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Fu JYL, Pukhari MH, Bador MK, Sam IC, Chan YF. Humoral and T Cell Immune Responses against SARS-CoV-2 after Primary and Homologous or Heterologous Booster Vaccinations and Breakthrough Infection: A Longitudinal Cohort Study in Malaysia. Viruses 2023; 15:v15040844. [PMID: 37112825 PMCID: PMC10146761 DOI: 10.3390/v15040844] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Vaccine efficacy against SARS-CoV-2 could be compromised by the emergence of SARS-CoV-2 variants and it is important to study how it impacts the booster vaccination regime. We investigated the humoral and T cell responses longitudinally in vaccinated uninfected (n = 25) and post-COVID-19 individuals (n = 8), and those who had received a BNT162b2 booster following complete two-doses regimes of either BNT162b2 (homologous) (n = 14) or ChAdOx1-S (heterologous) (n = 15) vaccines, by means of a SARS-CoV-2 pseudovirus neutralization test and QuantiFERON SARS-CoV-2 assay. Vaccinated post-COVID-19 individuals showed higher neutralizing antibodies with longer durability against SARS-CoV-2 wild type (WT) and Omicron spikes, but demonstrated similar declining T cell responses compared to the uninfected vaccinated. Two doses of BNT162b2 induced higher neutralizing antibodies against WT and T cell responses than ChAdOx1-S for six months. The BNT162b2 booster confers a greater humoral response against WT, but a similar cross-neutralizing antibody against Omicron and T cell responses in the homologous booster group compared to the heterologous booster group. Breakthrough infection in the homologous booster group (n = 11) significantly increased the neutralizing antibody, but T cell responses remained low. Our data may impact government public health policy regarding the administration of mix-and-match vaccines, where both vaccination regimes can be employed should there be shortages of certain vaccines.
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Affiliation(s)
- Jolene Yin Ling Fu
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.Y.L.F.); (M.H.P.); (M.K.B.); (I.-C.S.)
| | - Muhammad Harith Pukhari
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.Y.L.F.); (M.H.P.); (M.K.B.); (I.-C.S.)
| | - Maria Kahar Bador
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.Y.L.F.); (M.H.P.); (M.K.B.); (I.-C.S.)
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.Y.L.F.); (M.H.P.); (M.K.B.); (I.-C.S.)
- Department of Medical Microbiology, University Malaya Medical Centre, Kuala Lumpur 59100, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.Y.L.F.); (M.H.P.); (M.K.B.); (I.-C.S.)
- Correspondence:
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Wu J, Chen Z, Gao Y, Wang Z, Wang J, Chiang BY, Zhou Y, Han Y, Zhan W, Xie M, Jiang W, Zhang X, Hao A, Xia A, He J, Xue S, Mayer CT, Wu F, Wang B, Zhang L, Sun L, Wang Q. Fortuitous Somatic Mutations during Antibody Evolution Endow Broad Neutralization against SARS-CoV-2 Omicron Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.12.520172. [PMID: 36561175 PMCID: PMC9774204 DOI: 10.1101/2022.12.12.520172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Striking antibody evasion by emerging circulating SARS-CoV-2 variants drives the identification of broadly neutralizing antibodies (bNAbs). However, how a bNAb acquires increased neutralization breadth during antibody evolution is still elusive. Here, we identified a clonally-related antibody family from a convalescent individual. One of the members, XG005, exhibited potent and broad neutralizing activities against SARS-CoV-2 variants, while the other members showed significant reductions in neutralization breadth and potency, especially against the Omicron sublineages. Structural analysis visualizing the XG005-Omicron spike binding interface revealed how crucial somatic mutations endowed XG005 with greater neutralization potency and breadth. A single administration of XG005 with extended half-life, reduced antibody-dependent enhancement (ADE) effect, and increased antibody product quality, exhibited a high therapeutic efficacy in BA.2- and BA.5-challenged mice. Our results provided a natural example to show the importance of somatic hypermutation during antibody evolution for SARS-CoV-2 neutralization breadth and potency.
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Candido KL, Eich CR, de Fariña LO, Kadowaki MK, da Conceição Silva JL, Maller A, Simão RDCG. Spike protein of SARS-CoV-2 variants: a brief review and practical implications. Braz J Microbiol 2022; 53:1133-1157. [PMID: 35397075 PMCID: PMC8994061 DOI: 10.1007/s42770-022-00743-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.
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Affiliation(s)
- Kattlyn Laryssa Candido
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Caio Ricardo Eich
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Luciana Oliveira de Fariña
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Marina Kimiko Kadowaki
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - José Luis da Conceição Silva
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Alexandre Maller
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Rita de Cássia Garcia Simão
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
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4
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Zhang Z, Zhang J, Wang J. Surface charge changes in spike RBD mutations of SARS-CoV-2 and its variant strains alter the virus evasiveness via HSPGs: A review and mechanistic hypothesis. Front Public Health 2022; 10:952916. [PMID: 36091499 PMCID: PMC9449321 DOI: 10.3389/fpubh.2022.952916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/02/2022] [Indexed: 01/24/2023] Open
Abstract
With the COVID-19 pandemic continuing, more contagious SARS-CoV-2 variants, including Omicron, have been emerging. The mutations, especially those that occurred on the spike (S) protein receptor-binding domain (RBD), are of significant concern due to their potential capacity to increase viral infectivity, virulence, and breakthrough antibodies' protection. However, the molecular mechanism involved in the pathophysiological change of SARS-CoV-2 mutations remains poorly understood. Here, we summarized 21 RBD mutations and their human angiotensin-converting enzyme 2 (hACE2) and/or neutralizing antibodies' binding characteristics. We found that most RBD mutations, which could increase surface positive charge or polarity, enhanced their hACE2 binding affinity and immune evasion. Based on the dependence of electrostatic interaction of the epitope residue of virus and docking protein (like virus receptors or antibodies) for its invasion, we postulated that the charge and/or polarity changes of novel mutations on the RBD domain of S protein could affect its affinity for the hACE2 and antibodies. Thus, we modeled mutant S trimers and RBD-hACE2 complexes and calculated their electrotactic distribution to study surface charge changes. Meanwhile, we emphasized that heparan sulfate proteoglycans (HSPGs) might play an important role in the hACE2-mediated entry of SARS-CoV-2 into cells. Those hypotheses provide some hints on how SARS-CoV-2 mutations enhance viral fitness and immune evasion, which may indicate potential ways for drug design, next-generation vaccine development, and antibody therapies.
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Affiliation(s)
- Zhongyun Zhang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Juan Zhang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiqiu Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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5
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Kim YI, Casel MAB, Choi YK. Transmissibility and pathogenicity of SARS-CoV-2 variants in animal models. J Microbiol 2022; 60:255-267. [PMID: 35235177 PMCID: PMC8890026 DOI: 10.1007/s12275-022-2033-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 12/13/2022]
Abstract
As of February 2022, SARS-CoV-2 is still one of the most serious public health threats due to its high mortality rate and rapid spread of novel variants. Since the first outbreak in 2019, general understanding of SARS-CoV-2 has been improved through basic and clinical studies; however, knowledge gaps still exist in our understanding of the emerging novel SARSCoV-2 variants, which impacts the corresponding development of vaccines and therapeutics. Especially, accumulation of mutations in SARS-CoV-2 and rapid spread in populations with previous immunity has resulted in selection of variants that evade the host immune response. This phenomenon threatens to render current SARS-CoV-2 vaccines ineffective for controlling the pandemic. Proper animal models are essential for detailed investigations into the viral etiology, transmission and pathogenesis mechanisms, as well as evaluation of the efficacy of vaccine candidates against recent SARS-CoV-2 variants. Further, the choice of animal model for each research topic is important for researchers to gain better knowledge of recent SARS-CoV-2 variants. Here, we review the advantages and limitations of each animal model, including mice, hamsters, ferrets, and non-human primates, to elucidate variant SARS-CoV-2 etiology and transmission and to evaluate therapeutic and vaccine efficacy.
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Affiliation(s)
- Young-Il Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Mark Anthony B Casel
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Young Ki Choi
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea.
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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6
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Previous Infection Combined with Vaccination Produces Neutralizing Antibodies with Potency against SARS-CoV-2 Variants. mBio 2021; 12:e0265621. [PMID: 34872349 PMCID: PMC8649753 DOI: 10.1128/mbio.02656-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve in humans. Spike protein mutations increase transmission and potentially evade antibodies raised against the original sequence used in current vaccines. Our evaluation of serum neutralizing activity in both persons soon after SARS-CoV-2 infection (in April 2020 or earlier) or vaccination without prior infection confirmed that common spike mutations can reduce antibody antiviral activity. However, when the persons with prior infection were subsequently vaccinated, their antibodies attained an apparent biologic ceiling of neutralizing potency against all tested variants, equivalent to the original spike sequence. These findings indicate that additional antigenic exposure further improves antibody efficacy against variants.
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7
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Barona-Gómez F, Delaye L, Díaz-Valenzuela E, Plisson F, Cruz-Pérez A, Díaz-Sánchez M, García-Sepúlveda CA, Sanchez-Flores A, Pérez-Abreu R, Valencia-Valdespino FJ, Vega-Magaña N, Muñoz-Valle JF, García-González OP, Bernal-Silva S, Comas-García A, Cibrián-Jaramillo A. Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Microb Genom 2021; 7. [PMID: 34846283 PMCID: PMC8743546 DOI: 10.1099/mgen.0.000684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Understanding the evolution of the SARS-CoV-2 virus in various regions of the world during the Covid-19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A real-time quantitative PCR screening and phylogenomic reconstructions directed at sequence/structure analysis of the spike glycoprotein revealed mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show spike protein mutations in the N-terminal domain (i.e. R190M), in the receptor-binding motif (i.e. T478K, E484K), within the S1-S2 subdomains (i.e. P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of single nucleotide variants from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades. Our results highlight the dual and complementary role of spike and nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage.
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Affiliation(s)
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav-IPN, Irapuato, Guanajuato, México
| | - Erik Díaz-Valenzuela
- Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico
| | - Fabien Plisson
- Conacyt - Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, México
| | - Arely Cruz-Pérez
- Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico
| | - Mauricio Díaz-Sánchez
- Molecular Biology Research & Development Department, GrupoT, Irapuato, Guanajuato, México
| | | | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rafael Pérez-Abreu
- Centro de Investigación en Matemáticas AC (Cimat), Sede Aguascalientes, Aguascalientes, México
| | | | - Natali Vega-Magaña
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco, México
| | - José Francisco Muñoz-Valle
- Institute for Research in Biomedical Sciences, University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco, México
| | | | - Sofía Bernal-Silva
- Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis, San Luis Potosí, México
| | - Andreu Comas-García
- Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis, San Luis Potosí, México
- Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis, San Luis Potosí, México
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Lennerstrand J, Palanisamy N. Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Viruses 2021; 13:1974. [PMID: 34696404 PMCID: PMC8538289 DOI: 10.3390/v13101974] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Several vaccines with varying efficacies have been developed and are currently administered globally to minimize the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite having an RNA-dependent RNA polymerase with a proofreading activity, new variants of SARS-CoV-2 are on the rise periodically. Some of the mutations in these variants, especially mutations on the spike protein, aid the virus in transmission, infectivity and host immune evasion. Further, these mutations also reduce the effectiveness of some of the current vaccines and monoclonal antibodies (mAbs). In the present study, using the available 984,769 SARS-CoV-2 nucleotide sequences on the NCBI database from the end of 2019 till 28 July 2021, we have estimated the global prevalence of so-called 'adaptive mutations' and 'mutations identified in the prolonged infections', in the receptor-binding domain (RBD) of the spike (S) protein. Irrespective of the geographical region, in the case of the adaptive mutations, N501Y (48.38%) was found to be the dominant mutation followed by L452R (17.52%), T478K (14.31%), E484K (4.69%), S477N (3.29%), K417T (1.64%), N439K (0.7%) and S494P (0.7%). Other mutations were found to be less prevalent (less than 0.7%). Since the last two months, there has been a massive increase of L452R and T478K mutations (delta variant) in certain areas. In the case of prolonged infections' mutations (long-term SARS-CoV-2 infections), V483A (0.009%) was found to be dominant followed by Q493R (0.009%), while other mutations were found in less than 0.007% of the studied sequences. The data obtained in this study will aid in the development of better infection control policies, thereby curbing the spread of this virus.
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Affiliation(s)
- Johan Lennerstrand
- Department of Medical Sciences, Section of Clinical Microbiology, Uppsala University, 751 85 Uppsala, Sweden;
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9
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Purushotham JN, van Doremalen N, Munster VJ. SARS-CoV-2 vaccines: anamnestic response in previously infected recipients. Cell Res 2021; 31:827-828. [PMID: 34007056 PMCID: PMC8130209 DOI: 10.1038/s41422-021-00516-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Jyothi N Purushotham
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
- The Jenner Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Neeltje van Doremalen
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Vincent J Munster
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
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10
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Muecksch F, Wise H, Templeton K, Batchelor B, Squires M, McCance K, Jarvis L, Malloy K, Furrie E, Richardson C, MacGuire J, Godber I, Burns A, Mavin S, Zhang F, Schmidt F, Bieniasz P, Jenks S, Hatziioannou T. Longitudinal variation in SARS-CoV-2 antibody levels and emergence of viral variants: implications for the ability of serological assays to predict immunity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.07.02.21259939. [PMID: 34268524 PMCID: PMC8282113 DOI: 10.1101/2021.07.02.21259939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Serological assays are being deployed to monitor antibody responses in SARS-CoV-2 convalescents and vaccine recipients. There is a need to determine whether such assays can predict immunity, as antibody levels wane and viral variants emerge. METHODS We measured antibodies in a cohort of SARS-CoV-2 infected patients using several high-throughput serological tests and functional neutralization assays. The effects of time and spike protein sequence variation on the performance and predictive value of the various assays was assessed. FINDINGS Neutralizing antibody titers decreased over the first few months post-infection but stabilized thereafter, at about 30% of the level observed shortly after infection. Serological assays commonly used to measure antibodies against SARS-CoV-2 displayed a range of sensitivities that declined to varying extents over time. Quantitative measurements generated by serological assays based on the spike protein were better at predicting neutralizing antibody titers than assays based on nucleocapsid, but performance was variable and manufacturer positivity thresholds were not able to predict the presence or absence of detectable neutralizing activity. Even though there was some deterioration in correlation between serological measurements and functional neutralization activity, some assays maintained an ability to predict neutralizing titers, even against variants of concern. INTERPRETATION The ability of high throughput serological assays to predict neutralizing antibody titers is likely crucial for evaluation of immunity at the population scale. These data will facilitate the selection of the most suitable assays as surrogates of functional neutralizing activity and suggest that such measurements may have utility in clinical practice.
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Affiliation(s)
- Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Helen Wise
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Kate Templeton
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Becky Batchelor
- Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU
| | - Maria Squires
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Kirsty McCance
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Lisa Jarvis
- SNBTS Microbiology Reference Laboratory, The Jack Copland Centre, 52 Research Avenue North, Heriot Watt Research Park, Edinburgh, EH14 4AP
| | - Kristen Malloy
- SNBTS Microbiology Reference Laboratory, The Jack Copland Centre, 52 Research Avenue North, Heriot Watt Research Park, Edinburgh, EH14 4AP
| | - Elizabeth Furrie
- Ninewells Hospital and Medical School, NHS Tayside, Dundee, DD1 9SY
| | | | | | - Ian Godber
- Queen Elizabeth University Hospital, Govan Road, Glasgow, G51 4TF
| | - Alana Burns
- Queen Elizabeth University Hospital, Govan Road, Glasgow, G51 4TF
| | - Sally Mavin
- Scottish Microbiology Reference Laboratory, NHS Highland, Inverness, IV2 3UJ
| | - Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Paul Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | - Sara Jenks
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh EH16 4SA
| | - Theodora Hatziioannou
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 10065
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11
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Xu J, Xu K, Jung S, Conte A, Lieberman J, Muecksch F, Lorenzi JCC, Park S, Schmidt F, Wang Z, Huang Y, Luo Y, Nair MS, Wang P, Schulz JE, Tessarollo L, Bylund T, Chuang GY, Olia AS, Stephens T, Teng IT, Tsybovsky Y, Zhou T, Munster V, Ho DD, Hatziioannou T, Bieniasz PD, Nussenzweig MC, Kwong PD, Casellas R. Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Nature 2021; 595:278-282. [PMID: 34098567 PMCID: PMC8260353 DOI: 10.1038/s41586-021-03676-z] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/27/2021] [Indexed: 11/08/2022]
Abstract
Since the start of the COVID-19 pandemic, SARS-CoV-2 has caused millions of deaths worldwide. Although a number of vaccines have been deployed, the continual evolution of the receptor-binding domain (RBD) of the virus has challenged their efficacy. In particular, the emerging variants B.1.1.7, B.1.351 and P.1 (first detected in the UK, South Africa and Brazil, respectively) have compromised the efficacy of sera from patients who have recovered from COVID-19 and immunotherapies that have received emergency use authorization1-3. One potential alternative to avert viral escape is the use of camelid VHHs (variable heavy chain domains of heavy chain antibody (also known as nanobodies)), which can recognize epitopes that are often inaccessible to conventional antibodies4. Here, we isolate anti-RBD nanobodies from llamas and from mice that we engineered to produce VHHs cloned from alpacas, dromedaries and Bactrian camels. We identified two groups of highly neutralizing nanobodies. Group 1 circumvents antigenic drift by recognizing an RBD region that is highly conserved in coronaviruses but rarely targeted by human antibodies. Group 2 is almost exclusively focused to the RBD-ACE2 interface and does not neutralize SARS-CoV-2 variants that carry E484K or N501Y substitutions. However, nanobodies in group 2 retain full neutralization activity against these variants when expressed as homotrimers, and-to our knowledge-rival the most potent antibodies against SARS-CoV-2 that have been produced to date. These findings suggest that multivalent nanobodies overcome SARS-CoV-2 mutations through two separate mechanisms: enhanced avidity for the ACE2-binding domain and recognition of conserved epitopes that are largely inaccessible to human antibodies. Therefore, although new SARS-CoV-2 mutants will continue to emerge, nanobodies represent promising tools to prevent COVID-19 mortality when vaccines are compromised.
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MESH Headings
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/isolation & purification
- CRISPR-Cas Systems
- Camelids, New World/genetics
- Camelids, New World/immunology
- Female
- Gene Editing
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- Mutation
- Neutralization Tests
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/genetics
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/isolation & purification
- Somatic Hypermutation, Immunoglobulin/genetics
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Jianliang Xu
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA.
| | - Kai Xu
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Andrea Conte
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA
| | | | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - Solji Park
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yang Luo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jonathan E Schulz
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, CCR, NCI, NIH, Frederick, MD, USA
| | | | - Gwo-Yu Chuang
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - I-Ting Teng
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Vincent Munster
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Peter D Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA.
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD, USA.
- The NIH Regulome Project, NIH, Bethesda, MD, USA.
- Center for Cancer Research, NCI, NIH, Bethesda, MD, USA.
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12
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Wang Z, Muecksch F, Schaefer-Babajew D, Finkin S, Viant C, Gaebler C, Hoffmann HH, Barnes CO, Cipolla M, Ramos V, Oliveira TY, Cho A, Schmidt F, Da Silva J, Bednarski E, Aguado L, Yee J, Daga M, Turroja M, Millard KG, Jankovic M, Gazumyan A, Zhao Z, Rice CM, Bieniasz PD, Caskey M, Hatziioannou T, Nussenzweig MC. Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection. Nature 2021; 595:426-431. [PMID: 34126625 PMCID: PMC8277577 DOI: 10.1038/s41586-021-03696-9] [Citation(s) in RCA: 503] [Impact Index Per Article: 167.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/04/2021] [Indexed: 02/05/2023]
Abstract
More than one year after its inception, the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains difficult to control despite the availability of several working vaccines. Progress in controlling the pandemic is slowed by the emergence of variants that appear to be more transmissible and more resistant to antibodies1,2. Here we report on a cohort of 63 individuals who have recovered from COVID-19 assessed at 1.3, 6.2 and 12 months after SARS-CoV-2 infection, 41% of whom also received mRNA vaccines3,4. In the absence of vaccination, antibody reactivity to the receptor binding domain (RBD) of SARS-CoV-2, neutralizing activity and the number of RBD-specific memory B cells remain relatively stable between 6 and 12 months after infection. Vaccination increases all components of the humoral response and, as expected, results in serum neutralizing activities against variants of concern similar to or greater than the neutralizing activity against the original Wuhan Hu-1 strain achieved by vaccination of naive individuals2,5-8. The mechanism underlying these broad-based responses involves ongoing antibody somatic mutation, memory B cell clonal turnover and development of monoclonal antibodies that are exceptionally resistant to SARS-CoV-2 RBD mutations, including those found in the variants of concern4,9. In addition, B cell clones expressing broad and potent antibodies are selectively retained in the repertoire over time and expand markedly after vaccination. The data suggest that immunity in convalescent individuals will be very long lasting and that convalescent individuals who receive available mRNA vaccines will produce antibodies and memory B cells that should be protective against circulating SARS-CoV-2 variants.
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Affiliation(s)
- Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Charlotte Viant
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Hans- Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Justin Da Silva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Eva Bednarski
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Lauren Aguado
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Jim Yee
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mridushi Daga
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
| | | | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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13
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Duerr R, Crosse KM, Valero-Jimenez AM, Dittmann M. SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise. Microorganisms 2021; 9:1389. [PMID: 34198973 PMCID: PMC8307803 DOI: 10.3390/microorganisms9071389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 and HIV are zoonotic viruses that rapidly reached pandemic scale, causing global losses and fear. The COVID-19 and AIDS pandemics ignited massive efforts worldwide to develop antiviral strategies and characterize viral architectures, biological and immunological properties, and clinical outcomes. Although both viruses have a comparable appearance as enveloped viruses with positive-stranded RNA and envelope spikes mediating cellular entry, the entry process, downstream biological and immunological pathways, clinical outcomes, and disease courses are strikingly different. This review provides a systemic comparison of both viruses' structural and functional characteristics, delineating their distinct strategies for efficient spread.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA; (K.M.C.); (A.M.V.-J.); (M.D.)
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14
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Wang Z, Muecksch F, Schaefer-Babajew D, Finkin S, Viant C, Gaebler C, Hoffmann HH, Barnes CO, Cipolla M, Ramos V, Oliveira TY, Cho A, Schmidt F, da Silva J, Bednarski E, Aguado L, Yee J, Daga M, Turroja M, Millard KG, Jankovic M, Gazumyan A, Zhao Z, Rice CM, Bieniasz PD, Caskey M, Hatziioannou T, Nussenzweig MC. Naturally enhanced neutralizing breadth to SARS-CoV-2 after one year. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34100013 DOI: 10.1101/2021.05.07.443175] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Over one year after its inception, the coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains difficult to control despite the availability of several excellent vaccines. Progress in controlling the pandemic is slowed by the emergence of variants that appear to be more transmissible and more resistant to antibodies 1,2 . Here we report on a cohort of 63 COVID-19-convalescent individuals assessed at 1.3, 6.2 and 12 months after infection, 41% of whom also received mRNA vaccines 3,4 . In the absence of vaccination antibody reactivity to the receptor binding domain (RBD) of SARS-CoV-2, neutralizing activity and the number of RBD-specific memory B cells remain relatively stable from 6 to 12 months. Vaccination increases all components of the humoral response, and as expected, results in serum neutralizing activities against variants of concern that are comparable to or greater than neutralizing activity against the original Wuhan Hu-1 achieved by vaccination of naïve individuals 2,5-8 . The mechanism underlying these broad-based responses involves ongoing antibody somatic mutation, memory B cell clonal turnover, and development of monoclonal antibodies that are exceptionally resistant to SARS-CoV-2 RBD mutations, including those found in variants of concern 4,9 . In addition, B cell clones expressing broad and potent antibodies are selectively retained in the repertoire over time and expand dramatically after vaccination. The data suggest that immunity in convalescent individuals will be very long lasting and that convalescent individuals who receive available mRNA vaccines will produce antibodies and memory B cells that should be protective against circulating SARS-CoV-2 variants.
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15
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Jette CA, Cohen AA, Gnanapragasam PN, Muecksch F, Lee YE, Huey-Tubman KE, Schmidt F, Hatziioannou T, Bieniasz PD, Nussenzweig MC, West AP, Keeffe JR, Bjorkman PJ, Barnes CO. Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.23.441195. [PMID: 33948592 PMCID: PMC8095199 DOI: 10.1101/2021.04.23.441195] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many anti-SARS-CoV-2 neutralizing antibodies target the ACE2-binding site on viral spike receptor-binding domains (RBDs). The most potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly-emergent zoonotic sarbecoviruses and variants, but usually show only weak neutralization potencies. We characterized two class 4 anti-RBD antibodies derived from COVID-19 donors that exhibited broad recognition and potent neutralization of zoonotic coronavirus and SARS-CoV-2 variants. C118-RBD and C022-RBD structures revealed CDRH3 mainchain H-bond interactions that extended an RBD β-sheet, thus reducing sensitivity to RBD sidechain changes, and epitopes that extended from the cryptic epitope to occlude ACE2 binding. A C118-spike trimer structure revealed rotated RBDs to allow cryptic epitope access and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.
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Affiliation(s)
- Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | | | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
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16
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West AP, Wertheim JO, Wang JC, Vasylyeva TI, Havens JL, Chowdhury MA, Gonzalez E, Fang CE, Di Lonardo SS, Hughes S, Rakeman JL, Lee HH, Barnes CO, Gnanapragasam PNP, Yang Z, Gaebler C, Caskey M, Nussenzweig MC, Keeffe JR, Bjorkman PJ. Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.14.431043. [PMID: 33907745 PMCID: PMC8077570 DOI: 10.1101/2021.02.14.431043] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. Variants first detected in the United Kingdom, South Africa, and Brazil have spread to multiple countries. We developed the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detected an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020 when it represented <1% of sequenced coronavirus genomes that were collected in New York City (NYC). By February 2021, genomes from this lineage accounted for ~32% of 3288 sequenced genomes from NYC specimens. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage in NYC, notably the sub-clade defined by the spike mutation E484K, which has outpaced the growth of other variants in NYC. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, indicating the public health importance of this lineage.
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Affiliation(s)
- Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Jade C. Wang
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
| | | | - Jennifer L. Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093
| | - Moinuddin A. Chowdhury
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
| | - Edimarlyn Gonzalez
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
| | - Courtney E. Fang
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
| | - Steve S. Di Lonardo
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
| | - Scott Hughes
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
| | - Jennifer L. Rakeman
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, 10016 USA
| | - Henry H. Lee
- Pandemic Response Laboratory, Long Island City, NY 11101
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, 10065 USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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17
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Greaney AJ, Loes AN, Gentles LE, Crawford KH, Starr TN, Malone KD, Chu HY, Bloom JD. The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.14.439844. [PMID: 33880474 PMCID: PMC8057239 DOI: 10.1101/2021.04.14.439844] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The emergence of SARS-CoV-2 variants with mutations in key antibody epitopes has raised concerns that antigenic evolution will erode immunity. The susceptibility of immunity to viral evolution is shaped in part by the breadth of epitopes targeted. Here we compare the specificity of antibodies elicited by the mRNA-1273 vaccine versus natural infection. The neutralizing activity of vaccine-elicited antibodies is even more focused on the spike receptor-binding domain (RBD) than for infection-elicited antibodies. However, within the RBD, binding of vaccine-elicited antibodies is more broadly distributed across epitopes than for infection-elicited antibodies. This greater binding breadth means single RBD mutations have less impact on neutralization by vaccine sera than convalescent sera. Therefore, antibody immunity acquired by different means may have differing susceptibility to erosion by viral evolution. ONE SENTENCE SUMMARY Deep mutational scanning shows the mRNA-1273 RBD-binding antibody response is less affected by single viral mutations than the infection response.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington; Seattle, WA 98195, USA
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Lauren E. Gentles
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Microbiology, University of Washington; Seattle, WA 98195, USA
| | - Katharine H.D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington; Seattle, WA 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Keara D. Malone
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington; Seattle, Washington, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
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18
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