Cited by 538SARS-CoV-2 and COVID-19 ResearchEvolution and Genetic DynamicsAnimal Virus Infections Studies

The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

Open access

McCarthy, Kevin R., Rennick, Linda J., Nambulli, Sham, Robinson-McCarthy, Lindsey R., Bain, William G., Haidar, Ghady, Duprex, W. Paul·2021·Science

DOI 10.1126/science.abf6950PMC PMC7971772

Published version of a preprint

Open this paper in CoChat — free account

Abstract

Eluding detection: Influenza viruses evade immunity initiated by previous infection, which explains recurrent influenza pandemics. Unlike the error-prone RNA-dependent RNA polymerase of influenza, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related viruses contain polymerases with proofreading activity. However, proofreading cannot correct deletions, which during a long-term persistent infection could result in the generation of viruses showing alteration of entire stretches of amino acids and the structures they form. McCarthy et al. identified an evolutionary signature defined by prevalent and recurrent deletions in the spike protein of SARS-CoV-2 at four antigenic sites. Deletion variants show human-to-human transmission of viruses with altered antigenicity. Science , this issue p. 1139

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.abf6950

Cites

36 of 36 references verified0 citation errors · 0 not checkable

Statistics

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.

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
A novel coronavirus from patients with pneumonia in China, 2019
Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2001017 · Cited by 28,244
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027
A new coronavirus associated with human respiratory disease in China
Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2008-3 · Cited by 11,688
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Price, M. N., Dehal, P. S., & Arkin, A. P. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp077 · Cited by 5,602
Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus
Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.043 · Cited by 4,281
GISAID: Global initiative on sharing all influenza data – from vision to reality
Shu, Y., & McCauley, J. (2017) · Eurosurveillance · doi:10.2807/1560-7917.es.2017.22.13.30494 · Cited by 3,039
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
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2020) · doi:10.1101/2020.12.21.20248640 · Cited by 2,535 · cited 1×
“351 (28), first reported in the United Kingdom 159 and South Africa, have deletions in RDRs 1/2 and 4, respectively.”
Background
Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510

Flagged first, then by citations

Show all 33 references

Research works printed but not linked: 1

M. K. Hensley et al . Intractable COVID-19 and Prolonged SARS-CoV-2 Replication in a CAR-T-cell Therapy Recipient: A Case Study. Clin. Infect. Dis. ciab072 (2021).10.1093/cid/ciab07233507235 · DOI

Sorted by citations

Items 301–400 of 538

Hyper-Variable Spike Protein of Omicron Corona Virus and Its Differences with Alpha and Delta Variants: Prospects of RT-PCR and New Vaccine
Chakraborty, A. K. (2022) · Journal of Emerging Diseases and Virology · doi:10.16966/2473-1846.166 · Cited by 12
SARS-CoV-2 variants of concern: a review
Sarkar, M. S., & Madabhavi, I. (2022) · Monaldi Archives for Chest Disease · doi:10.4081/monaldi.2022.2337 · Cited by 14
Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes
Rogozin, I. B., Saura, A., Bykova, A., Brover, V. V., & Yurchenko, V. (2023) · Microorganisms · doi:10.3390/microorganisms11010229 · Cited by 12
Multivalent IgM scaffold enhances the therapeutic potential of variant-agnostic ACE2 decoys against SARS-CoV-2
Verstraete, M. M., Heinkel, F., Li, J., Cao, S., Tran, A., Halverson, E. C., Gene, R. W., Stangle, E., Silva‐Moreno, B., Arrafi, S., et al. (2023) · mAbs · doi:10.1080/19420862.2023.2212415 · Cited by 12
SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise
Duerr, R., Crosse, K. M., Valero-Jimenez, A. M., & Dittmann, M. (2021) · Microorganisms · doi:10.3390/microorganisms9071389 · Cited by 12
A systematic review on impact of SARS-CoV-2 infection
Gowripriya, T., Radhakrishnan, Y., Ramamurthi, S., Bhaskar, J. P., & Balamurugan, K. (2023) · Microbiological Research · doi:10.1016/j.micres.2023.127364 · Cited by 12
Mutations of SARS-CoV-2 Structural Proteins in the Alpha, Beta, Gamma, and Delta Variants: Bioinformatics Analysis
Khetran, S. R., & Mustafa, R. (2023) · JMIR Bioinformatics and Biotechnology · doi:10.2196/43906 · Cited by 13
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification
Class, J., Simons, L. M., Lorenzo-Redondo, R., Achi, J. G., Cooper, L. M., Dangi, T., Penaloza‐MacMaster, P., Ozer, E. A., Lutz, S. E., Rong, L., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01786-8 · Cited by 11
Impact of Ribosome Activity on SARS-CoV-2 LNP – Based mRNA Vaccines
Tsiambas, E., Chrysovergis, A., PAPANIKOLAOU, V. S., MASTRONIKOLIS, N. S., Ragos, V., Batistatou, A. K., Peschos, D., Kavantzas, N., Lazaris, A. C., & Kyrodimos, E. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.654866 · Cited by 11
Genetics of COVID-19
Vologzhanin, D. A., Голота, А. С., Kamilova, Т. A., Shneider, O. V., & Sherbak, S. G. (2021) · Journal of clinical practice · doi:10.17816/clinpract64972 · Cited by 11
Genome-Wide Variation in Betacoronaviruses
LaTourrette, K., Holste, N. M., Rodriguez-Peña, R., Leme, R. A., & García-Ruíz, H. (2021) · Journal of Virology · doi:10.1128/jvi.00496-21 · Cited by 12
Conserved Pattern and Potential Role of Recurrent Deletions in SARS-CoV-2 Evolution
Weng, S., Zhou, H., Ji, C., Li, L., Han, N., Yang, R., Shang, J., & Wu, A. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02191-21 · Cited by 11
SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection
McGowan, J., Borucki, M. K., Omairi, H., Varghese, M., Vellani, S. D., Chakravarty, S., Fan, S., Chattopadhyay, S., Siddiquee, M., Thissen, J. B., et al. (2022) · Viruses · doi:10.3390/v14092032 · Cited by 11
Characterization of intrinsic and effective fitness changes caused by temporarily fixed mutations in the SARS-CoV-2 spike E484 epitope and identification of an epistatic precondition for the evolution of E484A in variant Omicron
Schröder, S., Richter, A. M., Veith, T., Emanuel, J., Gudermann, L., Friedmann, K., Jeworowski, L. M., Mühlemann, B., Jones, T. C., Müller, M. A., et al. (2023) · Virology Journal · doi:10.1186/s12985-023-02154-4 · Cited by 10
Longitudinal Analysis and Comparison of Six Serological Assays up to Eight Months Post-COVID-19 Diagnosis
Aubry, A., Demey, B., François, C., Duverlie, G., Castelain, S., Helle, F., & Brochot, É. (2021) · Journal of Clinical Medicine · doi:10.3390/jcm10091815 · Cited by 10
SARS-CoV-2 gained a novel spike protein S1–N-Terminal Domain (S1-NTD)
Desingu, P. A., Nagarajan, K., & Dhama, K. (2022) · Environmental Research · doi:10.1016/j.envres.2022.113047 · Cited by 11
Recurrent independent emergence and transmission of SARS-CoV-2 Spike amino acid H69/V70 deletionsPreprint
Gupta, R. K., Kemp, S. A., Harvey, W. T., Lytras, S., Carabelli, A. M., & Robertson, D. L. (2021) · Research Square · doi:10.21203/rs.3.rs-136937/v1 · Cited by 12
An anti-SARS-CoV-2 non-neutralizing antibody with Fc-effector function defines a new NTD epitope and delays neuroinvasion and death in K18-hACE2 micePreprint
Beaudoin-Bussières, G., Chen, Y.-Z., Ullah, I., Prévost, J., Tolbert, W., Symmes, K., Ding, S.-L., Benlarbi, M., Gong, S., Tauzin, A., et al. (2021) · bioRxiv · doi:10.1101/2021.09.08.459408 · Cited by 15
Engineered ACE2 counteracts vaccine-evading SARS-CoV-2 Omicron variantPreprint
Ikemura, N., Taminishi, S., Inaba, T., Arimori, T., Motooka, D., Katoh, K., Kirita, Y., Higuchi, Y., Li, S., Suzuki, T., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.22.473804 · Cited by 11
Investigation of protein-protein interactions and hotspot region on the NSP7-NSP8 binding site in NSP12 of SARS-CoV-2
Neto, J. X., Bezerra, K. S., Barbosa, E. D., Araujo, R. L., Galvao, D. S., Lyra, M. L., Oliveira, J. I. N., Akash, S., Jardan, Y. A. B., Nafidi, H., et al. (2024) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1325588 · Cited by 11
Vero cell-adapted SARS-CoV-2 strain shows increased viral growth through furin-mediated efficient spike cleavage
Minami, S., Kotaki, T., Sakai, Y., Okamura, S., Torii, S., Ono, C., Motooka, D., Hamajima, R., Nouda, R., Nurdin, J. A., et al. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.02859-23 · Cited by 10
SARS-CoV-2 and Coronaviruses: Understanding Transmission, Impact, and Strategies for Prevention and Treatment
Tabatabaei, S. N., Keykhaee, Z., Nooraei, S., Ayati, M. A., Behzadmand, M., Azimi, S., Eskati, F., & Ahmadian, G. (2025) · Drugs and Drug Candidates · doi:10.3390/ddc4010005 · Cited by 13
SARS-CoV-2: Pathogenic Mechanisms and Host Immune Response
Yasmin, H., Saha, S., Butt, M. T., Modi, R. K., George, A. J. T., & Kishore, U. (2021) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-67452-6_6 · Cited by 10
Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2
Saunders, N., Planas, D., Bolland, W., Rodriguez, C., Fourati, S., Buchrieser, J., Planchais, C., Prot, M., Staropoli, I., Guivel‐Benhassine, F., et al. (2022) · EBioMedicine · doi:10.1016/j.ebiom.2022.103934 · Cited by 13
Viral Evolution and Immunology of SARS-CoV-2 in a Persistent Infection after Treatment with Rituximab
der Moeren, N. V., Selhorst, P., Ha, M. K., Heireman, L., Gaal, P.-J. V., Breems, D. A., Meysman, P., Laukens, K., Verstrepen, W. A., Gasse, N. V., et al. (2022) · Viruses · doi:10.3390/v14040752 · Cited by 10
Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples
Kimbrel, J. A., Moon, J. Y., Avila-Herrera, A., Martí, J. M., Thissen, J. B., Mulakken, N., Sandholtz, S. H., Ferrell, T., Daum, C. G., Hall, S., et al. (2022) · Viruses · doi:10.3390/v14122775 · Cited by 11
Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory
Ching, W. Y., Adhikari, P., Jawad, B., & Podgornik, R. (2023) · Biomedicines · doi:10.3390/biomedicines11020517 · Cited by 9
Transchromosomic bovine-derived anti-SARS-CoV-2 polyclonal human antibodies protects hACE2 transgenic hamsters against multiple variants
Gilliland, T. H., Dunn, M., Liu, Y., Alcorn, M. D. H., Terada, Y., Vasilatos, S. N., Lundy, J. D., Li, R., Nambulli, S., Larson, D. P., et al. (2023) · iScience · doi:10.1016/j.isci.2023.107764 · Cited by 10
Self-citation
Omicron Sub-Lineage BA.5 and Recombinant XBB Evasion from Antibody Neutralisation in BNT162b2 Vaccine Recipients
Brandolini, M., Gatti, G., Grumiro, L., Zannoli, S., Arfilli, V., Cricca, M., Dirani, G., Denicolò, A., Marino, M. M., Manera, M., et al. (2023) · Microorganisms · doi:10.3390/microorganisms11010191 · Cited by 10
Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7
Murugan, N. A., Javali, P. S., Pandian, C. J., Ali, M. A., Srivastava, V., & Jeyaraman, J. (2022) · Physical Chemistry Chemical Physics · doi:10.1039/d2cp00469k · Cited by 10
The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in severe models of COVID-19
Penrice-Randal, R., Bentley, E. G., Sharma, P., Kirby, A., Donovan-Banfield, I., Kipar, A., Mega, D. F., Bramwell, C., Sharp, J., Owen, A., et al. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.01829-24 · Cited by 8
Intra-host SARS-CoV-2 diversity in immunocompromised people living with HIV provides insight into the evolutionary trajectory of SARS-CoV-2
Joseph, R., Marais, G. J. K., Iranzadeh, A., Alisoltani, A., Hardie, D. R., Davies, M., Heekes, A., Chetty, N., Timmerman, V., Hsiao, M., et al. (2025) · Journal of Virology · doi:10.1128/jvi.00780-25 · Cited by 8
Biochemical Interface Engineering for Transistor-Based Point-of-Care Diagnostics
Kong, D., Xu, Z., Chen, C. Q., Liu, Y., & Wei, D. (2026) · Accounts of Chemical Research · doi:10.1021/acs.accounts.5c00732 · Cited by 9
Targeting spike glycans to inhibit SARS-CoV2 viral entry
Guseman, A. J., Rennick, L. J., Nambulli, S., Roy, C. N., Martinez, D. R., Yang, D. T., Bhinderwala, F., Vergara, S. V., Schaefer, A., Baric, R. S., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2301518120 · Cited by 11
Self-citation
Neutralisation resistance of SARS-CoV-2 spike-variants is primarily mediated by synergistic receptor binding domain substitutions
Pham, L. V., Underwood, A. P., Binderup, A., Fahnøe, U., Fernandez-Antunez, C., Mendez, B. L., Ryberg, L. A., Galli, A., Sølund, C. S., Weis, N. M., et al. (2024) · Emerging Microbes & Infections · doi:10.1080/22221751.2024.2412643 · Cited by 9
Degenerate CD8 Epitopes Mapping to Structurally Constrained Regions of the Spike Protein: A T Cell-Based Way-Out From the SARS-CoV-2 Variants Storm
Boni, C., Cavazzini, D., Bolchi, A., Rossi, M., Vecchi, A. L., Tiezzi, C., Barili, V., Fisicaro, P., Ferrari, C. I., & Ottonello, S. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.730051 · Cited by 9
Plasmonically Enhanced Ultrasensitive Epitope-Specific Serologic Assay for COVID-19
Wang, Z., Morrissey, J. J., Liu, L., Wang, Y., Zhou, Q., Naik, R. R., & Singamaneni, S. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c03676 · Cited by 9
High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination
Liao, Y.-C., Chen, F.-J., Chuang, M., Wu, H., Ji, W.-C., Yu, G., & Huang, T.-S. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23063257 · Cited by 9
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
Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency
Markarian, N. M., Galli, G., Patel, D., Hemmings, M., Nagpal, P., Berghuis, A. M., Abrahamyan, L. G., & Vidal, S. M. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.933983 · Cited by 10
Quantifying Mutational Response to Track the Evolution of SARS-CoV-2 Spike Variants: Introducing a Statistical-Mechanics-Guided Machine Learning Method
Sangeet, S., Sarkar, R., Mohanty, S. K., & Roy, S. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04574 · Cited by 9
Water-soluble tocopherol derivatives inhibit SARS-CoV-2 RNA-dependent RNA polymerasePreprint
Pacl, H. T., Tipper, J. L., Sevalkar, R. R., Crouse, A. B., Crowder, C. M., Ahmad, S., Ahmad, A. M., Holder, G. D., Kuhlman, C. J., Chinta, K. C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.13.449251 · Cited by 11
Lineage replacement and evolution captured by three years of the United Kingdom Covid Infection SurveyPreprint
Lythgoe, K., Golubchik, T., Hall, M. D., House, T., Cahuantzi, R., MacIntyre-Cockett, G., Fryer, H. R., Thomson, L., Nurtay, A., Ghafani, M., et al. (2022) · medRxiv · doi:10.1101/2022.01.05.21268323 · Cited by 9
SARS-CoV-2 Evolved Variants Bind to Sialylated Gangliosides and Are Inhibited by a Tetravalent Sialo-Glycocluster
Negi, G., Pandey, V. K., Potharaju, P. S., Jaiswal, M. K., Harshan, K. H., Tiwari, V. K., & Parveen, N. (2025) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.5c00143 · Cited by 8
Enhanced deep Convolutional Neural Network for SARS-CoV-2 variants classification
Awe, O. I., Obura, H. O., Charles, S., Mudibo, E. O., & Mwanga, M. J. (2025) · Frontiers in Artificial Intelligence · doi:10.3389/frai.2025.1512003 · Cited by 28
Standardized Two-Step Testing of Antibody Activity in COVID-19 Convalescent Plasma
Gilchuk, P., Thomsen, I. P., Yoder, S. M., Brady, E. J., Chappell, J. D., Stevens, L. J., Denison, M. R., Sutton, R. E., Chen, R. E., VanBlargan, L. A., et al. (2021) · iScience · doi:10.1016/j.isci.2021.103602 · Cited by 7
Molecular dynamics simulations of the SARS-CoV-2 Spike protein and variants of concern: structural evidence for convergent adaptive evolution
Neto, D. F. D. L., Fonseca, V., de Jesus, R., Dutra, L. H., Portela, L. M. D. O., de Freitas, C. S. M., Fillizola, E., Soares, B., de Abreu, A. L., Twiari, S., et al. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2097955 · Cited by 7
Intragenomic rearrangements involving 5′-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses
Patarca, R., & Haseltine, W. A. (2023) · Virology Journal · doi:10.1186/s12985-023-01998-0 · Cited by 8
Enhanced stability of the SARS CoV-2 spike glycoprotein following modification of an alanine cavity in the protein core
Poumbourios, P., Langer, C., Boo, I., Zakir, T., Akerman, A., Milogiannakis, V., Aggarwal, A., Johnstone, B. A., Ha, J., Coulibaly, F., et al. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1010981 · Cited by 8
Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2
Rogozin, I. B., Saura, A., Poliakov, E., Bykova, A., Roche-Lima, A., Pavlov, Y. I., & Yurchenko, V. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25073696 · Cited by 8
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
Genetic Path of the Emergence of SARS-CoV-2
Nasrin, T., & Ali, S. (2021) · Gene Cell and Tissue · doi:10.5812/gct.118302 · Cited by 8
Discovery of Highly Potent Fusion Inhibitors with Potential Pan-Coronavirus Activity That Effectively Inhibit Major COVID-19 Variants of Concern (VOCs) in Pseudovirus-Based Assays
Curreli, F., Ahmed, S., Victor, S. M. B., Drelich, A. K., Panda, S. S., Altieri, A., Kurkin, A. V., Tseng, C.-T. K., Hillyer, C. D., & Debnath, A. K. (2021) · Viruses · doi:10.3390/v14010069 · Cited by 9
Consecutive deletions in a unique Uruguayan SARS-CoV-2 lineage evidence the genetic variability potential of accessory genes
Panzera, Y., Calleros, L., Goñi, N., Marandino, A. E., Techera, C., Grecco, S., Ramos, N., Frabasile, S., Tomás, G., Condon, E., et al. (2022) · PLoS ONE · doi:10.1371/journal.pone.0263563 · Cited by 8
Predicting virus Fitness: Towards a structure-based computational model
Thakur, S., Kepp, K. P., & Mehra, R. (2023) · Journal of Structural Biology · doi:10.1016/j.jsb.2023.108042 · Cited by 8
AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Spike Protein Variants
Ali, M. A., & Caetano‐Anollés, G. (2024) · Biology · doi:10.3390/biology13030134 · Cited by 11
Pathogenesis and transmission of SARS-CoV-2 D614G, Alpha, Gamma, Delta, and Omicron variants in golden hamsters
Banete, A., Griffin, B. D., Corredor, J. C., Chien, E., Yip, L., Gunawardena, T. N. A., Nirmalarajah, K., Liang, J., Lee, Y., Leacy, A., et al. (2025) · npj Viruses · doi:10.1038/s44298-025-00092-2 · Cited by 8
The Role of Probiotics and Their Postbiotic Metabolites in Post-COVID-19 Syndrome
Jach, M. E., Sajnaga, E., Bumbul, M., Serefko, A., Borowicz, K. K., Golczyk, H., Kieliszek, M., & Wiater, A. (2025) · Molecules · doi:10.3390/molecules30204130 · Cited by 8
Challenges at the host-arthropod-coronavirus interface and COVID-19: a One Health approach
de la Fuente, J., de Mera, I. G. F., & Gortázar, C. (2021) · Frontiers in Bioscience-Landmark · doi:10.52586/4951 · Cited by 7
Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion
Panzera, Y., Ramos, N., Calleros, L., Marandino, A. E., Tomás, G., Techera, C., Grecco, S., Frabasile, S., Fuques, E., Cóppola, L., et al. (2021) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/0074-02760210275 · Cited by 7
High fusion and cytopathy of SARS-CoV-2 variant B.1.640.1
Bolland, W., Michel, V., Planas, D., Hubert, M., Guivel‐Benhassine, F., Porrot, F., Staropoli, I., N’Debi, M., Rodriguez, C., Fourati, S., et al. (2023) · Journal of Virology · doi:10.1128/jvi.01351-23 · Cited by 8
Endogenous viral mutations, evolutionary selection, and containment policy design
Mellacher, P. (2022) · Journal of Economic Interaction and Coordination · doi:10.1007/s11403-021-00344-3 · Cited by 7
Emergence of Novel SARS-CoV-2 variants in India: second wave
Adiga, R., & Nayak, V. R. (2021) · The Journal of Infection in Developing Countries · doi:10.3855/jidc.15484 · Cited by 5
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
Design and Immunoinformatic Assessment of Candidate Multivariant mRNA Vaccine Construct against Immune Escape Variants of SARS-CoV-2
Hussain, M., Amanullah, A., Aslam, A., Raza, F., Arzoo, S., Qureshi, I. W., Waheed, H., Jabeen, N., Shabbir, S., Sayeed, M. A., et al. (2022) · Polymers · doi:10.3390/polym14163263 · Cited by 8
Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants
Nörz, D. S., Grunwald, M., Tang, H. T., Weinschenk, C., Günther, T., Robitaille, A., Giersch, K., Fischer, N., Grundhoff, A. T., Aepfelbacher, M., et al. (2022) · Viruses · doi:10.3390/v14030608 · Cited by 7
The Emergence of SARS-CoV-2 Variants With a Lower Antibody Response: A Genomic and Clinical Perspective
Biswas, S., Mahmud, S., Mita, M. A., Afrose, S., Hasan, M. R., Paul, G. K., Shimu, M. S. S., Uddin, M. S., Zaman, S., Park, M. N., et al. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.825245 · Cited by 6
The Infectivity and Antigenicity of Epidemic SARS-CoV-2 Variants in the United KingdomPreprint
Wang, Y., Wu, J., Zhang, L., Zhang, Y., Wang, H., Ding, R., Nie, J., Li, Q., Liu, S., Yu, Y., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-153108/v1 · Cited by 7
Immunodominant B cell epitope in a hotspot mutation site and mechanism of immune escape for SARS-CoV-2Preprint
Oliveira, J. R., Machado, R. R. G., Arcuri, H. A., Magawa, J. Y., Daher, I. P., Urbanski, A. H., Schmitz, G. J. H., Silva, R. C. V., Durigon, E. L., Boscardin, S. B., et al. (2021) · medRxiv · doi:10.1101/2021.03.11.21253399 · Cited by 6
Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants that merit monitoringPreprint
Garushyants, S. K., Rogozin, I. B., & Koonin, E. V. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.23.441209 · Cited by 8
Herbal Compounds Dauricine and Isoliensinine Impede SARS-CoV-2 Viral Entry
Dabrell, S. N., Li, Y., Yamaguchi, H., Chen, H., & Hung, M. (2023) · Biomedicines · doi:10.3390/biomedicines11112914 · Cited by 6
Forecasting SARS-CoV-2 spike protein evolution from small data by deep learning and regression
King, S. B., Chen, X. E., Ng, S. W. S., Rostin, K., Hahn, S. V., Roberts, T., Schwab, J. C., Sekhon, P., Kagieva, M., Reilly, T., et al. (2024) · Frontiers in Systems Biology · doi:10.3389/fsysb.2024.1284668 · Cited by 7
Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs
Pontes, C. F. T., Ruiz‐Serra, V., Lepore, R., & Valencia, A. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.01.006 · Cited by 6
COVID-19 variants as moving targets and how to stop them by glycoengineered whole-virus vaccines
Galili, U. (2021) · Virulence · doi:10.1080/21505594.2021.1939924 · Cited by 6
Appraisal of SARS-CoV-2 mutations and their impact on vaccination efficacy: an overview
Hadizadeh, N., Naderi, M., Khezri, J., Yazdani, M., Shamsara, M., & Hashemi, E. (2022) · Journal of Diabetes & Metabolic Disorders · doi:10.1007/s40200-022-01002-6 · Cited by 7
Genomic epidemiology and emergence of SARS-CoV-2 variants of concern in the United Arab Emirates
AlSafar, H. S., Albreiki, M. S., Mousa, M., Azman, S. K., Vurivi, H., Waasia, F. Z., Ruta, D., Hosani, F. I. A., Mazrouei, S. A., Abuyadek, R. M., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-16967-w · Cited by 6
Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021
Khamadi, S. A., Opanda, S. M., Symekher, S. L., Konongoi, S. L., Langat, S. K., Cirindi, J., Mwangi, M., Mwikwabe, N. M., Okeyo, S., Koskei, E., et al. (2022) · Virology Journal · doi:10.1186/s12985-022-01895-y · Cited by 6
Cross-immunity against SARS-COV-2 variants of concern in naturally infected critically ill COVID-19 patients
Fraser, D. D., Patel, M. A., Nynatten, L. R. V., Martin, C. M., Seney, S. L., Miller, M. R., Daley, M., Slessarev, M., Cepinskas, G., Juneja, G. K., et al. (2022) · Heliyon · doi:10.1016/j.heliyon.2022.e12704 · Cited by 6
Mapping the Lipid Signatures in COVID-19 Infection: Diagnostic and Therapeutic Solutions
Dasgupta, A., Gangai, S., Narayan, R., & Kapoor, S. (2023) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.3c01238 · Cited by 6
Pathogen‐binding nanoparticles to inhibit host cell infection by heparan sulfate and sialic acid dependent viruses and protozoan parasites
Najer, A. (2024) · Smart Medicine · doi:10.1002/smmd.20230046 · Cited by 7
Variation in structural motifs within SARS-related coronavirus spike proteins
Hills, F. R., Eruera, A.-R., Hodgkinson‐Bean, J., Jorge, F., Easingwood, R. A., Brown, S. H. J., Bouwer, J. C., Li, Y., Burga, L. N., & Bostina, M. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012158 · Cited by 6
Antibody screening at reduced pH enables preferential selection of potently neutralizing antibodies targeting SARS‐CoV ‐2
Madan, B., Reddem, E. R., Wang, P., Casner, R. G., Nair, M. S., Huang, Y., Fahad, A. S., de Souza, M. O., Banach, B. B., Acevedo, S. N. L., et al. (2021) · AIChE Journal · doi:10.1002/aic.17440 · Cited by 6
Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia
Malune, P., Piras, G., Monne, M. I., Fiamma, M., Asproni, R., Fancello, T., Manai, A. L., Carta, F., Pira, G., Fancello, P., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.827799 · Cited by 6
Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2
Khalaf, R. A., Bernasconi, A., Pinoli, P., & Ceri, S. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.07.051 · Cited by 5
SARS-CoV-2 Mutations, Diagnosis and Their Concern
Artik, Y., Cesur, N. P., & Laçin, N. T. (2022) · Archives of Molecular Biology and Genetics · doi:10.33696/genetics.1.008 · Cited by 6
Development of highly potent non-covalent inhibitors of SARS-CoV-2 3CLproPreprint
Hou, N., Shuai, L., Zhang, L., Xie, X., Tang, K., Zhu, Y., Yin, Y., Zhang, W., Tan, Q., Zhong, G., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.10.503531 · Cited by 6
Evidence of SARS-CoV-2 convergent evolution in immunosuppressed patients treated with antiviral therapies
Feng, S., Reid, G., Clark, N. M., Harrington, A., Uprichard, S. L., & Baker, S. C. (2024) · Virology Journal · doi:10.1186/s12985-024-02378-y · Cited by 5
Advancements in the Development of Anti-SARS-CoV-2 Therapeutics
Huang, J., Ma, Q., Su, Z., & Cheng, X. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms251910820 · Cited by 5
The chimera of S1 and N proteins of SARS-CoV-2: can it be a potential vaccine candidate for COVID-19?
Kumar, A., Ladha, A., Choudhury, A., Ikbal, A. M. A., Bhattacharjee, B., Das, T., Gupta, G., Sharma, C., Sarbajna, A., Mandal, S. C., et al. (2022) · Expert Review of Vaccines · doi:10.1080/14760584.2022.2081156 · Cited by 5
Mapping of SARS-CoV-2 Spike Protein Evolution During the First and Second Waves of COVID-19 Infections in India
Rajpal, V. R., Sharma, S., Kumar, A., Vaishnavi, S., Singh, A., Sehgal, D., Tiwari, M., Goel, S., & Raina, S. N. (2022) · Future Virology · doi:10.2217/fvl-2021-0267 · Cited by 5
ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes
Alisoltani, A., Jaroszewski, L., Godzik, A., Iranzadeh, A., Simons, L. M., Dean, T. J., Lorenzo-Redondo, R., Hultquist, J., & Ozer, E. A. (2022) · Viruses · doi:10.3390/v14122714 · Cited by 5
Predicting spike protein NTD mutations of SARS-CoV-2 causing immune evasion by molecular dynamics simulations
Zhou, L., Wu, L., Peng, C., Yang, Y., Shi, Y., Gong, L., Xu, Z., & Zhu, W. (2022) · Physical Chemistry Chemical Physics · doi:10.1039/d1cp05059a · Cited by 6
Host–pathogen dynamics in longitudinal clinical specimens from patients with COVID-19
Lin, M. J., Rachleff, V. M., Xie, H. J., Shrestha, L., Lieberman, N. A. P., Peddu, V., Addetia, A., Casto, A. M., Breit, N., Mathias, P. C., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-09752-2 · Cited by 6
Mutational induction in SARS-CoV-2 major lineages by experimental exposure to neutralising sera
Brandolini, M., Dirani, G., Taddei, F., Zannoli, S., Denicolò, A., Arfilli, V., Battisti, A., Manera, M., Mancini, A., Grumiro, L., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-16533-4 · Cited by 5
Structural patterns of SARS-CoV-2 variants of concern (alpha, beta, gamma, delta) spike protein are influenced by variant-specific amino acid mutations: A computational study with implications on viral evolution
Cueno, M. E., Wada, K., Tsuji, A., Ishikawa, K., & Imai, K. (2022) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2022.111376 · Cited by 5
Effect of An 84-bp Deletion of the Receptor-Binding Domain on the ACE2 Binding Affinity of the SARS-CoV-2 Spike Protein: An In Silico Analysis
Kemenesi, G., Tóth, G. E., Bajusz, D., Keserű, G. M., Terhes, G., Burián, K., Zeghbib, S., Somogyi, B. A., & Jakab, F. (2021) · Genes · doi:10.3390/genes12020194 · Cited by 5
COVID‐19 vaccination in pediatric solid organ transplant recipients—Current state and future directions
L’Huillier, A. G., Ardura, M. I., Chaudhuri, A., Danziger‐Isakov, L. A., Dulek, D. E., Green, M., Michaels, M. G., Posfay-Barbe, K. M., Vásquez, L., & Benden, C. (2021) · Pediatric Transplantation · doi:10.1111/petr.14031 · Cited by 5
Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants of potential concernPreprint
Garushyants, S., Rogozin, I. B., & Koonin, E. V. (2021) · Research Square · doi:10.21203/rs.3.rs-456574/v1 · Cited by 5
Chronic Asymptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in the Immunocompromised Patient: New Challenges and Urgent Needs
Lodi, L., Moriondo, M., Pucci, A., Pisano, L., Ricci, S., Indolfi, G., & Azzari, C. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab538 · Cited by 5
A SARS-CoV-2 mini-genome assay based on negative-sense RNA to study replication inhibitors and emerging mutationsPreprint
Vial, T., Oade, M. S., Russell, C. A., Eggink, D., & Velthuis, A. J. W. T. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.28.450211 · Cited by 5

Authors: McCarthy, K. R., Rennick, L. J., Nambulli, S., Robinson-McCarthy, L. R., Bain, W. G., Haidar, G., & Duprex, W. P.
Affiliations: Boston Children's Hospital (US)
University of Pittsburgh (US)
Department of Genetics, Harvard Medical School, Boston, MA, USA.
Corresponding author: McCarthy, Kevin R.
Duprex, W. Paul
ORCID: McCarthy, Kevin R.
Rennick, Linda J.
Nambulli, Sham
Robinson-McCarthy, Lindsey R.
Bain, William G.
Haidar, Ghady
Duprex, W. Paul
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2021-03-12
Volume: 371
Issue: 6534
Pages: 1139-1142
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.abf6950
PMC: PMC7971772
OpenAlex: W3127143267
Cited by: 535
References: 33
Citations by year: 2026: 12 · 2025: 24 · 2024: 42 · 2023: 66 · 2022: 173 · 2021: 216
FWCI: 39.43
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: Science (publishedVersion, cc-by)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Science
Funders: U.S. Department of Veterans Affairs (IK2 BX004886)
Richard King Mellon Foundation
Hillman Foundation
UPMC Immune Transplant and Therapy Center
The Center for Vaccine Research
The University of Pittsburgh
Topics: Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
Keywords: SARS-CoV-2, spike protein, recurrent deletions, antibody escape, neutralizing antibodies, antigenic evolution, adaptive evolution, immune evasion, viral evolution, zoonotic spillover
MeSH terms: COVID-19, SARS-CoV-2, Amino Acid Sequence, Antibodies, Viral, Antigens, Viral, Humans, Protein Conformation, Sequence Deletion, Evolution, Molecular, Amino Acid Substitution, Genetic Drift, Immune Evasion, Antibodies, Neutralizing, 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

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks