PreprintCited by 1,178SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approachesSARS-CoV-2 detection and testing

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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies

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Greaney, Allison J., Loes, Andrea N., Crawford, Katharine H.D., Starr, Tyler N., Malone, Keara D., Chu, Helen Y., Bloom, Jesse D.·2021·Cell Host & Microbe

DOI 10.1101/2020.12.31.425021PMC PMC7869748

Preprint — published as 10.1016/j.chom.2021.02.003 · Paper page

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Abstract

The evolution of SARS-CoV-2 could impair recognition of the virus by human antibody-mediated immunity. To facilitate prospective surveillance for such evolution, we map how convalescent serum antibodies are impacted by all mutations to the spike’s receptor-binding domain (RBD), the main target of serum neutralizing activity. Binding by polyclonal serum antibodies is affected by mutations in three main epitopes in the RBD, but there is substantial variation in the impact of mutations both among individuals and within the same individual over time. Despite this inter- and intra-person heterogeneity, the mutations that most reduce antibody binding usually occur at just a few sites in the RBD’s receptor binding motif. The most important site is E484, where neutralization by some sera is reduced >10-fold by several mutations, including one in emerging viral lineages in South Africa and Brazil. Going forward, these serum escape maps can inform surveillance of SARS-CoV-2 evolution.

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BackgroundMethodResultInfluential
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“It was shown to have increased transmissibility and to possibly reduce vaccine efficacy (Greaney et al. 2021, Jangra et al. 2021, Liu et al. 2021).”
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The evolutionary ecology of SARS‐CoV‐2: A missing perspective in the One Health approach
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In Vitro Diagnostics for COVID-19: State-of-the-Art, Future Directions and Role in Pandemic Response
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Atypical N-glycosylation of SARS-CoV-2 impairs the efficient binding of Spike-RBM to the human-host receptor hACE2Preprint
Gámez, G., Hermoso, J. A., Carrasco‐López, C., Gómez-Mejía, A., Muskus, C., & Hammerschmidt, S. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.09.439154 · Cited by 1
RR:C19 Editorial: Immune Escape and Viral Evolution
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Overview of the first year of the SARS-CoV-2 pandemic in Serbia and the Pirot County
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“Јужноафрички и бразилски сој садрже мутације које узрокују антигенски померај и омогућавају избегавање имуног одговора код реконвалесцената и вакцинисаних индивидуа (Greaney et al., 2021; Hu et al., 2021).”
Design of a mutation-integrated trimeric RBD with broad protection against SARS-CoV-2
Liang, Y., Zhang, J., Yuan, R. Y., Wang, M. Y., He, P., Su, J. G., Han, Z. B., Jin, Y. Q., Hou, J. W., Zhang, H., et al. (2022) · Cell Discovery · doi:10.1038/s41421-022-00383-5 · Cited by 42
Updated vaccine protects from infection with SARS-CoV-2 variants, prevents transmission and is immunogenic against Omicron in hamstersPreprint
Sharma, S., Vercruysse, T., Sánchez-Felipe, L., Kerstens, W., Rasulova, M., Abdelnabi, R., Foo, C. S.-Y., Lemmens, V., Looveren, D. V., Maes, P., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.12.468374 · Cited by 7
“It is a challenging task to develop a universal vaccine that follows the evolution of emerging SARS-CoV-2 variants such as Omicron that carry increasingly complex combinations of old and new driver mutations responsible for both nAb escape (e.g., E484K/A) (10) and enhanced transmission (e.g., N501Y; P681R/H) (31).”
BackgroundInfluential
Antibody Dynamics, Seroreversion, and Persistence After Severe Acute Respiratory Syndrome Coronavirus 2: Another Answer
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“The implication is that it is quite likely, as one example, that recommendations for potential booster doses of COVID19 vaccines may differ between young and old, immunocompromised and healthy, one type of vaccine over another, and differential efficacy by circulating viral variant [11].”
Background
Surrogate virus neutralisation test based on nanoluciferase-tagged antigens to quantify inhibitory antibodies against SARS-CoV-2 and characterise Omicron-specific reactivity
Schoefbaenker, M., Neddermeyer, R., Guenther, T., et al. (2023) · medRxiv · doi:10.1101/2023.10.10.23296792
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Monoclonal antibodies lock down SARS-CoV-2 spike
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Comparison of L452R mutation variant diagnosis in SARS-COV-2 PCR positive samples with two different qPCR kits
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Introduction and effect of natural selection analysis at common mutations of SARS-CoV-2 spike gene in Iran
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Chronic Shedding of a SARS-CoV-2 Alpha Variant Lineage Q.3/Q.4 in WastewaterPreprint
Conway, M. J., Yang, H., Revord, L. A., Ward, A. S., Abel, J. D., Williams, M. R., Uzarski, R. L., & Alm, E. W. (2023) · medRxiv · doi:10.1101/2023.07.26.23293191
“E848V also reduced ACE2 binding (Greaney et al., 2021b).”
Background
Computational insights on the destabilizing mutations in the binding site of 3CL-protease SARS-CoV-2 Omicron (VOC)
Ullah, S., Amir, A., Ikram, A., et al. (2023) · bioRxiv · doi:10.1101/2023.05.24.542061
Rapidly Adaptable Multiplexed Yeast Surface Display Serological Assay for Immune Escape Screening of SARS-CoV-2 VariantsPreprint
López-Morales, J., Vanella, R., Utzinger, T., Schittny, V., Hirsiger, J. R., Osthoff, M. F., Berger, C. T., Guri, Y., & Nash, M. A. (2023) · medRxiv · doi:10.1101/2023.02.17.23286074
Underlying driving forces of the SARS-CoV-2 evolution: immune evasion and ACE2 binding affinityPreprint
Ma, W., Fu, H., Jian, F., Cao, Y., & Li, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.06.527236
SARS-CoV-2 vaccine-breakthrough infections (VBIs) by Omicron (B.1.1.529) variant and consequences in structural and functional impact
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SARS-CoV-2’NİN SÜREGELEN EVRİMİ: PANDEMİNİN SONUNA NE KADAR YAKINIZ?
Kilbaş, E. P. K., & Altındiş, M. (2022) · JOURNAL OF BIOTECHNOLOGY AND STRATEGIC HEALTH RESEARCH · doi:10.34084/bshr.1200144
Single‐center serological surveillance of SARS‐CoV‐2 in pregnant patients presenting to labor and delivery
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Development of pyrosequencing-based assay for genotyping of different coronavirus variants
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Investigating the role of binding free energy, binding affinity and antibody escape in the evolution of SARS-CoV-2 spike proteinPreprint
Young, M. R., & Lycett, S. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.15.512351
Memory B cells and memory T cells induced by SARS-CoV-2 booster vaccination or infection show different dynamics and efficacy to the Omicron variantPreprint
Mise‐Omata, S., Ikeda, M., Takeshita, M., Uwamino, Y., Wakui, M., Arai, T., Yoshifuji, A., Murano, K., Siomi, H., Nakagawara, K., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.31.500554
“which can alter viral transmission and immune recognition (7, 8).”
Background
Fc-modified SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal modelsPreprint
Takeshita, M., Fukuyama, H., Kamada, K., Matsumoto, T., Makino‐Okamura, C., Uchikubo‐Kamo, T., Tomabechi, Y., Hanada, K., Moriyama, S., Takahashi, Y., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.21.496751
“The unevenly distributed epitopes of the selected antibodies are consistent with previous reports (Greaney et al., 2021; Piccoli et al., 2020) that antibodies in the sera of patients infected with Wuhan strains mainly target the area around E484.”
Result
Rhenium complexes as antiviral agents for COVID-19
Karges, J. (2022) · Journal of Coordination Chemistry · doi:10.1080/00958972.2022.2084395 · Cited by 1
Uncovering the structural flexibility of SARS-CoV-2 glycoprotein spike variantsPreprint
Arruda, H. R. S., Lima, T. M., Alvim, R. G. F., Victorio, F. B. A., de Abreu, D. P. B., Marsili, F. F., Cruz, K. D., Sosa‐Acosta, P., Quiñones‐Vega, M., Guedes, J. D. S., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.20.488873
The mutational steps of SARS-CoV-2 to become like Omicron within seven months: the story of immune escape in an immunocompromised patient.
Sonnleitner, S., Prelog, M., Sonnleitner, S., et al. (2022) · medRxiv · doi:10.1101/2022.03.04.22271540
“E484K, a substitution in the receptor binding domain (RBD) appeared early in the course of 386 the infection and is described to impair neutralization resistance (39), potentially 387 compromising vaccines effectiveness (4, 6, 40-47).”
Background
An expanded high throughput RT-PCR assay to rapidly identify all known SARS-CoV-2 variants of concern using melting temperature codingPreprint
Banada, P. P., Green, R., Banik, S., Streck, D. L., Montalvan, I., Reiss, R., Jones, R., Marras, S. A. E., Chakravorty, S., & Alland, D. (2022) · medRxiv · doi:10.1101/2022.01.18.22269424
Determination of COVID-19 PCR positivity and mutation status in coronaVacvaccinated individuals in Turkey
ÇALIŞKAN, A., Seçme, M., Kaleli̇, İ., Sarı, T., Öner, S. Z., YAKA, S. K., & Dönmez, B. (2022) · TURKISH JOURNAL OF MEDICAL SCIENCES · doi:10.55730/1300-0144.5344
“The S protein (Spike) protein N501Y mutation increases the binding affinity of S protein and ACE2, while HV69-70del and Y144del deletions in the N-terminal domain (NTD) also play a role in ACE2 receptor binding or neutralizing antibody escape [7,8].”
Background
The Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614 Mutant: Conformational Plasticity and Frustration-Driven Allostery as Energetic Drivers of Highly Transmissible Spike VariantPreprint
Verkhivker, G. M., Agajanian, S., Kassab, R., & Krishnan, K. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.09.471953
Preclinical Efficacy of IMM-BCP-01, a Highly Active Patient-Derived Anti-SARS-CoV-2 Antibody CocktailPreprint
Nikitin, P. A., DiMuzio, J. M., Dowling, J. P., Patel, N. B., Bingaman, J. L., Heimbach, B. C., Henriquez, N., Nicolescu, C., Polley, A. M., Sikorski, E. L., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.18.464900 · Cited by 1
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Springstein, B. L., Deighan, P., Grabe, G., & Hochschild, A. (2021) · bioRxiv · doi:10.1101/2021.10.07.463611
Utility of Point‐of‐Care COVID‐19 Testing in an Outpatient Otolaryngology clinic
Ganesh, M., Brawley, C. C., Khanwalkar, A. R., Mycanka, J., Conley, D. B., Kern, R. C., & Tan, B. K. (2021) · OTO Open · doi:10.1177/2473974x211049328
“However, the risk of COVID-19 may well persist due to vaccine hesitancy and the development of new variants, which may even cause the pandemic to continue in a seasonal cycle.(42,43) As of this writing, India and Brazil continue to report high daily new case loads, and there are reports of a third-wave resurgence in A…”
Background
Разработка платформы для получения рекомбинантных белков – компонентов эпитопных вакцин для профилактики COVID-19
Карягина, А. С., Gromov, A. V., Grunina, T. M., Lyashchuk, A. M., Av, G., Strukova, N. V., Generalova, M. S., Galushkina, Z. M., Soboleva, L. A., Dobrynina, O. Y., et al. (2021) · Biochemistry (Moscow) · doi:10.31857/s0320972521100043
Persistence of robust humoral immune response in COVID-19 convalescent individuals over 12 months after infection
Miyakawa, K., Kubo, S., Jeremiah, S. S., et al. (2021) · medRxiv · doi:10.1101/2021.09.27.21264013
Persistent while declined neutralizing antibody responses in the convalescents of COVID-19 across clinical spectrum during the 16 months follow up
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Assessment of the potentially decreased neutralizing activities of intravenous immunoglobulin against future coronavirus variants
Inoue, T., Yunoki, M., Kubota‐Koketsu, R., & Shioda, T. (2021) · Transfusion · doi:10.1111/trf.16553 · Cited by 1
“V2 harbors the concerning E484K mutation in the spike protein, which allows the virus to escape from certain VN monoclonal antibodies and also decreases VN activities in convalescent serum by 10-fold.(4) However, the introduction of the E484K, N501Y, and D614G mutations in live SARS-CoV-2 only slightly diminished the…”
Background
Dissecting Molecular Determinants of Mutational Escape Mechanisms in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Atomistic Simulations and Ensemble-Based Deep Mutational Scanning of Protein Stability and Binding InteractionsPreprint
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“While cross-immunity between Sars-CoV-2 and other types of coronavirus can stimulate immune response [2], new variants may be able to evade immunity acquired in previous infections [3].”
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Endonuclease-based genotyping of the RBM, a first-line method for the surveillance of emergence or evolution of SARS-CoV-2 Variants.
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Authors: Greaney, A. J., Loes, A. N., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D.
Affiliations: University of Washington (US)
Howard Hughes Medical Institute (US)
Fred Hutch Cancer Center (US)
Corresponding author: Bloom, Jesse D.
ORCID: Greaney, Allison J.
Loes, Andrea N.
Crawford, Katharine H.D.
Starr, Tyler N.
Chu, Helen Y.
Bloom, Jesse D.
Venue: Cell Host & Microbe
Publisher: openRxiv
Published: 2021-01-04
Volume: 29
Issue: 3
Pages: 463-476.e6
ISSN: 1931-3128 (ISSN-L)
DOI: 10.1101/2020.12.31.425021
PMC: PMC7869748
OpenAlex: W3127852352
Cited by: 1,178
References: 58
Citations by year: 2026: 43 · 2025: 64 · 2024: 79 · 2023: 158 · 2022: 361 · 2021: 459
FWCI: 83.77
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Cell Host & Microbe (publishedVersion)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Howard Hughes Medical Institute
Bill and Melinda Gates Foundation (INV-004949)
Damon Runyon Cancer Research Foundation (DRG-2381-19)
Washington Research Foundation
Vanderbilt University
University of Washington
National Institutes of Health (1s10od028685-01)
National Institute of Allergy and Infectious Diseases (R01AI127893, T32AI083203, F30AI149928, R01AI140891, R01AI141707)
Office of Research Infrastructure Programs, National Institutes of Health (S10OD028685)
Topics: Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
Keywords: SARS-CoV-2, spike protein receptor-binding domain, antibody escape mutations, neutralizing antibodies, E484K mutation, antibody epitopes, convalescent plasma, humoral immunity
MeSH terms: Protein Domains, COVID-19, SARS-CoV-2, Adult, Aged, Antibodies, Monoclonal, Antibodies, Viral, Binding Sites, Cell Line, Female, Humans, Male, Middle Aged, Mutation, Prospective Studies, Protein Binding, Receptors, Virus, Young Adult, Antibodies, Neutralizing, Spike Glycoprotein, Coronavirus

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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies

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