARS-CoV-2 strains 14”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [14] Sahin U. et al. BNT162b2 induces SARS-CoV-2-neutralising antibodies and T cells in humans. Preprint at https://www.medrxiv.org/content/10.1101/2020.12.09.20245175v1 (2020).
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- Premisecitation§ Main text
The E484K substitution alone confers resistance to several monoclonal antibodies.
“The E484K substitution alone confers resistance to several monoclonal antibodies 9,10 .”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [9] Ku, Z. et al. Molecular determinants and mechanism for antibody cocktail preventing SARS-CoV-2 escape. Nat. Commun. 12, 469 (2021). source
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- cites [10] Baum, A. et al. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science 369, 1014–1018 (2020). source
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- Premisecitation§ Main text
Rapidly spreading variants of SARS-CoV-2 have arisen in the UK, South Africa and other regions.
“rapidly spreading variants of SARS-CoV-2 have arisen in the UK, SA and other regions 3,4 .”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [3] MRC Centre for Global Infectious Disease Analysis. Report 42 - Transmission of SARS-CoV-2 lineage B.1.1.7 in England: insights from linking epidemiological and genetic data. https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-42-sars-cov-2-variant/ (2021).
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- cites [4] Tegally H. et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. Preprint at https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 (2020).
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- Study design and conductcitation§ Main text
The engineered viruses do not include the full set of spike mutations found in the UK or SA variants, which is a limitation of the study.
“A limitation of the current study is that the engineered viruses do not include the full set of spike mutations found in the UK or SA variants 3,4 .”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [3] MRC Centre for Global Infectious Disease Analysis. Report 42 - Transmission of SARS-CoV-2 lineage B.1.1.7 in England: insights from linking epidemiological and genetic data. https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-42-sars-cov-2-variant/ (2021).
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- cites [4] Tegally H. et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. Preprint at https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 (2020).
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- Premisecitation§ Main text
BNT162b2 elicited dose-dependent SARS-CoV-2-neutralizing GMTs that were similar to or higher than the GMT of a panel of SARS-CoV-2 convalescent human serum samples.
“BNT162b2, a nucleoside-modified RNA vaccine that encodes the SARS-CoV-2 full-length, prefusion-stabilized spike glycoprotein, elicited dose-dependent SARS-CoV-2-neutralizing GMTs that were similar to or higher than the GMT of a panel of SARS-CoV-2 convalescent human serum samples 1 .”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [1] Walsh E. E. et al. Safety and immunogenicity of two RNA-based Covid-19 vaccine candidates. N. Engl. J. Med. 383, 2439–2450 (2020). source
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- May combine two claims. 5
- Classified as probably not a substantial claim. 11
- The quote only partly states this claim. 1
May combine two claims.
Findingown data§ Main textThe ratios of the sera's neutralization GMTs against the N501Y, Δ69/70 + N501Y + D614G and E484K + N501Y + D614G viruses to their GMT against the USA-WA1/2020 virus were 1.46, 1.41 and 0.81, respectively.
“The ratios of the neutralization GMTs of the sera against the N501Y, Δ69/70 + N501Y + D614G and E484K + N501Y + D614G viruses to their GMTs against the USA-WA1/2020 virus were 1.46, 1.41 and 0.81, respectively (Supplementary Fig. 4).”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown data§ Main textThe three engineered mutant viruses showed plaque morphologies on Vero E6 cells similar to those of the wild-type USA-WA1/2020 strain.
“Compared to the wild-type (WT) USA-WA1/2020 strain, the three mutant viruses showed similar plaque morphologies on Vero E6 cells (Supplementary Fig. 2).”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ Main textThe D614G mutation is dominant in circulating strains around the world.
“The D614G mutation is dominant in circulating strains around the world 7,8 .”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [7] Plante J. A. et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature https://doi.org/10.1038/s41586-020-2895-3 (2020). source
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- cites [8] Korber B. et al. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell 182, 812–827 (2020). source
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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Interpretationcitation§ Main textThe emergence of N501Y from different geographical regions, together with the previously emerged globally dominant D614G mutation, suggests that these mutations might improve viral fitness.
“The emergence of the common mutation N501Y from different geographical regions, as well as the previously emerged globally dominant D614G mutation, suggest that these mutations might improve viral fitness”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [7] Plante J. A. et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature https://doi.org/10.1038/s41586-020-2895-3 (2020). source
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- cites [15] Hou Y. J. et al. SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Science 370, 1464–1468 (2020). source
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Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ Main textAmino acids 69 and 70 are located in the N-terminal domain of the spike S1 fragment.
“Amino acids 69 and 70 are located in the N-terminal domain of the spike S1 fragment;”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [6] Wrapp, D. et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367, 1260–1263 (2020). source
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The quote only partly states this claim.
Interpretationown data§ Main textThe magnitude of the differences in neutralization GMTs against the mutant viruses (0.81- to 1.41-fold) was small compared with the greater than four-fold differences in hemagglutination-inhibition titers used to signal a potential need for a strain change in influenza vaccines.
“hemagglutination-inhibition titers that have been used to signal potential need for a strain change in influenza vaccines 13 .”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [13] Smith, D. J. et al. Mapping the antigenic and genetic evolution of influenza virus. Science 305, 371–376 (2004). source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone given§ Serum specimens and neutralization assay.Each serum was tested in duplicates.
“Each serum was tested in duplicates.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone given§ Construction of isogenic viruses.The genome sequences of the P1 viruses were validated by Sanger sequencing.
“The genome sequences of the P1 viruses were validated by Sanger sequencing.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductnone given§ Serum specimens and neutralization assay.The study was conducted in compliance with International Council for Harmonisation Good Clinical Practice guidelines and the ethical principles of the Declaration of Helsinki.
“The study was conducted in compliance with all International Council for Harmonisation Good Clinical Practice guidelines and the ethical principles of the Declaration of Helsinki.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ Main textDeletion of residues 69 and 70 might allosterically change the conformation of S1.
“deletion of these residues might allosterically change S1 conformation 6 .”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [6] Wrapp, D. et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367, 1260–1263 (2020). source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation§ Main textThe N501Y mutation is shared by both the UK and SA variants.
“Mutant N501Y virus contains the N501Y mutation that is shared by both the UK and SA variants.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [3] MRC Centre for Global Infectious Disease Analysis. Report 42 - Transmission of SARS-CoV-2 lineage B.1.1.7 in England: insights from linking epidemiological and genetic data. https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-42-sars-cov-2-variant/ (2021).
Not checked in the free run.
- cites [4] Tegally H. et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. Preprint at https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 (2020).
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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductnone given§ Serum specimens and neutralization assay.The PRNT50 assay was performed at a Biosafety Level-3 facility with approval from the Institutional Biosafety Committee at the University of Texas Medical Branch.
“The PRNT 50 assay was performed at the Biosafety Level-3 facility with the approval from the Institutional Biosafety Committee at the University of Texas Medical Branch.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone given§ Serum specimens and neutralization assay.The protocol and informed consent were approved by institutional review boards for each of the investigational centers participating in the study.
“The protocol and informed consent were approved by institutional review boards for each of the investigational centers participating in the study.”
Quote in the paperNot a substantial claimMay combine two claims.
Premisecitation§ Main textN501Y is located in the viral receptor-binding domain for cell entry and increases binding to the angiotensin-converting enzyme 2 receptor.
“This mutation is located in the viral receptor-binding domain (RBD) for cell entry, increases binding to the angiotensin-converting enzyme 2 receptor”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [5] Xie X. et al. An infectious cDNA clone of SARS-CoV-2. Cell Host Microbe 27, 841–848 (2020). source
Not checked in the free run.
- cites [6] Wrapp, D. et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367, 1260–1263 (2020). source
Not checked in the free run.
The paper relies on this without support.
No serological correlate of protection against COVID-19 has been defined.
“A second limitation of the study is that no serological correlate of protection against COVID-19 has been defined.”
The paper relies on this without support.
The spike glycoproteins of SARS-CoV-2 are key targets of virus-neutralizing antibodies.
“These variants have multiple mutations in their spike glycoproteins, which are key targets of virus-neutralizing antibodies.”
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SARS-CoV-2 spike-derived CD8+ T cell epitopes after natural infection, including the immunodominant HLA-A*0201-restricted peptide YLQPRTFLL also identified here, have been published, but this is to our knowledge the first report of epitopes recognized by vaccine-induced T cells.
“Although SARS-CoV-2 S-derived CD8 + T cell epitopes after natural infection have previously been published (including the immunodominant HLA-A*0201-restricted peptide YLQPRTFLL that is also identified in this Article) 37,38 , to our knowledge this is the first report of epitopes recognized by vaccine-induced T cells.”
From BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans (2021) · cites this paper as [37]
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Experimental — accuracy not yet measuredAuthentic SARS-CoV-2 bearing two mutations present in B.1.1.7 S protein (69/70-deletion + N501Y) was still robustly neutralized by antibodies induced by BNT162b2 vaccination.
“Xie and coworkers found that authentic SARS-CoV-2 bearing two mutations present in the S protein of the B.1.1.7 variant (69/70-deletion + N501Y) was still robustly neutralized by antibodies induced by vaccination with BNT162b2.”
From SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies (2021) · cites this paper as Xie et al., 2021
Neutralization of a virus bearing changes found in the RBD of B.1.351 and P.1 (E484K + N501Y) was moderately reduced.
“Similarly, neutralization of a virus bearing changes found in the RBD of the B.1.351 and P.1 variants (E484K + N501Y) was moderately reduced (Liu et al., 2021; Wang et al., 2021; Xie et al., 2021), again in keeping with our findings.”
From SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies (2021) · cites this paper as Xie et al., 2021
The RBD mutation N501Y increases affinity to ACE2 and is present in B.1.1.7 and B.1.351, but does not impair post-vaccine serum neutralization on its own.
“The RBD mutation N501Y, which increases affinity to ACE2 and is present in B.1.1.7 and B.1.351(ref.20 ), does not impair on its own post-vaccine serum neutralization 21 .”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [21]
Earlier work using Vero E6-produced viruses carrying some or all South African spike changes found only 1.2- to 2.7-fold drops in neutralization by human sera after BNT162b2 vaccination.
“As an example, recent studies with Vero E6 cell-derived SARS-CoV-2 with spike proteins containing some (E484K, N501Y, and D614G) or all of the South African mutations showed smaller 1.2 to 2.7-fold decreases in neutralization potency by BNT162b2 mRNA vaccine-elicited human immune sera22,46.”
From Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies (2021) · cites this paper as [22]
These results are generally aligned with in vitro neutralization assays showing a large reduction in neutralization against B.1.351 and little to no reduction against B.1.1.7 in fully vaccinated individuals.
“These results are generally aligned with those from in vitro neutralization assays that have shown a large reduction in neutralization against B.1.351,and little to no reduction against B.1.1.7 in fully vaccinated individuals [7][8][9][10][11]17 .”
From Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals (2021) · cites this paper as [8]
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Self-citationThe biological and clinical significance of emerging SARS-CoV-2 variants
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BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans
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Self-citationSensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies
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Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
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Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
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SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern
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BNT162b2 mRNA COVID-19 Vaccine: First Approval
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BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants
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Self-citationStructural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
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SARS-CoV-2 spreads through cell-to-cell transmission
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Immune Responses Induced by mRNA Vaccination in Mice, Monkeys and Humans
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The N501Y spike substitution enhances SARS-CoV-2 transmission
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Self-citationEscape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
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- Authors
- Xie, X., Liu, Y., Liu, J., Zhang, X., Zou, J., Fontes-Garfias, C. R., Xia, H., Swanson, K. A., Cutler, M., Cooper, D., Menachery, V. D., Weaver, S. C., Dormitzer, P. R., & Shi, P.-Y.
- Affiliations
- The University of Texas Medical Branch at Galveston (US)
- Pfizer (United States) (US)
- Corresponding author
- Dormitzer, Philip R.
- Shi, Pei-Yong
- ORCID
- Venue
- Nature Medicine
- Published
- 2021-02-08
- Volume
- 27
- Issue
- 4
- Pages
- 620-621
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- PMC
- PMC7814835
- OpenAlex
- W3127401064
- Cited by
- 628
- References
- 18
- Citations by year
- 2026: 3 · 2025: 14 · 2024: 20 · 2023: 42 · 2022: 159 · 2021: 388 · 2020: 1
- FWCI
- 48.22
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Medicine (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Research Square (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (submittedVersion, cc-by-nc-nd)
- PubMed Central (submittedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Funders
- Foundation for the National Institutes of Health (AI42759)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- SARS-CoV-2, spike protein mutations, BNT162b2, neutralizing antibodies, Omicron variant, E484K, N501Y, D614G, variants of concern, vaccine escape, neutralization titers
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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.
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