Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies

Tada, Takuya; Dcosta, Belinda M.; Samanovic-Golden, Marie; Herati, Ramin S.; Cornelius, Amber; Mulligan, Mark J.; Landau, Nathaniel R.

doi:10.1101/2021.02.05.430003

PreprintCited by 153SARS-CoV-2 and COVID-19 ResearchAnimal Virus Infections Studiesvaccines and immunoinformatics approaches

Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies

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Tada, Takuya, Dcosta, Belinda M., Samanovic-Golden, Marie, Herati, Ramin S., Cornelius, Amber, Mulligan, Mark J., Landau, Nathaniel R.·2021·mBio

DOI 10.1101/2021.02.05.430003PMC PMC7872356

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Abstract

The increasing prevalence of SARS-CoV-2 variants with mutations in the spike protein has raised concerns that recovered individuals may not be protected from reinfection and that current vaccines will become less effective. The B.1.1.7 isolate identified in the United Kingdom and B.1.351 isolate identified in the Republic of South Africa encode spike proteins with multiple mutations in the S1 and S2 subunits. In addition, variants have been identified in Columbus, Ohio (COH.20G/677H), Europe (20A.EU2) and in domesticated minks. Analysis by antibody neutralization of pseudotyped viruses showed that convalescent sera from patients infected prior to the emergence of the variant viruses neutralized viruses with the B.1.1.7, B.1.351, COH.20G/677H Columbus Ohio, 20A.EU2 Europe and mink cluster 5 spike proteins with only a minor decrease in titer compared to that of the earlier D614G spike protein. Serum specimens from individuals vaccinated with the BNT162b2 mRNA vaccine neutralized D614G virus with titers that were on average 7-fold greater than convalescent sera. Vaccine elicited antibodies neutralized virus with the B.1.1.7 spike protein with titers similar to D614G virus and neutralized virus with the B.1.351 spike with, on average, a 3-fold reduction in titer (1:500), a titer that was still higher than the average titer with which convalescent sera neutralized D614G (1:139). The reduction in titer was attributable to the E484K mutation in the RBD. The B.1.1.7 and B.1.351 viruses were not more infectious than D614G on ACE2.293T cells in vitro but N501Y, an ACE2 contacting residue present in the B.1.1.7, B.1.351 and COH.20G/677H spike proteins caused higher affinity binding to ACE2, likely contributing to their increased transmissibility. These findings suggest that antibodies elicited by primary infection and by the BNT162b2 mRNA vaccine are likely to maintain protective efficacy against B.1.1.7 and most other variants but that the partial resistance of virus with the B.1.351 spike protein could render some individuals less well protected, supporting a rationale for the development of modified vaccines containing E484K.

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The 10.3-12.4-fold loss of activity against B.1.351 is larger than reported results using mutant pseudoviruses.
“On the other hand, the loss in activity by 10.3-12.4-foldagainst B.1.351 is larger than results that were reported using mutant pseudoviruses 34,42,43 .”
From Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 (2021) · cites this paper as [43]
The E484K mutation appears to result in a lower neutralising ability of mRNA vaccine sera.
“The E484K mutation appears to result in a lower neutralising ability of mRNA vaccine sera.48”
From Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial (2021) · cites this paper as [48]

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A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses
Tauzin, A., Nayrac, M., Benlarbi, M., Gong, S. Y., Gasser, R., Beaudoin-Bussières, G., Brassard, N., Laumaea, A., Vézina, D., Prévost, J., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.06.001 · Cited by 187 · see citing works
“, 2021) and confers resistance to neutralization mediated by monoclonal antibodies (mAbs) and plasma from naturally infected and vaccinated individuals (Ku et al., 2021; Stamatatos et al., 2021; Tada et al., 2021; Wang et al., 2021).”
Antibody Response to the BNT162b2 mRNA COVID-19 Vaccine in Subjects with Prior SARS-CoV-2 Infection
Gobbi, F. G., Buonfrate, D., Moro, L., Rodari, P., Piubelli, C., Caldrer, S., Riccetti, S., Sinigaglia, A., & Barzon, L. (2021) · Viruses · doi:10.3390/v13030422 · Cited by 178 · see citing works
Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy
Ramesh, S., Govindarajulu, M., Parise, R. S., Neel, L. T., Shankar, T., Patel, S., Lowery, P., Smith, F., Dhanasekaran, M., & Moore, T. (2021) · Vaccines · doi:10.3390/vaccines9101195 · Cited by 152 · see citing works
Neutralising antibody escape of SARS‐CoV‐2 spike protein: Risk assessment for antibody‐based Covid‐19 therapeutics and vaccines
Focosi, D., & Maggi, F. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2231 · Cited by 148 · see citing works
An intranasal vaccine durably protects against SARS-CoV-2 variants in mice
Hassan, A. O., Shrihari, S., Gorman, M. J., Ying, B., Yuan, D., Raju, S., Chen, R. E., Dmitriev, I. P., Kashentseva, E. A., Adams, L. J., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109452 · Cited by 129 · see citing works
Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis
Thye, A. Y.-K., Law, J. W., Pusparajah, P., Letchumanan, V., Chan, K., & Lee, L. (2021) · Biomedicines · doi:10.3390/biomedicines9101303 · Cited by 116 · see citing works
“351, greater than those using mutant pseudoviruses [71,79,150].”
Background
Partial resistance of SARS-CoV-2 Delta variants to vaccine-elicited antibodies and convalescent sera
Tada, T., Zhou, H., Dcosta, B. M., Samanovic, M. I., Mulligan, M. J., & Landau, N. R. (2021) · iScience · doi:10.1016/j.isci.2021.103341 · Cited by 101 · see citing works
Self-citation
Comparison of Neutralizing Antibody Titers Elicited by mRNA and Adenoviral Vector Vaccine against SARS-CoV-2 Variants
Tada, T., Zhou, H., Samanovic, M., et al. (2021) · bioRxiv · doi:10.1101/2021.07.19.452771 · Cited by 97 · see citing works
Self-citation
Variant SARS-CoV-2 mRNA vaccines confer broad neutralization as primary or booster series in mice
(2021) · doi:10.1016/j.vaccine.2021.11.001 · Cited by 101 · see citing works
Decreased neutralization of SARS-CoV-2 global variants by therapeutic anti-spike protein monoclonal antibodiesPreprint
Tada, T., Dcosta, B. M., Zhou, H., Vaill, A., Kazmierski, W., & Landau, N. R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.18.431897 · Cited by 59 · see citing works
Self-citation
Potency of BNT162b2 and mRNA‐1273 vaccine‐induced neutralizing antibodies against severe acute respiratory syndrome‐CoV‐2 variants of concern: A systematic review of in vitro studies
Noori, M., Nejadghaderi, S. A., Arshi, S., Carson‐Chahhoud, K., Ansarin, K., Kolahi, A., & Safiri, S. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2277 · Cited by 64 · see citing works
mRNA vaccines: Past, present, future
Karam, M., & Daoud, G. (2022) · Asian Journal of Pharmaceutical Sciences · doi:10.1016/j.ajps.2022.05.003 · Cited by 74 · see citing works
“Xie et al. engineered 3 SARS-CoV-2 viruses containing key spike mutations from the United Kingdom and South African variants: N501Y; 69/70-deletion + N501Y + D614G; and E484K + N501Y + D614G.”
BackgroundInfluential
The Spike Proteins of SARS-CoV-2 B.1.617 and B.1.618 Variants Identified in India Provide Partial Resistance to Vaccine-elicited and Therapeutic Monoclonal Antibodies
Tada, T., Zhou, H., Dcosta, B. M., Samanovic, M. I., Mulligan, M. J., & Landau, N. R. (2021) · doi:10.1101/2021.05.14.444076 · Cited by 101 · see citing works
“293T cells relative to that 144 of virus with the D614G mutation, an assay that we have used previously to analyze 145 variant spike protein affinity [11].”
Self-citation
B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies
Zhou, H., Dcosta, B. M., Samanovic, M. I., Mulligan, M. J., Landau, N. R., & Tada, T. (2021) · mBio · doi:10.1128/mbio.01386-21 · Cited by 68 · see citing works
“351 variant spike protein has been found to reduce the level of protection provided by vaccination in populations in which the variant has become prevalent (17, 20).”
BackgroundSelf-citation
Molecular Aspects Concerning the Use of the SARS-CoV‑2 Receptor Binding Domain as a Target for Preventive Vaccines
Valdés-Balbín, Y., Santana-Mederos, D., Paquet, F., Fernández-Castillo, S., Climent, Y., Chiodo, F., Rodríguez, L., Ramírez, B. S., León, K., Hernández, T., et al. (2021) · ACS Central Science · doi:10.1021/acscentsci.1c00216 · Cited by 53 · see citing works
An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by several therapeutic monoclonal antibodies
VanBlargan, L., Errico, J., Halfmann, P., et al. (2021) · bioRxiv · doi:10.1101/2021.12.15.472828 · Cited by 59
“529 isolates with R346K mutations may be 172 warranted if the substitution becomes more prevalent; (4) Our data is derived from experiments 173”
Method
mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates
Corbett, K. S., Werner, A. P., Connell, S. O., Gagné, M., Lai, L., Moliva, J. I., Flynn, B. J., Choi, A., Koch, M., Foulds, K. E., et al. (2021) · Nature Immunology · doi:10.1038/s41590-021-01021-0 · Cited by 53 · see citing works
SARS-CoV-2 Lambda Variant Remains Susceptible to Neutralization by mRNA Vaccine-elicited Antibodies and Convalescent SerumPreprint
Tada, T., Zhou, H., Dcosta, B. M., Samanovic, M. I., Mulligan, M. J., & Landau, N. R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.02.450959 · Cited by 51 · see citing works
Self-citation
The ins and outs of SARS-CoV-2 variants of concern (VOCs)
Salehi-Vaziri, ‪., Fazlalipour, M., Khorrami, S. M. S., Azadmanesh, K., Pouriayevali, M. H., Jalali, T., Shoja, Z., & Maleki, A. (2022) · Archives of Virology · doi:10.1007/s00705-022-05365-2 · Cited by 58 · see citing works
“A deletion at positions 69 and 70 of the spike protein (Δ69–70), which is associated with diagnostic realtime PCR failure (S gene target failure: SGTF), has been reported to be a marker for the Alpha variant, which was given the name VOC 202012/01 by Public Health England (PHE) [23, 24].”
Background
Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B
Liu, J., Budylowski, P., Samson, R., Griffin, B. D., Babuadze, G., Rathod, B., Colwill, K., Abioye, J. A., Schwartz, J. A., Law, R., et al. (2022) · Science Advances · doi:10.1126/sciadv.abj9815 · Cited by 56 · see citing works
An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination statusPreprint
Lumley, S., Rodger, G., Constantinides, B., Sanderson, N., Chau, K. K., Street, T. L., O’Donnell, D., Howarth, A., Hatch, S. B., Marsden, B. D., et al. (2021) · medRxiv · doi:10.1101/2021.03.09.21253218 · Cited by 48 · see citing works
An Observational Cohort Study on the Incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and B.1.1.7 Variant Infection in Healthcare Workers by Antibody and Vaccination Status
Lumley, S., Rodger, G., Constantinides, B., Sanderson, N. D., Chau, K., Street, T. L., O’Donnell, D., Howarth, A., Hatch, S. B., Marsden, B. D., et al. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab608 · Cited by 70 · see citing works
The evolutionary dynamics of endemic human coronaviruses
Jo, W. K., Drosten, C., & Drexler, J. F. (2021) · Virus Evolution · doi:10.1093/ve/veab020 · Cited by 57 · see citing works
Development and preclinical evaluation of virus‐like particle vaccine against COVID‐19 infection
Yilmaz, I. C., İpekoğlu, E. M., Bulbul, A., Turay, N., Yıldırım, M., Evcili, İ., Yilmaz, N. S., Guvencli, N., Aydin, Y., Gungor, B., et al. (2021) · Allergy · doi:10.1111/all.15091 · Cited by 59 · see citing works
Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B
Liu, J., Budylowski, P., Samson, R., Griffin, B., Babuadze, G., Rathod, B., Colwill, K., Abioye, J., Schwartz, J., Law, R., et al. (2021) · bioRxiv · doi:10.1101/2021.05.11.443286 · Cited by 51 · see citing works
Protective roles and protective mechanisms of neutralizing antibodies against SARS-CoV-2 infection and their potential clinical implications
Abebe, E. C., & Dejenie, T. A. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1055457 · Cited by 56 · see citing works
SARS-CoV-2 variants and effectiveness of vaccines: a review of current evidence
Tatsi, E., Filippatos, F., & Michos, A. G. (2021) · Epidemiology and Infection · doi:10.1017/s0950268821002430 · Cited by 63 · see citing works
“351 compared to those with wild-type virus, but still more enhanced than titres in convalescent individuals infected by wild-type virus [78].”
Result
Protective activity of mRNA vaccines against ancestral and variant SARS-CoV-2 strains
Ying, B.-L., Whitener, B. M., VanBlargan, L., et al. (2021) · bioRxiv · doi:10.1101/2021.08.25.457693 · Cited by 45 · see citing works
Physicochemical effect of the N501Y, E484K/Q, K417N/T, L452R and T478K mutations on the SARS-CoV-2 spike protein RBD and its influence on agent fitness and on attributes developed by emerging variants of concern
Pondé, R. A. D. A. (2022) · Virology · doi:10.1016/j.virol.2022.05.003 · Cited by 52 · see citing works
Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccinationPreprint
Suryawanshi, R., Chen, I. P., Ma, T., Syed, A. M., Simoneau, C., Ciling, A., Khalid, M., Sreekumar, B., Chen, P.-Y., George, A. F., et al. (2022) · medRxiv · doi:10.1101/2022.01.13.22269243 · Cited by 45 · see citing works
Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern
Long, S. W., Olsen, R. J., Christensen, P. A., Subedi, S., Olson, R., Davis, J. J., Saavedra, M. O., Yerramilli, P., Pruitt, L., Reppond, K., et al. (2021) · American Journal Of Pathology · doi:10.1016/j.ajpath.2021.03.004 · Cited by 46 · see citing works
Protective activity of mRNA vaccines against ancestral and variant SARS-CoV-2 strains
Ying, B., Whitener, B., VanBlargan, L. A., Hassan, A. O., Shrihari, S., Liang, C.-Y., Karl, C. E., Mackin, S., Chen, R. E., Kafai, N. M., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abm3302 · Cited by 85 · see citing works
Resistance of SARS-CoV-2 variants to neutralization by antibodies induced in convalescent patients with COVID-19
Kaku, Y., Kuwata, T., Zahid, H. M., Hashiguchi, T., Noda, T., Kuramoto, N., Biswas, S., Matsumoto, K., Shimizu, M., Kawanami, Y., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109385 · Cited by 26 · see citing works
“Mink cluster 5 was neutralized by plasma samples from convalescent patients at the same level as prototypic SARS-CoV-2, as reported previously (Tada et al., 2021; Wu et al., 2021).”
A single BNT162b2 mRNA dose elicits antibodies with Fc-mediated effector functions and boost pre-existing humoral and T cell responsesPreprint
Tauzin, A., Nayrac, M., Benlarbi, M., Gong, S. Y., Gasser, R., Beaudoin-Bussières, G., Brassard, N., Laumaea, A., Vézina, D., Prévost, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.18.435972 · Cited by 41 · see citing works
Immunogenic and efficacious SARS-CoV-2 vaccine based on resistin-trimerized spike antigen SmT1 and SLA archaeosome adjuvant
Akache, B., Renner, T. M., Tran, A., Deschatelets, L., Dudani, R., Harrison, B. A., Duque, D., Haukenfrers, J., Rossotti, M. A., Gaudreault, F., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-01363-7 · Cited by 41 · see citing works
B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies
(2021) · doi:10.1101/2021.03.24.436620 · Cited by 68 · see citing works
“351 which also bears the mutation [24-28, 32-34].”
BackgroundSelf-citation
SARS-CoV-2 Variants: A Synopsis of In Vitro Efficacy Data of Convalescent Plasma, Currently Marketed Vaccines, and Monoclonal Antibodies
Focosi, D., Tuccori, M., Baj, A., & Maggi, F. (2021) · Viruses · doi:10.3390/v13071211 · Cited by 37 · see citing works
Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern
Voss, C., Esmail, S., Liu, X., Knauer, M. J., Ackloo, S. Z., Kaneko, T., Lowes, L. E., Stogios, P. J., Seitova, A., Hutchinson, A., et al. (2021) · JCI Insight · doi:10.1172/jci.insight.148855 · Cited by 53 · see citing works
“While it has been shown that mutations result in more fit, and likely more contagious, viruses (15, 16, 40), the serological consequences of the mutations found in VOCs are unclear (40).”
Influential
Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests
Rodgers, M. A., Batra, R., Snell, L., et al. (2021) · medRxiv · doi:10.1101/2021.04.24.21256045 · Cited by 36
“1 lineages that have been 136 linked to increased transmissibility and immune escape [1-7].”
Reduced antibody activity against SARS-CoV-2 B.1.617.2 delta virus in serum of mRNA-vaccinated individuals receiving tumor necrosis factor-α inhibitors
Chen, R. E., Gorman, M. J., Zhu, D. Y., Carreño, J. M., Yuan, D., VanBlargan, L. A., Burdess, S., Lauffenburger, D. A., Kim, W., Turner, J. S., et al. (2021) · Med · doi:10.1016/j.medj.2021.11.004 · Cited by 36 · see citing works
Immunodominant linear B cell epitopes in the spike and membrane proteins of SARS-CoV-2 identified by immunoinformatics prediction and immunoassay
Polyiam, K., Phoolcharoen, W., Butkhot, N., Srisaowakarn, C., Thitithanyanont, A., Auewarakul, P., Hoonsuwan, T., Ruengjitchatchawalya, M., Mekvichitsaeng, P., & Roshorm, Y. M. (2021) · Scientific Reports · doi:10.1038/s41598-021-99642-w · Cited by 35 · see citing works
SARS-CoV-2 protein subunit vaccination of mice and rhesus macaques elicits potent and durable neutralizing antibody responses
Mandolesi, M., Sheward, D., Hanke, L., Ma, J.-J., Pushparaj, P., Vidakovics, L. P., Kim, C., Ádori, M., Lenart, K., Loré, K., et al. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100252 · Cited by 32 · see citing works
Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2Preprint
Dicken, S. J., Murray, M. J., Thorne, L., Reuschl, A., Forrest, C., Ganeshalingham, M., Muir, L., Kalemera, M. D., Palor, M., McCoy, L. E., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.22.436468 · Cited by 30 · see citing works
“However, we used a limited panel of antibodies and we note that many other reports demonstrate that B.1.1.7 does not escape neutralisation by the majority of COVID-19 patient serum or human mAbs (2, 11, 22, 44–46).”
BackgroundMethodInfluential
The Emergence and Spread of Novel SARS-CoV-2 Variants
Yi, H., Wang, J., Wang, J., Lu, Y., Zhang, Y., Peng, R., Lu, J., & Chen, Z. (2021) · Frontiers in Public Health · doi:10.3389/fpubh.2021.696664 · Cited by 28 · see citing works
“Three mutations in S gene of these mutations have potential biological effects: First, mutation N501Y is located in the receptor-binding motif (RBM), one of the six key contact residues within the receptor-binding domain (RBD), and has been identified to enhance the affinity of the virus to ACE2 (20, 21).”
BackgroundInfluential
Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations
Showers, W. M., Leach, S. M., Kechris, K., & Strong, M. (2021) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2021.105153 · Cited by 26 · see citing works
Evolution of Antiviral Drug Resistance in SARS-CoV-2
Dinata, R., Baindara, P., & Mandal, S. M. (2025) · Viruses · doi:10.3390/v17050722 · Cited by 29 · see citing works
“It has been observed that activity loss of convalescent sera and vaccine-elicited antibodies against B.1.351 is higher than the results reported using mutant pseudoviruses [70,71].”
Influential
An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern
Morris, C. P., Luo, C. H., Amadi, A., Schwartz, M. C., Gallagher, N., Ray, S. C., Pekosz, A. S., & Mostafa, H. H. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab636 · Cited by 23 · see citing works
Optimised non-coding regions of mRNA SARS-CoV-2 vaccine CV2CoV improves homogeneous and heterogenous neutralising antibody responses
Roth, N., Schön, J., Hoffmann, D., Thran, M., Thess, A., Mueller, S. O., Petsch, B., & Rauch, S. (2021) · doi:10.1101/2021.05.13.443734 · Cited by 18 · see citing works
The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom
Wu, J., Zhang, L., Zhang, Y., Wang, H., Ding, R., Nie, J., Li, Q., Liu, S., Yu, Y., Yang, X., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.687869 · Cited by 22 · see citing works
The challenge of emerging SARS-CoV-2 mutants to vaccine development
Li, R., Liu, J., & Zhang, H. (2021) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2021.03.001 · Cited by 24 · see citing works
Molecular variants of SARS-CoV-2: antigenic properties and current vaccine efficacy
Damavandi, A. R., Dowran, R., Sharif, S. A., Kashanchi, F., & Jafari, R. (2022) · Medical Microbiology and Immunology · doi:10.1007/s00430-022-00729-6 · Cited by 21 · see citing works
Facing the wrath of enigmatic mutations: a review on the emergence of severe acute respiratory syndrome coronavirus 2 variants amid coronavirus disease‐19 pandemic
Chadha, J., Khullar, L., & Mittal, N. (2021) · Environmental Microbiology · doi:10.1111/1462-2920.15687 · Cited by 32 · see citing works
“In a similar context, the E484K mutation in B.1.351 variant (VOC) has been shown to lower the protective efficacy of the BNT162b2 mRNA vaccine (Pfizer) in populations with a prevalence of B.1.351 variant (Tada et al., 2021).”
BackgroundInfluential
Neutralizing Antibodies Against SARS-CoV-2 Variants Induced by Natural Infection or Vaccination: A Systematic Review and Individual Data Meta-AnalysisPreprint
Chen, X., Chen, Z., Azman, A. S., Sun, R., Lu, W., Zheng, N., Zhou, J., Wu, Q., Deng, X., Zhao, Z., et al. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3858816 · Cited by 11 · see citing works
Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays
Virtanen, J. M. E., Uusitalo, R., Korhonen, E. M., Aaltonen, K., Smura, T., Kuivanen, S. H., Pakkanen, S. H., Mero, S., Patjas, A., Riekkinen, M., et al. (2021) · Viruses · doi:10.3390/v13060996 · Cited by 24 · see citing works
“7) or the older dominant strains, including studies in vaccinees [5,8,11,13,26,27].”
Background
Efficacy and Safety of COVID-19 Vaccines—An Update
Sharma, E., Revinipati, S., Bhandari, S., Thakur, S., Goyal, S., Ghose, A., Bajpai, S., Muhammad, W., & Boussios, S. (2022) · Diseases · doi:10.3390/diseases10040112 · Cited by 15 · see citing works
“Serum samples of vaccinated individuals neutralized D164G strain with seven-fold raised antibody titer than convalescent serum [33].”
Evaluation of mRNA-1273 against SARS-CoV-2 B.1.351 Infection in Nonhuman PrimatesPreprint
Corbett, K. S., Werner, A. P., Connell, S. O., Gagné, M., Lai, L., Moliva, J. I., Flynn, B. J., Choi, A., Koch, M. J., Foulds, K. E., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.21.445189 · Cited by 11 · see citing works
Pre-Omicron Vaccine Breakthrough Infection Induces Superior Cross-Neutralization against SARS-CoV-2 Omicron BA.1 Compared to Infection Alone
da Silva, E. S., Kohnen, M., Gilson, G., Staub, T., Arendt, V., Hilger, C., Servais, J.-Y., Charpentier, É., Domingues, O., Snoeck, C. J., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23147675 · Cited by 12 · see citing works
Deep dissection of the antiviral immune profile of patients with COVID-19
Atanackovic, D., Avila, S. V., Lutfi, F. U., de Miguel‐Pérez, D., Fan, X., Sanchez‐Petitto, G., Mause, E. R. V., Siglin, J., Baddley, J. W., Mannuel, H. D., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-02852-1 · Cited by 10 · see citing works
Longitudinal variation in SARS-CoV-2 antibody levels and emergence of viral variants: implications for the ability of serological assays to predict immunityPreprint
Muecksch, F., Wise, H., Templeton, K., Batchelor, B., Squires, M., McCance, K., Jarvis, L., Malloy, K., Furrie, E., Richardson, C., et al. (2021) · medRxiv · doi:10.1101/2021.07.02.21259939 · Cited by 12 · see citing works
Serum Neutralizing Activity against B.1.1.7, B.1.351, and P.1 SARS-CoV-2 Variants of Concern in Hospitalized COVID-19 Patients
Trombetta, C. M., Marchi, S., Viviani, S., Manenti, A., Benincasa, L., Ruello, A., Bombardieri, E., Vicenti, I., Zazzi, M., & Montomoli, E. (2021) · Viruses · doi:10.3390/v13071347 · Cited by 14 · see citing works
“The immunoevasion could lead to reinfection of subjects who recovered from a previous infection [16] and could reduce the protection induced by vaccination and/or natural infection [27].”
BackgroundResult
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 · see citing works
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 · see citing works
“In contrast to British variant, other recently isolated spike protein mutant patterns (South African and Brazilian) seem to influence partially the effectiveness of the first generation v-mRNA vaccines in sub-groups of individuals that demonstrate a level or resistance (Tada et al., 2021).”
Result
Detection of Mutations Associated with Variants of Concern Via High Throughput Sequencing of SARS-CoV-2 Isolated from NYC WastewaterPreprint
Smyth, D. S., Trujillo, M., Cheung, K., Gao, A., Hoxie, I., Kannoly, S., Kubota, N., Markman, M., San, K. M., Sompanya, G., et al. (2021) · medRxiv · doi:10.1101/2021.03.21.21253978 · Cited by 10 · see citing works
“Even more concerning are reports of decreased antibody59 mediated neutralization of these variants (7-9).”
Background
Atomistic insights into the binding of SARS-CoV-2 spike receptor binding domain with the human ACE2 receptor: The importance of residue 493
Carter, C., Airas, J., & Parish, C. A. (2022) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2022.108360 · Cited by 10 · see citing works
A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivoPreprint
Hanke, L., Das, H., Sheward, D. J., Vidakovics, L. P., Urgard, E., Moliner-Morro, A., Kim, C., Karl, V., Pankow, A. P., Smith, N. L., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.20.436243 · Cited by 5 · see citing works
Spike-directed vaccination elicits robust spike-specific T-cell response, including to mutant strains
Stanojevic, M., Geiger, A. E., Ostermeier, B., Sohai, D. K., Lazarski, C. A., Lang, H., Jensen-Wachspress, M. A., Webber, K., Burbelo, P. D., Cohen, J. I., et al. (2021) · Cytotherapy · doi:10.1016/j.jcyt.2021.07.006 · Cited by 9 · see citing works
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 · see citing works
“Some of these second-wave Spike mutations seem to confer partial neutralization resistance, as measured in in vitro assays with convalescent or vaccine sera [292-297].”
Background
High Seroprevalence of Anti-SARS-CoV-2 IgM/IgG among Inhabitants of Sakaka City, Aljouf, Saudi Arabia
Taha, A. E., Alduraywish, A. A., Almaeen, A. H., El‐Metwally, T. H., Alayyaf, M., Mallick, A., & Abouelkheir, M. M. (2022) · Vaccines · doi:10.3390/vaccines11010026 · Cited by 6 · see citing works
Neutralization Heterogeneity of Circulating SARS-CoV-2 Variants to Sera Elicited by a Vaccinee or Convalescent
Zhang, M., Gong, Y., & Jiao, S. (2022) · Future Virology · doi:10.2217/fvl-2021-0100 · Cited by 7 · see citing works
“Beta is more worrisome when compared with Alpha in that it is not only refractory to neutralization by most NTD antibodies and multiple RBD antibodies [20,48] but also exhibits varying degrees of resistance to convalescent serum and vaccine-elicited antibodies [20,31,65,66,70,72,73].”
Background
COVID-19 Cases from the First Local Outbreak of the SARS-CoV-2 B.1.1.7 Variant in China May Present More Serious Clinical Features: A Prospective, Comparative Cohort Study
Song, Y., Ge, Z., Cui, S., Tian, D., Wan, G., Zhu, S., Wang, X., Wang, Y., Zhao, X., Xiang, P., et al. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00273-21 · Cited by 12 · see citing works
In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains
Diamond, M. S., Chen, R. E., Winkler, E. S., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-448370/v1 · Cited by 6
Passive Immunity Should and Will Work for COVID-19 for Some Patients
Cimolai, N. (2021) · Clinical Hematology International · doi:10.2991/chi.k.210328.001 · Cited by 6 · see citing works
Reduced antibody activity against SARS-CoV-2 B.1.617.2 Delta virus in serum of mRNA-vaccinated patients receiving TNF-alpha inhibitors
Chen, R. E., Gorman, M., Zhu, D. Y., et al. (2021) · medRxiv · doi:10.1101/2021.09.28.21264250 · Cited by 5
“; https://doi.org/10.1101/2021.09.28.21264250doi: medRxiv preprint 13 L452, E484, and elsewhere (Chen et al., 2021b; McCallum et al., 2021; Tada et al., 2021; Wang 256 et al., 2021a; Wang et al., 2021b; Wibmer et al., 2021).”
Influential
Progressive Evolutionary Dynamics of Gene-Specific ω Led to the Emergence of Novel SARS-CoV-2 Strains Having Super-Infectivity and Virulence with Vaccine Neutralization
Maiti, A. K. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25126306 · Cited by 3 · see citing works
Antibodies Induced by Homologous or Heterologous Inactivated (CoronaVac/BBIBP-CorV) and Recombinant Protein Subunit Vaccines (ZF2001) Dramatically Enhanced Inhibitory Abilities against B.1.351, B.1.617.2, and B.1.1.529 Variants
Xu, X., Hong, Y., Chen, E., Wang, Y., Ma, B., Li, J., Su, W., Zhou, Y., & Zhang, M. (2022) · Vaccines · doi:10.3390/vaccines10122110 · Cited by 4 · see citing works
COVID-19 cases from the first local outbreak of SARS-CoV-2 B.1.1.7 variant in China presented more serious clinical features: a prospective, comparative cohort study
Song, Y., Ge, Z.-R., Cui, S., et al. (2021) · medRxiv · doi:10.1101/2021.05.04.21256655 · Cited by 4
“7 variant cases with non-variant cases, (1) there were more patients 315 with body temperature over 38°C; (2) the laboratory tests of the level of CRP, SAA, CK 316 and DD was significantly higher; (3) the abnormal proportion of CD4T was 317 significantly higher; (4) the patients that had ground glass opacity in the lu…”
Result
Epitope-resolved serology test differentiates the clinical outcome of COVID-19 and identifies defects in antibody response in SARS-CoV-2 variants
Voss, C., Esmail, S., Liu, X., et al. (2021) · medRxiv · doi:10.1101/2021.03.16.21253716 · Cited by 4
“This may explain why recent studies have shown the Pfizer and Moderna mRNA vaccines are effective in protecting from infection by the variant (37-39).”
Result
Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests
Rodgers, M. A., Olivo, A., Harris, B. J., Lark, C., Luo, X., Berg, M. G., Meyer, T. V., Mohaimani, A., Orf, G. S., Goldstein, D. Y., et al. (2022) · Journal of Clinical Virology · doi:10.1016/j.jcv.2022.105080 · Cited by 43 · see citing works
Multifactorial Traits of SARS-CoV-2 Cell Entry Related to Diverse Host Proteases and Proteins
You, J., Seok, J. H., Joo, M., Bae, J., Kim, J. I., Park, M., & Kim, K. (2021) · Biomolecules & Therapeutics · doi:10.4062/biomolther.2021.048 · Cited by 3 · see citing works
“An amino acid residue “R” is constantly exposed at the C-terminus of the S1/ S2 cleavage site by the host protease furin, commonly known as the C-end rule (CendR) (Teesalu et al., 2009).”
Review of: "Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera"
Banoun, H. (2021) · Qeios · doi:10.32388/hgi4le
Development of highly potent neutralising nanobodies against multiple SARS-CoV-2 variants including the variant of concern B.1.351Preprint
Sziemel, A. M., Hwa, S.-H., Sigal, A., Tyson, G. B., Logan, N. A., Willett, B. J., & Durcan, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.11.439360 · Cited by 2 · see citing works
SARS-CoV-2 spike RBD and nucleocapsid encoding DNA vaccine elicits T cell and neutralising antibody responses that cross react with variantsPreprint
Brentville, V. A., Vankemmelbeke, M., Metheringham, R. L., Symonds, P., Cook, K., Urbanowicz, R. A., Tsoleridis, T., Coleman, C., Chang, K.-C., Skinner, A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.18.448932 · Cited by 5 · see citing works
“Data have suggested that although the approved vaccines induce responses that can provide some cross-reactivity with the Alpha variant, they are less effective against the Beta, Delta and Gamma variants [27,32-34].”
Background
Mathematical artificial intelligence design of mutation-proof COVID-19 monoclonal antibodies
Chen, J.-H., & Wei, G.-S. (2022) · arXiv.org · doi:10.48550/arxiv.2204.09471 · Cited by 2
Impffortschritt in Deutschland und der Welt: Chancen und Risiken
Grimm, V., Lembcke, F. K., & Schwarz, M. (2021) · Wirtschaftsdienst · doi:10.1007/s10273-021-2894-5 · Cited by 5 · see citing works
Sequence Analysis of 20,453 SARS-CoV-2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern
Long, S., Olsen, R., Christensen, P., et al. (2021) · medRxiv · doi:10.1101/2021.02.26.21252227 · Cited by 2 · see citing works
“20 These variants also are of concern because they contain a mutation 88 (E484K) in the spike protein that decreases efficacy of some therapeutic mAbs, decreases in 89 vitro virus neutralization, and may result in potential escape from immunity induced by natural 90 infection or vaccination.(29-37) All three variants…”
Pre-Omicron vaccine breakthrough infection induces superior cross-neutralization against SARS-CoV-2 Omicron BA.1 than primo infection
da Silva, E. E. S., Kohnen, M., Gilson, G., et al. (2022) · medRxiv · doi:10.1101/2022.06.21.22276659 · Cited by 1
“in neutralizing activity is modest (2-3-fold) [48, 72-77], while it reaches ~10-fold to full escape for Beta and Gamma [48, 72-79].”
BackgroundResult
Outbreak of infections with the COVID-19 virus mutation B.1.351 about four weeks after the second successful vaccination with BNT162b2
Ortloff, A., & Harsch, I. (2021) · GMS Hygiene and Infection Control · doi:10.3205/dgkh000387 · Cited by 1
High-Potency Polypeptide-based Inhibition of Enveloped-virus GlycoproteinsPreprint
Ma, J., Acevedo, A. C., & Wang, Q. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.05.438537 · Cited by 3 · see citing works
Epitope Profiling of SARS-CoV-2 Spike Antigen Provides a Novel Strategy for Developing ELISAs Specific for Different Spike Protein Variants in Bivalent Vaccine Formulations
Ettorre, L., Williams, T., Houy, C., Zhu, S., Kishko, M., Azizi, A., James, D. A., Gajewska, B., & Szeto, J. (2025) · Vaccines · doi:10.3390/vaccines13080794
“These mutations imparted conformational changes to the ACE2 binding region and decreased susceptibility to sero-neutralization [14].”
'Geno-to-pheno' SARS-CoV-2 genome-COVID-19 association studies
Tang, J. W.-T. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103333
“However, there is still some protection offered by these vaccines against severe disease and death [4,5].”

Brief Report: Prediction of Serum HIV-1 Neutralization Titers After Passive Administration of VRC01
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Heterogeneity in the Properties of 7 S and 19 S Rabbit-Neutralizing Antibodies to Herpes Simplex Virus
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Neutralization of SARS-CoV-2 with IgG from COVID-19-convalescent plasma
Maeda, K., Higashi‐Kuwata, N., Kinoshita, N., Kutsuna, S., Tsuchiya, K., Hattori, S.-I., Matsuda, K., Takamatsu, Y., Gatanaga, H., Oka, S., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-84733-5 · Cited by 46 · see citing works

Authors: Tada, T., Dcosta, B. M., Samanovic-Golden, M., Herati, R. S., Cornelius, A., Mulligan, M. J., & Landau, N. R.
Affiliations: New York University (US)
Corresponding author: Landau, Nathaniel R.
ORCID: Tada, Takuya
Dcosta, Belinda M.
Herati, Ramin S.
Mulligan, Mark J.
Landau, Nathaniel R.
Venue: mBio
Publisher: openRxiv
Published: 2021-02-07
Volume: 12
Issue: 3
Pages: e0069621-e0069621
ISSN: 2150-7511 (ISSN-L)
DOI: 10.1101/2021.02.05.430003
PMC: PMC7872356
OpenAlex: W3164611210
Cited by: 153
References: 35
Citations by year: 2025: 4 · 2024: 5 · 2023: 11 · 2022: 45 · 2021: 88
FWCI: 11.88
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
www.biorxiv.org/about/FAQ#license (vor)
Locations: mBio (publishedVersion, cc-by)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
PubMed Central (submittedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: National Institutes of Health (AI122390)
National Institute on Drug Abuse (DP1DA046100)
National Institute of Allergy and Infectious Diseases (K08AI120898, R21AI122390, U01AI047996, R33AI122390, UM1AI148574)
Common Fund (AI122390, AI120898, DA046100, UM1AI148574)
Topics: Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Keywords: SARS-CoV-2 variants, neutralizing antibodies, convalescent sera, vaccine-elicited antibodies, B.1.351 variant, anti-spike antibodies, antibody escape, combination therapy, vaccine effectiveness, variant surveillance

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Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies

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