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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Specific CD4+ T Cell Responses to Ancestral SARS-CoV-2 in Children Increase With Age and Show Cross-Reactivity to Beta Variant
Paul, K., Sibbertsen, F., Weiskopf, D., Lütgehetmann, M., Barroso, M., Danecka, M. K., Glau, L., Hecher, L., Hermann, K., Kohl, A., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.867577 · Cited by 13
“T cell response to the beta variant may serve as a model for immune escaping variants, as immune escape is mainly attributed to its mutation on position E484 within the spike domain, which is associated with reduced affinity of neutralizing antibodies (44) and mutations on this site are also found in SARS-CoV-2 strain…”
Background
Molecular epidemiological features of SARS-CoV-2 in Japan, 2020–1
Ode, H., Nakata, Y., Nagashima, M., Hayashi, M., Yamazaki, T., Asakura, H., Suzuki, J., Kubota, M., Matsuoka, K., Matsuda, M., et al. (2022) · Virus Evolution · doi:10.1093/ve/veac034 · Cited by 18
Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants
Verkhivker, G. M., Agajanian, S., Kassab, R., & Krishnan, K. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00124 · Cited by 16
T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components
Jing, L., Wu, X., Krist, M. P., et al. (2022) · medRxiv · doi:10.1101/2022.01.23.22269497 · Cited by 10
“SARS-CoV-2 S Wu-1 with the D614G mutation, 497 HDM_Spikedelta21_D614G (Addgene #158762), and isogenic mutant K417N are described 498 (86, 87).”
Background
SARS-CoV-2 Variants: Mutations and Effective Changes
Park, G., & Hwang, B. H. (2021) · Biotechnology and Bioprocess Engineering · doi:10.1007/s12257-021-0327-3 · Cited by 17
“It also aids the virus in avoiding antibody neutralization, especially by convalescent and vaccine sera, requiring higher titers overall [18-20] and reducing plasma neutralization up to 10 fold in some instances [20].”
Background
Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution
Nunes, D. R., Braconi, C. T., Ludwig‐Begall, L. F., Arns, C. W., & Durães‐Carvalho, R. (2022) · PLoS ONE · doi:10.1371/journal.pone.0268389 · Cited by 14
Global Prevalence of Adaptive and Prolonged Infections’ Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein
Lennerstrand, J., & Palanisamy, N. (2021) · Viruses · doi:10.3390/v13101974 · Cited by 12
“As mentioned before, E484K is one of the prime RBM mutations found in several SARS-CoV-2 variants, and mutations at E484 reduce the binding and neutralization by RBD targeting polyclonal plasma antibodies significantly (>10-fold) [34].”
Background
Smartphone screen testing, a novel pre-diagnostic method to identify SARS-CoV-2 infectious individuals
Young, R., Solis, C. J., Barriga-Fehrman, A., Abogabir, C., Thadani, A. R., Labarca, M., Bustamante, E. I., Tapia, C. V., Sarda, A. G., Sepúlveda, F., et al. (2021) · eLife · doi:10.7554/elife.70333 · Cited by 9
“Moreover, the development of this pandemic is still difficult to predict considering the emergence of SARS-CoV-2 mutations located in the receptor-binding domain of the surface spike protein, which creates a new hazard as evolved viral strains may be more infectious or evade the immune response and hinder vaccination…”
Background
COVID-19: Structural Considerations for Virus Pathogenesis, Therapeutic Strategies and Vaccine Design in the Novel SARS-CoV-2 Variants Era
Volkan, E. (2021) · Molecular Biotechnology · doi:10.1007/s12033-021-00353-4 · Cited by 12
“E484K amino acid change was demonstrated to interfere with efficient neutralization by convalescent sera and confer resistance to SARS-CoV-2 neutralizing antibodies, potentially preventing therapeutic approaches both by monoclonal antibody therapeutics and via convalescent plasma [37, 38, 40, 41].”
Background
Increased elastase sensitivity and decreased intramolecular interactions in the more transmissible 501Y.V1 and 501Y.V2 SARS-CoV-2 variants’ spike protein–an in silico analysis
Pokhrel, S., Kraemer, B. R., Lee, L., Samardzic, K., & Mochly‐Rosen, D. (2021) · PLoS ONE · doi:10.1371/journal.pone.0251426 · Cited by 12
“V2 lineage reduces serum binding and neutralization in circulating SARS-CoV-2 isolates [38].”
Background
Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoringPreprint
Maier, W., Bray, S. A., van den Beek, M., Bouvier, D., Coraor, N., Miladi, M., Singh, B., Rambla, J., Baker, D., Roach, N. P., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.25.437046 · Cited by 10
“Only two of the mutations reported by Greaney et al. 20 are observed at appreciable frequency.”
BackgroundMethodInfluential
ACE2 receptor polymorphism in humans and animals increases the risk of the emergence of SARS-CoV-2 variants during repeated intra- and inter-species host-switching of the virus
Devaux, C. A., & Fantini, J. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1199561 · Cited by 10
Online news regarding the spread of the omicron variant in Southeast Asia
Rulinawaty, R., Sjuchro, D. W., Syahrial, S., Badollahi, M. Z., & Hussain, Z. (2022) · Jurnal Studi Komunikasi (Indonesian Journal of Communications Studies) · doi:10.25139/jsk.v6i2.4865 · Cited by 10
“Compared to the previously described SARS-CoV-2 strain, the Omicron variation had 37 substitution residues in the learning protein on the dominant haplotype (Piccoli et al., 2020; Greaney et al., 2021).”
Result
Large Scale SARS-CoV-2 Molecular Testing and Genomic Surveillance Reveal Prolonged Infections, Protracted RNA shedding, and Viral Reinfections
Morris, C. P., Luo, C. H., Sachithanandham, J., Li, M., Schwartz, M. C., Gaston, D. C., Gniazdowski, V., Giraldo, N. A., Amadi, A., Norton, J. M., et al. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.809407 · Cited by 10
High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2
Bhadane, R. N., & Salo‐Ahen, O. M. H. (2022) · Biomedicines · doi:10.3390/biomedicines10112779 · Cited by 10
“06(38) T478K  Yes(32,34) E484Q  Yes (slightly)(39) Yes(14,35,40) -”
Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern
Abdulnoor, M., Eshaghi, A., Perusini, S. J., Broukhanski, G., Corbeil, A., Cronin, K. I., Fittipaldi, N., Forbes, J. D., Guthrie, J. L., Kus, J. V., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00681-21 · Cited by 9
“This lineage is associated with antigenic escape (12).”
Background
In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape
Pretti, M. A. M., Galvani, R. G. A., Scherer, N. D. M., Farias, A. S., & Boroni, M. (2022) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2022.105236 · Cited by 14
Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia
Farès, W., Ghedira, K., Gdoura, M., Chouikha, A., Boubaker, S., Khedhiri, M., Ayouni, K., Lamari, A., Touzi, H., Hammemi, W., et al. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00639-21 · Cited by 13
Early insight into antibody-dependent enhancement after SARS-CoV-2 mRNA vaccination
Hasan, A., Al-Mulla, M. R., Abubaker, J. A., & Al‐Mulla, F. (2021) · Human Vaccines & Immunotherapeutics · doi:10.1080/21645515.2021.1969855 · Cited by 6
Association of E484K Spike Protein Mutation With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Vaccinated Persons: Maryland, January–May 2021
Feder, K. A., Patel, A. B., Vepachedu, V. R., Dominguez, C. E., Keller, E. N., Klein, L., Kim, C., Blood, T., Hyun, J. K., Williams, T. W., et al. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab762 · Cited by 13
“This is in contrast to in vitro studies showing L452R is associated with reduced neutralization from polyclonal antibodies, albeit less strongly than E484K [10], and to epidemiologic evidence of reduced vaccine efficacy for lineage B.”
Result
Jumping a Moving Train: SARS-CoV-2 Evolution in Real Time
Moustafa, A. M., & Planet, P. J. (2021) · Journal of the Pediatric Infectious Diseases Society · doi:10.1093/jpids/piab051 · Cited by 8
“Most notable of these are mutations at the E484 position [130, 153, 154].”
Background
Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection
Sulbarán, G., Maisonnasse, P., Amen, A., Effantin, G., Guilligay, D., Dereuddre‐Bosquet, N., Burger, J. A., Poniman, M., Grobben, M., Buisson, M., et al. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100528 · Cited by 11
The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study
Rueca, M., Giombini, E., Messina, F., Bartolini, B., Di, A., Capobianchi, M. R., & Gruber, C. E. M. (2022) · JMIR Bioinformatics and Biotechnology · doi:10.2196/31536 · Cited by 11
“Next-generation sequencing (NGS) has reached a pivotal role in the field of emerging infectious diseases by enhancing the development capacity of new diagnostic methods, vaccines, and drugs [1,2].”
Background
SARS-CoV-2 Reinfection among Healthcare Workers in Mexico: Case Report and Literature Review
Garduño-Orbe, B., Sánchez-Rebolledo, J. M., Cortés-Rafael, M., García-Jiménez, Y., Perez-Ortiz, M., Mendiola-Pastrana, I. R., López‐Ortiz, E., & López-Ortiz, G. (2021) · Medicina · doi:10.3390/medicina57050442 · Cited by 16
“; (2) deficient immune responses to new variants: it has been pointed out that new lineages of SARS-CoV-2 could evade immune responses acquired in past infections or reduce the capacity for neutralization by polyclonal antibodies [25,26], and (3) infectious behavior of other coronaviruses: the susceptibility to reinfe…”
Background
Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2
Mast, F. D., Fridy, P. C., Ketaren, N. E., Wang, J., Jacobs, E. Y., Olivier, J. P., Sanyal, T., Molloy, K., Schmidt, F., Rutkowska, M., et al. (2021) · bioRxiv · doi:10.1101/2021.04.08.438911 · Cited by 9
“Nanobodies are derived from the variable domain (VHH) of variant heavy chain-only IgGs (HCAb) found in camelids (e.g. llamas, alpacas, and camels), can bind in modes different from typical antibodies, covering more chemical space and binding with very high affinities (comparable to the very best antibodies) (Jovcevska…”
MethodInfluential
Linked transmission chains of imported SARS-CoV-2 variant B.1.351 across mainland France, January 2021
The SARS-CoV-2 variant with lineage B.1.351 clusters investigation team (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.13.2100333 · Cited by 14
“First-line positive-RT-qPCR nasopharyngeal samples were forwarded to the National Reference Laboratory for viral genome sequencing and/or to selected reference laboratories of Paris Hospitals (AP-HP) and/or to the University Hospital in Toulouse, France where a specific RT-qPCR was used to identify the N501Y and E484K…”
BackgroundInfluential
Functional Antibodies in COVID-19 Convalescent Plasma
Herman, J. D., Wang, C., Loos, C., et al. (2021) · medRxiv · doi:10.1101/2021.03.08.21253157 · Cited by 9
The Host Interactome of Spike Expands the Tropism of SARS-CoV-2Preprint
Bamberger, C., Pankow, S., Martínez‐Bartolomé, S., Diedrich, J. K., Park, S. K. R., & Yates, J. R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.16.431318 · Cited by 12
Sharp Reductions in COVID-19 Case Fatalities and Excess Deaths in Peru in Close Time Conjunction, State-By-State, with Ivermectin TreatmentsPreprint
Chamie-Quintero, J. J., Hibberd, J. A., & Scheim, D. E. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3765018 · Cited by 8
Rapid, tunable, and multiplexed detection of RNA using convective array PCR
Sullivan, A. T., Rao, V., Rockwood, T., Gandhi, J., Gruzka, S., O’Connor, L., Wang, B., Ragan, K. B., Zhang, D. Y., & Khodakov, D. A. (2023) · Communications Biology · doi:10.1038/s42003-023-05346-4 · Cited by 9
Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking
Cheng, Y., Ji, C., Zhou, H., Zheng, H., & Wu, A. (2023) · Viruses · doi:10.3390/v15051158 · Cited by 11
“Deep mutational scanning can also measure how mutations in the SARS-CoV-2 RBD affect binding by antibodies [78,106,107].”
Background
Understanding the challenges to COVID-19 vaccines and treatment options, herd immunity and probability of reinfection
Al-Hatamleh, M. A. I., Abusalah, M. A. H., Hatmal, M. M., Alshaer, W., Ahmad, S., Mohd-Zahid, M. H., Rahman, E. N. S. E. A., Yean, C. Y., Alias, I. Z., Uskoković, V., et al. (2022) · Journal of Taibah University Medical Sciences · doi:10.1016/j.jtumed.2022.11.007 · Cited by 8
“These mutations may decrease the binding affinity of anti-SARS-CoV-2 antibodies.(31) Therefore, the growing number of more transmissible SARS-CoV-2 variants may cause more reinfections.”
A flow cytometry-based neutralization assay for simultaneous evaluation of blocking antibodies against SARS-CoV-2 variants
Egia‐Mendikute, L., Bosch, A., Prieto‐Fernández, E., Vila-Vecilla, L., Zanetti, S. R., Lee, S. Y., Jiménez-Lasheras, B., Río, A. G.-D., Antoñana-Vildosola, A., de Blas, A., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1014309 · Cited by 9
“1, a variant that emerged in South Africa in late 2021 (10) that presents several mutations that affect key residues on the RBD, leading to escape from neutralizing antibodies (11, 12).”
Background
Divergent Antibody Repertoires Found for Omicron versus Wuhan SARS-CoV-2 Strains Using Ig-MS
Forte, E., Soye, B. J. D., Melani, R. D., Hollas, M. A. R., Kafader, J. O., Sha, B. E., Schneider, J. R., & Kelleher, N. L. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00514 · Cited by 8
The Functional Landscape of SARS-CoV-2 3CL ProteasePreprint
Iketani, S., Hong, S. J., Sheng, J., Bahari, F., Culbertson, B., Atanaki, F. F., Aditham, A. K., Kratz, A. F., Luck, M. I., Tian, R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.23.497404 · Cited by 5
Detailed analysis of antibody responses to SARS-CoV-2 vaccination and infection in macaques
Willcox, A. C., Sung, K., Garrett, M. E., Galloway, J., O’Connor, M. A., Erasmus, J. H., Logue, J. K., Hawman, D. W., Chu, H. Y., Hasenkrug, K. J., et al. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010155 · Cited by 9
“In general, we did not detect responses in the RBD because many epitopes in this region are known to be conformational, and Phage-DMS only has the power to detect epitopes that include linear sequences.”
BackgroundInfluentialSelf-citation
Antigen–Antibody Complex-Guided Exploration of the Hotspots Conferring the Immune-Escaping Ability of the SARS-CoV-2 RBD
Fung, K.-M., Lai, S.-J., Lin, T.-L., & Tseng, T. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.797132 · Cited by 9
Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing
Singh, L., San, J. E., Tegally, H., Brzoska, P. M., Anyaneji, U. J., Wilkinson, E., Clark, L. V., Giandhari, J., Pillay, S., Lessells, R. J., et al. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000774 · Cited by 7
“This is especially useful when regions of low read coverage correspond to key sites of the genome known to harbour mutations of interest, such as the spike E484K and N501Y, which are mutations associated with escape of neutralizing and monoclonal antibodies, respectively [16, 17], and the K417N/T, which has been impli…”
Background
Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy)
Dolci, M., Signorini, L., Cason, C., Campisciano, G., Kunderfranco, P., Pariani, E., Galli, C., Petix, V., Ferrante, P., Delbue, S., et al. (2022) · Microorganisms · doi:10.3390/microorganisms10030612 · Cited by 11
“As for N439K, S477N occurs in the RBD region and seems to confer enhanced binding ability to the ACE2 receptor [35], but it does not seem to be associated with the loss of neutralizing activities of convalescent serum antibodies [35,48,49].”
Background
Analysis of the Neutralizing Activity of Antibodies Targeting Open or Closed SARS-CoV-2 Spike Protein Conformations
Cia, G., Pucci, F., & Rooman, M. J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23042078 · Cited by 9
“Indeed, it is highly variable among COVID-19 patients, as shown in Figure 3 and Figure S1 of Supplementary Material, and moreover, it evolves over time [26].”
BackgroundMethodInfluential
Capturing a Crucial ‘Disorder-to-Order Transition’ at the Heart of the Coronavirus Molecular Pathology—Triggered by Highly Persistent, Interchangeable Salt-Bridges
Roy, S., Ghosh, P., Bandyopadhyay, A., & Basu, S. (2022) · Vaccines · doi:10.3390/vaccines10020301 · Cited by 11
High activity of an affinity-matured ACE2 decoy against Omicron SARS-CoV-2 and pre-emergent coronaviruses
Sims, J. J., Lian, S., Meggersee, R., Kasimsetty, A., & Wilson, J. M. (2022) · PLoS ONE · doi:10.1371/journal.pone.0271359 · Cited by 10
Collaboration between Clinical and Academic Laboratories for Sequencing SARS-CoV-2 Genomes
Wang, J., Hawken, S. E., Jones, C. D., Hagan, R. S., Bushman, F., Everett, J. K., Miller, M. B., & Rodino, K. G. (2022) · Journal of Clinical Microbiology · doi:10.1128/jcm.01288-21 · Cited by 7
Variantes del SARS-CoV-2: epidemiología, fisiopatología y la importancia de las vacunas
Bedoya-Sommerkamp, M., Medina-Ranilla, J., Rodriguez, V. H. C., Li-Soldevilla, R., Vera-Albújar, Á., & Garcia, P. J. (2021) · Revista Peruana de Medicina Experimental y Salud Pública · doi:10.17843/rpmesp.2021.383.8734 · Cited by 13
“Por otro lado, al hacer el análisis filogenético de las mutaciones compartidas por las nuevas variantes (N501Y, E484K, P681H, L452R, T478K) se ve que han ocurrido de manera independiente en tiempo y espacio (evolución convergente), lo que apunta nuevamente a una presión selectiva poblacional que lleva a una mejor adap…”
BackgroundInfluential
A Novel Real-Time RT-PCR-Based Methodology for the Preliminary Typing of SARS-CoV-2 Variants, Employing Non-Extendable LNA Oligonucleotides and Three Signature Mutations at the Spike Protein Receptor-Binding Domain
Chaintoutis, S. C., Chassalevris, T., Balaska, S., Mouchtaropoulou, E., Tsiolas, G., Vlatakis, I., Tychala, A., Koutsioulis, D., Argiriou, A., Skoura, L., et al. (2021) · Life · doi:10.3390/life11101015 · Cited by 15
Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India
Shrivastava, S., Mhaske, S. T., Modak, M. S., Virkar, R., Pisal, S. S., Mishra, A. C., & Arankalle, V. A. (2022) · Archives of Virology · doi:10.1007/s00705-021-05320-7 · Cited by 7
Outbreak of P.3 (Theta) SARS-CoV-2 emerging variant of concern among service workers in Louisiana
Rose, R., Nolan, D. J., LaFleur, T. M., & Lamers, S. L. (2021) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2021.11.011 · Cited by 11
“351) in the spike protein, including E484K, N501Y, and P681H [6], which have been linked to increased transmissibility and immune escape [7, 8].”
Background
Murine Monoclonal Antibodies against the Receptor Binding Domain of SARS-CoV-2 Neutralize Authentic Wild-Type SARS-CoV-2 as Well as B.1.1.7 and B.1.351 Viruses and Protect In Vivo in a Mouse Model in a Neutralization-Dependent Manner
Amanat, F., Strohmeier, S., Lee, W.-H., Bangaru, S., Ward, A. B., Coughlan, L., & Krammer, F. (2021) · mBio · doi:10.1128/mbio.01002-21 · Cited by 16
Global Discrepancies between Numbers of Available SARS-CoV-2 Genomes and Human Development Indexes at Country Scales
Colson, P., & Raoult, D. (2021) · Viruses · doi:10.3390/v13050775 · Cited by 8
Amino acids 484 and 494 of SARS-CoV-2 spike are hotspots of immune evasion affecting antibody but not ACE2 bindingPreprint
Alenquer, M., Ferreira, F., Lousa, D., Valério, M., Medina-Lopes, M., Bergman, M., Gonçalves, J., Demengeot, J., Leite, R. B., Lilue, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.22.441007 · Cited by 8
Novel SARS-CoV-2 Variants in Italy: The Role of Veterinary Public Health Institutes
Lorusso, A., Calistri, P., Savini, G., Morelli, D., Ambrosij, L., Migliorati, G., & D’Alterio, N. (2021) · Viruses · doi:10.3390/v13040549 · Cited by 8
“Such mutations could have a role in evading the host immune response [4].”
Background
SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2Preprint
Weekley, C. M., Purcell, D. F. J., & Parker, M. W. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.16.434488 · Cited by 6
“Its neighbouring residue E484 is of great interest to the scientific community with the mutation E484K contributing to antigenic escape (Greaney et al., 2021; Liu et al., 2021).”
BackgroundInfluential

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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