Cited by 535SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approachesAnimal Virus Infections Studies

The DOI matches its Crossref record; 89 of the 90 references it cites were found in a registry or an index, and 1 are not checked yet.

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

Open access

McCallum, Matthew, Czudnochowski, Nadine, Rosen, Laura E., Zepeda, Samantha K., Bowen, John E., Walls, Alexandra C., Hauser, Kevin, Joshi, Anshu, Stewart, Cameron, Dillen, Josh R., Powell, Abigail E., Croll, Tristan I., Nix, Jay, Virgin, Herbert W., Corti, Davide, Snell, Gyorgy, Veesler, David·2022·Science

DOI 10.1126/science.abn8652PMC PMC9427005

Published version of a preprint

Open this paper in CoChat — free account

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo–electron microscopy and x-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a blueprint for understanding the marked reduction of binding of other therapeutic mAbs that leads to dampened neutralizing activity. Remodeling of interactions between the Omicron receptor-binding domain and human ACE2 likely explains the enhanced affinity for the host receptor relative to the ancestral virus.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1126/science.abn8652

Cites

89 of 90 references verified0 citation errors · 0 not checkable

Statistics

Fig. 1. CryoEM structure of the SARS-CoV-2 Omicron S trimer reveals a remodeling of the NTD antigenic supersite. (A) Surface rendering in two orthogonal orientations of the Omicron S trimer with one open RBD bound to the S309 (grey) and S2L20 (green) Fabs shown as ribbons. The three S protomers are colored light blue, pink or gold. N-linked glycans are shown as dark blue surfaces. (B) Ribbon diagrams in two orthogonal orientations of the S trimer with one open RBD with Omicron residues mutated relative to Wuhan-Hu-1 shown as red spheres (except D614G which is not shown). (C) The S2L20-bound Omicron NTD with mutated, deleted, or inserted residues rendered or indicated as red spheres. Segments with notable structural changes are shown in orange and labeled. (D) Zoomed-in view of the Omicron NTD antigenic supersite overlaid with the S2X333 Fab (used here as an example of prototypical NTD neutralizing mAb (22)) highlighting the binding incompatibility; the modeled clash between S2X333 W106 and NTD G142D is indicated with an asterisk.CC BY · PubMed Central

Fig. 2. SARS-CoV-2 Omicron S mutations outside the NTD and RBD. Ribbon diagram showing a cross-section of the Omicron S glycoprotein (the location of this slice on the S trimer is indicated on the left). Mutated residues T547K, N764K, N856K, N969K, and L981F are shown as red spheres whereas the residues they contact are shown as spheres colored as the protomer they belong to. Black asterisks show the position of residues involved in the prefusion-stabilizing 2P mutations (K986P and V987P) used in all three vaccines deployed in the US. The three S protomers are colored light blue, pink or gold. N-linked glycans are shown as dark blue surfaces.CC BY · PubMed Central

Fig. 3. SARS-CoV-2 Omicron RBD mutations promote escape from a panel of clinical mAbs. (A, RBD antigenic map as determined elsewhere (13). (B) Ribbon diagram of the RBD crystal structure with residue mutated relative to the Wuhan-Hu-1 RBD shown as red spheres. The N343 glycan is rendered as blue spheres. (C to J) Zoomed-in view of the Omicron RBD (blue) superimposed on structures of clinical mAbs (grey) highlighting (black circles) selected residues that interfere with the mAbs: (C) REGN10933, (D) REGN10987, (E) COV2-2196, (F) COV2-2130, (G) LY-CoV555, (H) LY-CoV16, (I) CT-P59, and (J) S309 which does not clash with G339D. Panels A-I were rendered with the crystal structure whereas panel J was generated using the cryoEM model. Binding of the Wuhan-Hu-1 (gray line) or Omicron (red line) RBD to the corresponding mAb was evaluated using surface plasmon resonance (single-cycle kinetics) and is shown underneath each structural superimposition. White and gray stripes are association and dissociation phases, respectively. The black line is a fit to a kinetic model. The decrease in affinity between Wuhan-Hu-1 and Omicron binding is indicated in red. Results are consistent with IgG binding to S ectodomains (fig. S3).CC BY · PubMed Central

Fig. 4. Molecular basis of human ACE2 recognition by the SARS-CoV-2 Omicron RBD. (A) Ribbon diagram of the crystal structure of the Omicron RBD in complex with the ACE2 ectodomain. The S309 and S304 Fab fragments are not shown for clarity. (B to E) Zoomed-in views of the RBD/ACE2 interface highlighting modulation of interactions due to introduction of the N501Y (B), K417N (C), Q493R/Q498R (D) and S477N (E) residue substitutions.CC BY · PubMed Central

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,882
Features and development of Coot
Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 29,915
Phaser crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612
MolProbity : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Punjani, A., Rubinstein, J. L., Fleet, D. J., & Brubaker, M. A. (2017) · Nature Methods · doi:10.1038/nmeth.4169 · Cited by 11,626
Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation
Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020) · Science · doi:10.1126/science.abb2507 · Cited by 8,897
Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020) · doi:10.1101/2020.02.19.956581 · Cited by 8,586 · cited 1×
“However, the region comprising residues 366 to 375, which harbors the S371L/S373P/S375F substitutions, deviates markedly from the conformation observed for the Wuhan-Hu-1 RBD, irrespective of the presence of bound linoleic acid ( 4 , 42 , 43 ).”
Self-citation
REFMAC 5 for the refinement of macromolecular crystal structures
Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M., Long, F., & Vagin, A. A. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444911001314 · Cited by 8,415
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Liebschner, D., Afonine, P. V., Baker, M. L., Bunkóczi, G., Chen, V. B., Croll, T. I., Hintze, B., Hung, L.-W., Jain, S., McCoy, A. J., et al. (2019) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798319011471 · Cited by 7,953
Self-citation
Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor
Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., et al. (2020) · Nature · doi:10.1038/s41586-020-2180-5 · Cited by 5,983 · cited 2×
“The Omicron RBD is structurally similar to the Wuhan-Hu-1 RBD and both structures can be superimposed with an r.m.s.d. of 0.8Å over 183 aligned C ɑ residues (as compared to PDB 6m0j ( 42 )).”

Show all 85 references

Research works printed but not linked: 2

10.1016/j.cell.2020.02.058 · DOI · Paper page
10.1126/science.abh1139 · DOI · Paper page

Sorted by citations

Items 301–400 of 535

Potent antibodies against immune invasive SARS-CoV-2 Omicron subvariants
Wang, L., Wang, Y., & Zhou, H. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.125997 · Cited by 8
SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode
Goike, J., Hsieh, C., Horton, A. P., Gardner, E. C., Zhou, L., Bartzoka, F., Wang, N., Javanmardi, K., Herbert, A. S., Abbasi, S. A., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-05649-6 · Cited by 8
“Instead, altered RBD conformational dynamics contribute to the antigenic drift observed by evading conformational binders 12,13 .”
Up, up, down, down: the structural biology of the SARS-CoV-2 spike protein and how it cheats the immune system
Stäb, S., Pearce, N. M., Tronrud, D. E., Ginn, H. M., Fadda, E., Santoni, G., & Thorn, A. (2024) · Crystallography Reviews · doi:10.1080/0889311x.2024.2363756 · Cited by 7
“For Omicron and Delta , recent studies suggest that due to their mutations, both strains are less sensitive to neutralizing monoclonal antibodies from recovered patients and capable of evading immunity conferred through prior infections [252,253].”
Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike
Duyvesteyn, H. M. E., Dijokaite-Guraliuc, A., Liu, C., Supasa, P., Kronsteiner, B., Jeffery, K. J., Stafford, L., Klenerman, P., Dunachie, S. J., Mongkolsapaya, J., et al. (2024) · Structure · doi:10.1016/j.str.2024.07.020 · Cited by 7
SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals
Gen, R., Addetia, A., Asarnow, D. E., Park, Y., Quispe, J. D., Chan, M. C., Brown, J. T., Lee, J., Campbell, M. G., Lapointe, C. P., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115696 · Cited by 7
“The conserved nsp1-binding site on the 40S ribosomal subunit along with the reduced nsp1 genetic drift among SARS-CoV-2 variants 98 , relative to the spike glycoprotein 94,96,99 , suggest the possibility of targeting this key virulence factor to develop next-generation COVID-19 countermeasures.”
Self-citation
Integrative Computational Modeling of Distinct Binding Mechanisms for Broadly Neutralizing Antibodies Targeting SARS-CoV-2 Spike Omicron Variants: Balance of Evolutionary and Dynamic Adaptability in Shaping Molecular Determinants of Immune Escape
Alshahrani, M., Parikh, V., Foley, B., & Verkhivker, G. M. (2025) · Viruses · doi:10.3390/v17060741 · Cited by 7
From single-sequences to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2
Lamb, K. D., Hughes, J., Lytras, S., Young, F., Koci, O., Herzig, J. C., Lovell, S. C., Grove, J., Yuan, K., & Robertson, D. L. (2026) · Nature Communications · doi:10.1038/s41467-026-69569-9 · Cited by 20
“N969K forms electrostatic contacts with Q755 on the adjacent protomer in the pre-fusion state 27 , as well as interacting with and displacing the HR2 backbone in the post-fusion spike structure 22 .”
Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS‐CoV ‐2
Planchais, C., Reyes‐Ruiz, A., Lacombe, R. V., Zarantonello, A., Lecerf, M., Revel, M., Roumenina, L. T., Atanasov, B. P., Mouquet, H., & Dimitrov, J. D. (2022) · Protein Science · doi:10.1002/pro.4447 · Cited by 7
“15,17,19 This His residue might be an important contributor for overall energy of binding, and it may control the interaction with ACE2.”
Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein
Shikha, S., Jogi, M. K., Jha, R., Kumar, R. A., Sah, T., Singh, P., Sagar, R., Kumar, A., Marwal, R., Ponnusamy, K., et al. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1209513 · Cited by 8
“and NTD mutations to retain ACE2 binding affinity similar to the Delta variant with a remarkable antibody evasion (3, 4).”
The paradigm of immune escape by SARS-CoV-2 variants and strategies for repositioning subverted mAbs against escaped VOCs
Shah, M., & Woo, H. G. (2022) · Molecular Therapy · doi:10.1016/j.ymthe.2022.08.020 · Cited by 7
A bias of Asparagine to Lysine mutations in SARS-CoV-2 outside the receptor binding domain affects protein flexibility
Boer, J. C., Pan, Q., Holien, J. K., Nguyen, T., Ascher, D. B., & Plebanski, M. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.954435 · Cited by 7
“For instance, SARS-CoV-2 Omicron G339D and N440K mutations are located in a neighbouring site called antigenic site IV, which in turn is a known recognition site by the S309 mAb (76).”
High-throughput saturation mutagenesis generates a high-affinity antibody against SARS-CoV-2 variants using protein surface display assay on a human cell
Yang, Y., Liu, S., Luo, Y., Wang, B., Wang, J., Li, J., Li, J., Ye, B., Wang, Y., & Xi, J. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1011119 · Cited by 7
Effect of Conformational Variability on Seasonable Thermal Stability and Cell Entry of Omicron Variants
Izumi, H., Aoki, H., Nafié, L. A., & Dukor, R. K. (2023) · ACS Omega · doi:10.1021/acsomega.2c08075 · Cited by 6
Digital PCR Discriminates between SARS-CoV-2 Omicron Variants and Immune Escape Mutations
Holland, S. C., Holland, L., Smith, M. F., Lee, M. B., Hu, J. C., & Lim, E. (2022) · medRxiv · doi:10.1128/spectrum.05258-22 · Cited by 7
A potent and broad‐spectrum neutralizing nanobody for SARS‐CoV‐2 viruses, including all major Omicron strains
Yao, H., Wang, H., Zhang, Z., Lu, Y., Zhang, Z., Zhang, Y., Xiong, X., Wang, Y., Wang, Z., Yang, H., et al. (2023) · MedComm · doi:10.1002/mco2.397 · Cited by 6
Up or down: where comes Omicron?
Liu, Z., Lu, L., & Jiang, S. (2022) · Cell Research · doi:10.1038/s41422-022-00675-1 · Cited by 7
Effectiveness of Naturally Acquired and Vaccine-Induced Immune Responses to SARS-CoV-2 Mu Variant
de Oliveira-Filho, E. F., Rincón‐Orozco, B., Jones-Cifuentes, N. A., Peña-López, B. O., Mühlemann, B., Drosten, C., Moreira‐Soto, A., & Drexler, J. F. (2022) · Emerging infectious diseases · doi:10.3201/eid2808.220584 · Cited by 7
“In addition, the mutation leading to the amino acid exchange R346K in Mu is known to be involved in the evasion of monoclonal antibody–mediated neutralization (9), and genomic exchanges occurring at 3 adjacent sites (Y144T, Y145S, and insertion of the amino acid asparagine [N] between spike residues 145 and 146) have…”
Potent bivalent nanobody constructs that protect against the SARS-CoV-2 XBB variant
Halfmann, P., Lee, J. S., McArthur, N., Gupta, O., Kawaoka, Y., & Kane, R. S. (2025) · npj Viruses · doi:10.1038/s44298-025-00101-4 · Cited by 6
Molecular mechanisms of SARS-CoV-2 entry: implications for biomedical strategies
Santamaria-Castro, I., Leiva-Rebollo, R., Marín‐Wong, S., Jiménez-Guardeño, J. M., & Ortega‐Prieto, A. M. (2025) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00260-24 · Cited by 7
ADME analysis, metabolic prediction, and molecular docking of lipoic acid with SARS-CoV-2 Omicron spike protein
dos Santos, C. A. L., Monteiro, A. A. D. A., Costa, A. R., Barros, L. M., Aloufi, A. D., Almutairi, M. M., Hassan, W., Kamdem, J. P., Duarte, A. E., Ali, A., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-93121-2 · Cited by 6
“SARS-CoV-2 enters cells by utilizing the ACE2 receptor 86 .”
Multiscale Modeling and Dynamic Mutational Profiling of Binding Energetics and Immune Escape for Class I Antibodies with SARS-CoV-2 Spike Protein: Dissecting Mechanisms of High Resistance to Viral Escape Against Emerging Variants
Alshahrani, M., Parikh, V., Foley, B., & Verkhivker, G. M. (2025) · Viruses · doi:10.3390/v17081029 · Cited by 6
RAMIHM generates fully human monoclonal antibodies by rapid mRNA immunization of humanized mice and BCR-seq
Ren, P., Peng, L., Yang, L., Suzuki, K., Fang, Z., Renauer, P. A., Lin, Q., Bai, M., Li, T., Clark, P. R., et al. (2023) · Cell chemical biology · doi:10.1016/j.chembiol.2022.12.005 · Cited by 6
Vaccine- and Breakthrough Infection-Elicited Pre-Omicron Immunity More Effectively Neutralizes Omicron BA.1, BA.2, BA.4 and BA.5 Than Pre-Omicron Infection Alone
da Silva, E. S., Servais, J.-Y., Kohnen, M., Arendt, V., Gilson, G., Staub, T., Seguin‐Devaux, C., & Perez-Bercoff, D. (2023) · Current Issues in Molecular Biology · doi:10.3390/cimb45020112 · Cited by 6
“The Omicron Spike also adopts a distinct, more compact conformation and glycosylation patterns which shield it from type 1, 2 and 3 Neutralizing antibodies (NAbs) [33,36,37].”
Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage
Paulino-Ramírez, R., López, P. L., Mueses, S., Cuevas, P., Jabier, M., & Rivera‐Amill, V. (2023) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph20085503 · Cited by 6
“The high number of mutations raised much concern because this region mediates host entry and is the main target of neutralizing antibodies [57].”
Structure and dynamics of the interaction of Delta and Omicron BA.1 SARS-CoV-2 variants with REGN10987 Fab reveal mechanism of antibody action
Lyukmanova, E. N., Pichkur, E., Nolde, D. E., Kocharovskaya, M. V., Manuvera, V. A., Shirokov, D. A., Kharlampieva, D. D., Grafskaia, E. N., Svetlova, J. I., Лазарев, В. Н., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-07422-9 · Cited by 6
A Meta-Analysis on the Immunogenicity of Homologous versus Heterologous Immunization Regimens against SARS-CoV-2 Beta, Delta, and Omicron BA.1 VoCs in Healthy Adults
Ndzouboukou, J. B., Kamara, A. A., Ullah, N., Lei, Q., & Fan, X. (2025) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.2411.11059 · Cited by 7
Immune evasion, infectivity, and membrane fusion of the SARS-CoV-2 JN.1 variant
Tang, H., Zhuo, Y., Chen, J., Zhang, R., Zheng, M., Huang, X., Chen, Y., Huang, M., Zeng, Z., Huang, X., et al. (2025) · Virology Journal · doi:10.1186/s12985-025-02737-3 · Cited by 7
“Furthermore, structural analyses demonstrate that Q493R and Q498R mutations establish new electrostatic interactions with ACE2 residues Glu35 and Asp38, respectively, while the S477N mutation facilitates hydrogen bond formation with ACE2 Ser19 [12, 35].”
Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction
Teruel, N., Crown, M. R., Rajsbaum, R., Bashton, M., & Najmanovich, R. (2025) · Virus Evolution · doi:10.1093/ve/veaf027 · Cited by 7
“…provide a limited view of functional aspects, as they typically rely on a single or few structures (Hong et al. 2022, Mannar et al. 2022, McCallum et al. 2022) that fail to capture the full variability and dynamic nature of a moving protein, a limitation that can be seen when comparing…”
Does pre-existing immunity determine the course of SARS-CoV-2 infection in health-care workers? Single-center experience
Laura, L., Dalmatin-Dragišić, M., Martinović, K., Tutiš, B., Herceg, I., Arapović, M., & Arapović, J. (2022) · Infection · doi:10.1007/s15010-022-01859-y · Cited by 7
Immune Evasion by the Highly Mutated SARS-CoV-2 Omicron Variant
Mengist, H. M., Kombe, A. J. K., & Jin, T. (2022) · Infection and Drug Resistance · doi:10.2147/idr.s366437 · Cited by 6
Physical-Chemical Regulation of Membrane Receptors Dynamics in Viral Invasion and Immune Defense
Qin, R., An, C., & Chen, W. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167800 · Cited by 6
A Heterologous Challenge Rescues the Attenuated Immunogenicity of SARS-CoV-2 Omicron BA.1 Variant in Syrian Hamster Model
Ma, J., Liu, X., Zhou, M., Chen, P., Chen, R., Wang, J., Zhu, H., Wu, K., Ye, J., Zhang, Y., et al. (2023) · Journal of Virology · doi:10.1128/jvi.01684-22 · Cited by 6
Molecular recognition of SARS-CoV-2 spike protein with three essential partners: exploring possible immune escape mechanisms of viral mutants
Cheng, Y., Zheng, D., Zhang, D., Guo, D., Wang, Y., Liu, W. Y., Liang, L., Hu, J., Shi, H., & Luo, T. (2023) · Journal of Molecular Modeling · doi:10.1007/s00894-023-05509-4 · Cited by 6
Kinetics and ability of binding antibody and surrogate virus neutralization tests to predict neutralizing antibodies against the SARS-CoV-2 Omicron variant following BNT162b2 booster administration
Simon, G., Favresse, J., Gillot, C., Closset, M., Catry, É., Dogné, J., Douxfils, J., Wieërs, G., & Bayart, J. (2023) · Clinical Chemistry and Laboratory Medicine (CCLM) · doi:10.1515/cclm-2022-1258 · Cited by 7
Update on Remdesivir in the Treatment of Novel Coronavirus Pneumonia
Feng, H., Lakshmi, K. V., Ng, C. T., Sasikumar, M., Arip, M., Hassan, M., Chin, V. K., Rajagopal, M. S., Fatokun, O. O., Parvathi, N., et al. (2023) · Progress In Microbes & Molecular Biology · doi:10.36877/pmmb.a0000341 · Cited by 6
“Both transcription and genome replication of RNA viruses are dominated by RdRp [27, 42] .”
mRNA vaccines against SARS-CoV-2 induce divergent antigen-specific T-cell responses in patients with lung cancer
Song, N., Chakravarthy, K. B., Jeon, H., Bolyard, C. M., Reynolds, K., Weller, K. P., Reisinger, S. A., Wang, Y., Li, A., Jiang, S., et al. (2024) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2023-007922 · Cited by 6
Long-term levels of protection of different types of immunity against the Omicron variant: a rapid literature review
Velásquez, S. R., Biru, L., Hakiza, S., Al‐Gobari, M., Triulzi, I., Dalal, J., Valera, C. B., Mesa, S. B., & Keiser, O. (2024) · Swiss Medical Weekly · doi:10.57187/s.3732 · Cited by 7
“Of the five variants of concern, Omicron has accumulated the highest number of mutations and has mediated the greatest level of immune escape [6].”
Valuable Contributions and Lessons Learned from Proteomics and Metabolomics Studies of COVID-19
Chatterjee, B., & Thakur, S. S. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00340 · Cited by 5
Dynamic mutational profiling of binding interactions and allosteric networks in conformational ensembles of the SARS-CoV-2 spike protein complexes with classes of antibodies targeting cryptic binding sites: confluence of binding and allostery determines molecular mechanisms and hotspots of immune escape
Alshahrani, M., Parikh, V., Foley, B., & Verkhivker, G. M. (2025) · Physical Chemistry Chemical Physics · doi:10.1039/d5cp02468d · Cited by 5
Repeated COVID-19 vaccine boosters elicit variant-specific memory B cells in humans
Tortorici, M. A., Sprouse, K. R., Addetia, A., Brown, J. T., Lee, J., Stewart, C., Merz, B., Harteloo, A., Elias-Warren, A., Chu, H. Y., et al. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117052 · Cited by 8
Self-citation
Investigating the structural impact of Omicron RBD mutation on antibody escape and receptor management
Saini, S., Pareekh, S., & Kumar, Y. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2222174 · Cited by 5
“The conformational geometry of RBD plays an essential role in the spatial chemistry of interaction between human ACE-2 and RBD of SARS-CoV-2 and its variants.”
Influential
Evolution of SARS-CoV-2 Spikes shapes their binding affinities to animal ACE2 orthologs
Yao, W., Li, Y., Ma, D., Hou, X.-D., Wang, H., Tang, X., Cheng, D., Zhang, H., Du, C., Pan, H., et al. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.02676-23 · Cited by 5
“Since both K417N and Y505H mutations are present in Omicron’s major sublineages (47, 73, 74), the above data also suggest that, in contrast to the WHU01 and Delta variants, the Omicron lineage might be generally less hazardous to livestock and pet animals.”
Vaccine-induced strain replacement: theory and real-life implications
Mahroum, N., Karaoglan, B. S., Ulucam, E. S., & Shoenfeld, Y. (2024) · Future Microbiology · doi:10.1080/17460913.2024.2345003 · Cited by 5
An integrated multiscale computational framework deciphers SARS-CoV-2 resistance to sotrovimab
Sharma, A., Maurya, S., Kumar, S., Tripathi, T., Kar, R. K., & Padhi, A. K. (2025) · Biophysical Journal · doi:10.1016/j.bpj.2025.05.015 · Cited by 6
Analyzing the interaction of human ACE2 and RBD of spike protein of SARS-CoV-2 in perspective of Omicron variantPreprint
Samanta, A., Alam, S. S. M., Ali, S., & Hoque, M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.17179/excli2022-4721 · Cited by 14
Permissive omicron breakthrough infections in individuals with binding or neutralizing antibodies to ancestral SARS-CoV-2
Williams, E., Colson, J., Valiathan, R., Carreño, J. M., Krammer, F., Hoffer, M. E., Pallikkuth, S., Pahwa, S. G., & Andrews, D. M. (2022) · Vaccine · doi:10.1016/j.vaccine.2022.08.058 · Cited by 5
Continued Complexity of Mutations in Omicron Sublineages
Spratt, A. N., Kannan, S. R., Sharma, K., Sachdev, S., Kandasamy, S. L., Sönnerborg, A. B., Lorson, C. L., & Singh, K. (2022) · Biomedicines · doi:10.3390/biomedicines10102593 · Cited by 4
“The loop harboring F486 also has another Omicron signature mutation (E484A), which abrogates the binding of the LYCoV555 monoclonal antibody (mAb) to S-RBD [23].”
A comparative analysis exposes an amplification delay distinctive to SARS-CoV-2 Omicron variants of clinical and public health relevance
Brown, K. L., Ceci, A., Roby, C. D., Briggs, R., Ziolo, D., Korba, R., Mejia, R., Kelly, S., TONEY, D. M., Friedlander, M. J., et al. (2022) · Emerging Microbes & Infections · doi:10.1080/22221751.2022.2154617 · Cited by 5
“activity among vaccinated and previously infected individuals [15-19].”
A systematic study on the binding affinity of SARS-CoV-2 spike protein to antibodies
An, K., Zhu, X., Yan, J., Xu, P., Hu, L., & Bai, C. (2022) · AIMS Microbiology · doi:10.3934/microbiol.2022038 · Cited by 5
Successful clearance of persistent SARS-CoV-2 asymptomatic infection following a single dose of Ad5-nCoV vaccine
Qiu, S., Chen, Z., Zhu, A., Zeng, Q., Liu, H., Liu, X., Ye, F., Jin, Y., Wu, J., Yang, C., et al. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01345-3 · Cited by 5
“Single-vaccination dose induced durable and broad nAbs against various SARS-CoV-2 VOCs in PA cases The ongoing transmission of SARS-CoV-2 has led to the emergence of VOCs with higher transmissibility or resistance to prior immunity.(26,27) To further investigate the protection efficiency of this vaccine in facing emer…”
Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson–Boltzmann Theories
Hsieh, Y.-C., Delarue, M. H., Orland, H., & Koehl, P. (2023) · Viruses · doi:10.3390/v15061366 · Cited by 6
Update on Central Nervous System Effects of the Intersection of HIV-1 and SARS-CoV-2
Ocampo, F. F., Promsena, P., & Chan, P. (2023) · Current HIV/AIDS Reports · doi:10.1007/s11904-023-00676-8 · Cited by 5
“Compared to pre-Omicron (wild-type, Alpha, Beta, and Delta) variants, Omicron and its subvariants exhibit high immune evasion [10, 11] and increased transmissibility [9].”
Peroxide derivatives as SARS-CoV-2 entry inhibitors
Zhang, D., Ma, Q., Yang, M.-C., Belyakova, Y. Y., Yang, Z., Radulov, P. S., Chen, R., Yang, L., Wei, J., Peng, Y.-T., et al. (2023) · Virus Research · doi:10.1016/j.virusres.2023.199295 · Cited by 5
Differential pathogenic and molecular features in neurological infection of SARS‐CoV‐2 Omicron BA.5.2 and BA.2.75 and Delta
Wang, E., Yang, Q., Xu, X., Zou, Q., Long, Y., Ma, G., Deng, Z., Zhao, J., Li, M., & Zeng, J. (2024) · Journal of Medical Virology · doi:10.1002/jmv.29357 · Cited by 5
Tracking vaccine effectiveness in an evolving pandemic, countering misleading hot takes and epidemiologic fallacies
Morris, J. S. (2024) · American Journal of Epidemiology · doi:10.1093/aje/kwae280 · Cited by 5
Structure/Function Analysis of Truncated Amino-Terminal ACE2 Peptide Analogs That Bind to SARS-CoV-2 Spike Glycoprotein
Mackin, R. T., Edwards, J. V., Atuk, E. B., Beltrami, N., Condon, B., Jayawickramarajah, J., & French, A. D. (2022) · Molecules · doi:10.3390/molecules27072070 · Cited by 5
“These mutations correspond to positive charge changes and allow for the formation of new salt bridges and hydrogen bonds, while other mutations improve antibody evasion [20,83].”
Reduced neutralization against Delta, Gamma, Mu, and Omicron BA.1 variants of SARS-CoV-2 from previous non-Omicron infection
Pidal, P., Fernández, J. O., Airola, C., Araujo, M., Menjiba, A. M., Martín, H. S., Bruneau, N., Balanda, M., Elgueta, C., Fasce, R., et al. (2022) · Medical Microbiology and Immunology · doi:10.1007/s00430-022-00753-6 · Cited by 5
Humoral and cellular immune responses against SARS-CoV-2 variants of concern induced by heterologous CoronaVac/ChAdOx-1 versus homologous ChAdOx-1 vaccination in the elderly
Liwsrisakun, C., Pata, S., Laopajon, W., Takheaw, N., Chaiwong, W., Duangjit, P., Inchai, J., Chuensirikulchai, K., Cheyasawan, P., Pothirat, C., et al. (2023) · Asian Pacific Journal of Allergy and Immunology · doi:10.12932/ap-120822-1434 · Cited by 5
“26 Vaccine effectiveness for the Omicron was reported to be lower than WT and other VOCs.”
Novel ACE2 fusion protein with adapting activity against SARS-CoV-2 variants in vitro
Zekri, L., Ruétalo, N., Christie, M., Walker, C., Manz, T., Rammensee, H., Salih, H. R., Schindler, M., & Jung, G. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1112505 · Cited by 5
Understanding the host-pathogen evolutionary balance through Gaussian process modeling of SARS-CoV-2
Loguercio, S., Calverley, B. C., Wang, C., Shak, D., Zhao, P., Sun, S., Budinger, G. R. S., & Balch, W. E. (2023) · Patterns · doi:10.1016/j.patter.2023.100800 · Cited by 5
“This can be done through the prism of GP-based SCV and EWAD to advance understanding of viral pathology and/or advancing new therapeutics, 63,65,66 as our GP analysis treats the virus as whole (the collective sum of its covariate parts) in driving the rapid evolution of the pandemic.”
The SARS-CoV-2 Spike is a virulence determinant and plays a major role on the attenuated phenotype of Omicron virus in a feline model of infection
Martins, M., Nooruzzaman, M., Cunningham, J. L., Ye, C., Caserta, L. C., Jackson, N. D., Martínez‐Sobrido, L., Fāng, Y., & Diel, D. G. (2024) · Journal of Virology · doi:10.1128/jvi.01902-23 · Cited by 5
Comparative Dynamics of Delta and Omicron SARS-CoV-2 Variants across and between California and Mexico
Mehta, S. R., Smith, D. M., Boukadida, C., & Chaillon, A. (2022) · Viruses · doi:10.3390/v14071494 · Cited by 5
Differential vaccine-induced kinetics of humoral and cellular immune responses in SARS-CoV-2 naive and convalescent health care workers
Smit, W. L., Thijsen, S. F. T., van der Kieft, R., van Tol, S., Reimerink, J. H. J., Reusken, C. B. E. M., Rümke, L. W., Bossink, A. W. J., Limonard, G. J. M., & Heron, M. (2022) · Pathogens and Disease · doi:10.1093/femspd/ftac035 · Cited by 5
Durable protection against SARS-CoV-2 Omicron induced by an adjuvanted subunit vaccinePreprint
Arunachalam, P. S., Feng, Y., Ashraf, U., Hu, M., Edara, V. V., Zarnitsyna, V. I., Aye, P. P., Golden, N., Green, K. M., Threeton, B., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.18.484950 · Cited by 5
“Protection against Omicron Omicron is characterized by high resistance to vaccine-induced nAbs and therapeutic monoclonal nAbs (Cameroni et al., 2022; McCallum et al., 2022), which results in a striking decline in vaccine efficacy against Omicron (Andrews et al., 2022).”
Self-citation
Limited Neutralization of Omicron by Antibodies from the BNT162b2 Vaccination against SARS-CoV-2Preprint
Lanz, T. V., Brewer, R. C., Jahanbani, S., & Robinson, W. H. (2022) · Research Square · doi:10.21203/rs.3.rs-1518378/v1 · Cited by 5
Structural and functional characteristics of SARS-CoV-2 Omicron subvariant BA.2 spikePreprint
Zhang, J., Tang, W., Gao, H., Lavine, C. L., Shi, W., Peng, H., Zhu, H., Anand, K., Kosikova, M., Kwon, H. J., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.28.489772 · Cited by 5
“Q493R and Q498R have been shown to enhance ACE2 affinity by creating additional contacts with the receptor (38-42), while K417N and E484A eliminate ionic interactions with ACE2 and may reduce the ACE2 affinity (27, 43).”
Atomic-scale Quantum Chemical Calculation of Omicron Mutations Near Cleavage Sites of the Spike ProteinPreprint
Adhikari, P., Jawad, B., Podgornik, R., & Ching, W. Y. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.03.494698 · Cited by 5
Genome-first detection of emerging resistance to novel therapeutic agents for SARS-CoV-2Preprint
Ragonnet‐Cronin, M., Nutalai, R., Huo, J., Dijokaite-Guraliuc, A., Das, R., Tuekprakhon, A., Supasa, P., Liu, C., Selvaraj, M., Groves, N., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.14.500063 · Cited by 5
Attenuated humoral responses in HIV infection after SARS-CoV-2 vaccination are linked to global B cell defects and cellular immune profilesPreprint
Touizer, E., Alrubayyi, A., Ford, R., Hussain, N., Gerber, P. P., Shum, H.-L., Rees-Spear, C., Muir, L., Gea‐Mallorquí, E., Kopycinski, J. T., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.11.516111 · Cited by 5
Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics SimulationsPreprint
Raisinghani, N., Alshahrani, M., Gupta, G., Xiao, S., Tao, P., & Verkhivker, G. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.02.587850 · Cited by 6
Living Cell Surfacome Lysine Footprinting (LiFT) Captures Virus-Induced Conformational Dynamics and Uncovers Influenza A Virus Host Factors
Ma, S., Liang, Y., Song, H., Wang, T., Zhang, Y., Zhang, L., Chen, J., Lu, H., & Zhang, Y. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.5c14196 · Cited by 4
Structural Insights into the SARS-CoV-2 Spike Protein and Its Implications for Antibody Resistance
Yamamoto, Y., & Noguchi, K. (2025) · Biomolecules · doi:10.3390/biom15111489 · Cited by 5
“Although REGN10987 (Class 3) is primarily impaired by other Omicron mutations such as G446S, Q493R in combination with adjacent substitutions contributes to the extensive immune escape phenotype observed in Omicron [78,80].”
Genomic surveillance of SARS-CoV-2 upsurge in India due to Omicron sub-lineages BA.2.74, BA.2.75 and BA.2.76
Singh, U. B., Deb, S., Rani, L., Bhardwaj, D., Gupta, R., Kabra, M., Bala, K., Kumari, L., Perumalla, S., Shukla, J., et al. (2023) · The Lancet Regional Health - Southeast Asia · doi:10.1016/j.lansea.2023.100148 · Cited by 4
Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps
Remesh, S. G., Merz, G. E., Brilot, A. F., Chio, U. S., Rizo, A. N., Pospiech, T. H., Lui, I., Laurie, M. T., Glasgow, J. E., Le, C. Q., et al. (2023) · Structure · doi:10.1016/j.str.2023.01.009 · Cited by 4
“3,4,28 For example, while the Y505H mutation leads to loss in hydrogen bond interactions with WT-ACE2 residue E37, there are several compensatory mutations in the Omicron-RBD.”
Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers: Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants
Verkhivker, G. M., Alshahrani, M., & Gupta, G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24076642 · Cited by 4
“4 various functional states and complexes with antibodies revealed a remarkable versatility of molecular mechanisms and diversity of binding epitopes that underlie binding affinity of S proteins with different classes of antibodies [19-28].”
A Unique mRNA Vaccine Elicits Protective Efficacy against the SARS-CoV-2 Omicron Variant and SARS-CoV
Guan, X., Verma, A. K., Wang, G., Roy, A., Perlman, S. M., & Du, L. (2024) · Vaccines · doi:10.3390/vaccines12060605 · Cited by 4
SARS-CoV-2 ferritin nanoparticle vaccines produce hyperimmune equine sera with broad sarbecovirus activity
Martinez, E. J., Chang, W. C., Chen, W., Hajduczki, A., Thomas, P. V., Jensen, J. L., Choe, M., Sankhala, R. S., Peterson, C. E., Rees, P. A., et al. (2024) · iScience · doi:10.1016/j.isci.2024.110624 · Cited by 3
Characterization of key spike RBD residues influencing SARS-CoV-2 variant adaptation to avian ACE2
Yao, W., Li, Y., Sun, H., Ma, D., Tang, X., Zeng, A., & Huang, F. (2025) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1631926 · Cited by 4
Being a Public Health Statistician During a Global Pandemic
Mukherjee, B. (2022) · Statistical Science · doi:10.1214/22-sts859 · Cited by 4
Molecular Insights into Striking Antibody Evasion of SARS-CoV-2 Omicron Variant
Yan, Z., Xu, Y., Ding, H., & Ma, Y. (2022) · Chinese Physics Letters · doi:10.1088/0256-307x/39/10/108701 · Cited by 4
Computational analysis of interior mutations of SARS-CoV-2 Spike protein suggest a balance of protein stability and S2: S1 separation propensity
Li, Z., & Buck, M. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.10.044 · Cited by 4
“For the Omicron variant, the current electron microscope results indicate the existence of both 2 RBD ‘‘open” and 1 RBD ‘‘open” states, but the relative ratio is unknown [10].”
Mapping the Accessory Proteins (Orfs) of Severe Acute Respiratory Syndrome Coronavirus 2
Thomas, S. (2023) · Re GEN Open · doi:10.1089/regen.2022.0056 · Cited by 4
Genomic evidence for reinfection with different Omicron subvariants
Hirotsu, Y., & Omata, M. (2023) · Journal of Infection · doi:10.1016/j.jinf.2023.01.010 · Cited by 4
An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variantsPreprint
Du, W., Hurdiss, D. L., Drabek, D., Mykytyn, A. Z., Kaiser, F. K., González-Hernández, M. C., Muñoz‐Santos, D., Lamers, M. M., van Haperen, R., Li, W., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.17.480751 · Cited by 4
Structural dynamics in the evolution of SARS-CoV-2 spike glycoproteinPreprint
Calvaresi, V., Wrobel, A. G., Toporowska, J., Hammerschmid, D., Doores, K. J., Bradshaw, R. T., Parsons, R. B., Benton, D. J., Roustan, C., Reading, E., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-2049401/v1 · Cited by 4
Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2Preprint
Bianchini, F., Crivelli, V., Abernathy, M. E., Guerra, C., Palus, M., Muri, J., Marcotte, H., Piralla, A., Pedotti, M., Gasparo, R. D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.24.515932 · Cited by 4
Editorial: COVID-19 booster vaccination: increasing immunity against life-threatening infection
Yorsaeng, R., Atsawawaranunt, K., & Riad, A. (2024) · Frontiers in Public Health · doi:10.3389/fpubh.2023.1342118 · Cited by 4
Phylogeny-driven design of broadly protective sarbecovirus receptor-binding domain nanoparticle vaccinesPreprint
Addetia, A., Schäfer, A., Sprouse, K. R., Valdez, A., Taylor, A., Navarro, M.-J., Brown, J. T., Leaf, E. M., Miranda, M. C., Walls, A. C., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.11.652904 · Cited by 4
Self-citation
Population immunity enhances the evolution of SARS-CoV-2 in Beijing revealed by wastewater genomic surveillance
Wang, C., Chen, W., Yu, L., Wang, X., Zhang, L., Zhang, X., Tang, S., Han, J., Gao, W., Huang, X., et al. (2025) · Water Research · doi:10.1016/j.watres.2025.123649 · Cited by 3
Design of Entry Inhibitor Peptides Covalently Bonding SARS-CoV-2 Variants in Wastewater
Xue, B., Li, R., Zhu, Q., Yang, Y., Wang, F., Cheng, Z., & Zhou, X. (2025) · Environmental Science & Technology · doi:10.1021/acs.est.5c02307 · Cited by 3
A single-dose intranasal immunization with a novel bat influenza A virus-vectored MERS vaccine provides effective protection against lethal MERS-CoV challenge
Shi, L., Roy, S., Lang, Y., Wen, Y., Mitchell, W. J., Yang, W., Wang, L., Zhang, J., Liu, H., Driver, J. P., et al. (2025) · mBio · doi:10.1128/mbio.01107-25 · Cited by 3
Differentiating Cell Entry Potentials of SARS-CoV-2 Omicron Subvariants on Human Lung Epithelium Cells
Katte, R. H., Ao, Y., Wang, X., Han, Y., Zhong, G., Ghimire, D., Florence, J., Tucker, T. A., & Lu, M. (2024) · Viruses · doi:10.3390/v16030391 · Cited by 3
“BA.1 and its descendants harbor an unusually large number of mutations (over 30) in S [11,35,36].”
Mutational Scanning and Binding Free Energy Computations of the SARS-CoV-2 Spike Complexes with Distinct Groups of Neutralizing Antibodies: Energetic Drivers of Convergent Evolution of Binding Affinity and Immune Escape Hotspots
Alshahrani, M., Parikh, V., Foley, B., Raisinghani, N., & Verkhivker, G. M. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26041507 · Cited by 3
The implications of host–pathogen co-evolutionary outcomes on macro-epidemics based on a combined-host strategy
Liu, Q., Xiao, Y., & Smith, R. J. (2025) · Bulletin of Mathematical Biology · doi:10.1007/s11538-025-01517-y · Cited by 3
“2 (McCallum et al. 2022; Day et al. 2022).”
A Pathway Model to Understand the Evolution of Spike Protein Binding to ACE2 in SARS-CoV-2 Variants
Pipitò, L., Reynolds, C. A., Mobarec, J. C., Vickery, O. N., & Deganutti, G. (2022) · Biomolecules · doi:10.3390/biom12111607 · Cited by 3
“Mutations K417N, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, and Y505H are part of the immunodominant antigenic site I [8].”
Preclinical safety and efficacy of a therapeutic antibody that targets SARS-CoV-2 at the sotrovimab face but is escaped by Omicron
Kreye, J., Reincke, S. M., Edelburg, S., Jeworowski, L. M., Kornau, H., Trimpert, J., Hombach, P., Halbe, S., Nölle, V., Meyer, M., et al. (2023) · iScience · doi:10.1016/j.isci.2023.106323 · Cited by 3
Efficacy of novel SARS-CoV-2 rapid antigen tests in the era of omicron outbreak
Widyasari, K., & Kim, S. (2023) · PLoS ONE · doi:10.1371/journal.pone.0289990 · Cited by 3
“In comparison to the prior SARS-CoV-2 variants, the Omicron showed a significant number of mutations [30], with a greater rate of transmissibility [31, 32] and the ability to evade the efficacy of the currently administered COVID-19 vaccines or monoclonal antibody therapies [33, 34].”
Designing peptides predicted to bind to the omicron variant better than ACE2 via computational protein design and molecular dynamics
Sitthiyotha, T., Treewattanawong, W., & Chunsrivirot, S. (2023) · PLoS ONE · doi:10.1371/journal.pone.0292589 · Cited by 3
A human antibody derived from original SARS-CoV-2 infection effectively neutralizes omicron
Li, T., Zhou, B., Dong, H., Lavillette, D., & Li, D. (2024) · Advanced Biotechnology · doi:10.1007/s44307-024-00011-1 · Cited by 3
COVID-19 point-of-care tests can identify low-antibody individuals: In-depth immunoanalysis of boosting benefits in a healthy cohort
Mallory, M. L., Munt, J. E., Narowski, T. M., Castillo, I. N., Cuadra, E., Pisanic, N., Fields, P., Powers, J. M., Dickson, A. M., Harris, R., et al. (2024) · Science Advances · doi:10.1126/sciadv.adi1379 · Cited by 5
“Some spike RBD mutations enhanced viral interaction with the host cell surface receptor, angiotensin-converting enzyme 2 (ACE2) ( 7 ).”

Authors: McCallum, M., Czudnochowski, N., Rosen, L. E., Zepeda, S. K., Bowen, J. E., Walls, A. C., Hauser, K., Joshi, A., Stewart, C., Dillen, J. R., Powell, A. E., Croll, T. I., Nix, J., Virgin, H. W., Corti, D., Snell, G., & Veesler, D.
Affiliations: University of Washington (US)
VIR Biotechnology (United States) (US)
Howard Hughes Medical Institute (US)
University of Cambridge (GB)
Lawrence Berkeley National Laboratory (US)
Washington University in St. Louis (US)
Vir Biotechnology (Switzerland) (CH)
Corresponding author: McCallum, Matthew
Czudnochowski, Nadine
Snell, Gyorgy
Veesler, David
ORCID: McCallum, Matthew
Czudnochowski, Nadine
Rosen, Laura E.
Zepeda, Samantha K.
Bowen, John E.
Walls, Alexandra C.
Hauser, Kevin
Stewart, Cameron
Dillen, Josh R.
Powell, Abigail E.
Croll, Tristan I.
Nix, Jay
Virgin, Herbert W.
Corti, Davide
Snell, Gyorgy
Veesler, David
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2022-02-25
Volume: 375
Issue: 6583
Pages: 864-868
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.abn8652
PMC: PMC9427005
OpenAlex: W4220861013
Cited by: 535
References: 85
Citations by year: 2026: 25 · 2025: 56 · 2024: 85 · 2023: 122 · 2022: 246
FWCI: 62.11
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
Locations: Science (publishedVersion, cc-by)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, cc-by)
eScholarship (California Digital Library) (submittedVersion)
Funders: Howard Hughes Medical Institute (DE-AC02-05CH11231)
U.S. Department of Energy (-AC02-05CH11231, Contract No. DE-AC02-05-CH11231, 05CH11231, No. DE-AC02-05-CH11231, DE AC02 05CH11231, DE-AC02-)
Burroughs Wellcome Fund (DE-AC02-05CH11231)
University of Washington
Wellcome Trust (Z/17/Z, 209407/Z/17/Z)
Fast Grants
National Institutes of Health (S10 OD032290, DE-AC02–05CH11231, 1s10od023476-01, HHSN272201700059C)
Office of Science (No. DE-AC02- 05-CH11231, DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231, Contract No. DE-AC02-05CH11231)
National Institute of General Medical Sciences (DE-AC02-05CH11231, R01GM120553, T32GM008268, P30GM124169)
National Institute of Allergy and Infectious Diseases (HHSN272201700059C, DP1AI158186)
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
Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
Keywords: Omicron variant, spike protein, receptor binding domain, antibody escape, sotrovimab, ACE2 receptor, antigenic shift, spike protein mutations, antibody affinity
MeSH terms: Protein Domains, Broadly Neutralizing Antibodies, Receptors, Coronavirus, Angiotensin-Converting Enzyme 2, SARS-CoV-2, Antigenic Drift and Shift, Antibodies, Monoclonal, Antibodies, Viral, Humans, Models, Molecular, Mutation, Protein Binding, Protein Conformation, Crystallography, X-Ray, Amino Acid Substitution, Cryoelectron Microscopy, Protein Interaction Domains and Motifs, Immune Evasion, Spike Glycoprotein, Coronavirus

About these checks

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.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

Abstract

Overview

Integrity signals

Figures

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks