Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients

SUMMARYThe SARS-CoV-2 pandemic has unprecedented implications for public health, social life, and world economy. Since approved drugs and vaccines are not available, new options for COVID-19 treatment and prevention are highly demanded. To identify SARS-CoV-2 neutralizing antibodies, we analysed the antibody response of 12 COVID-19 patients from 8 to 69 days post diagnosis. By screening 4,313 SARS-CoV-2-reactive B cells, we isolated 255 antibodies from different time points as early as 8 days post diagnosis. Among these, 28 potently neutralized authentic SARS-CoV-2 (IC100 as low as 0.04 μg/ml), showing a broad spectrum of V genes and low levels of somatic mutations. Interestingly, potential precursors were identified in naïve B cell repertoires from 48 healthy individuals that were sampled before the COVID-19 pandemic. Our results demonstrate that SARS-CoV-2 neutralizing antibodies are readily generated from a diverse pool of precursors, fostering the hope of rapid induction of a protective immune response upon vaccination.

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Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability

Science ◽

10.1126/science.abc5902 ◽

2020 ◽

Vol 369 (6504) ◽

pp. 643-650 ◽

Cited By ~ 167

Author(s):

Philip J. M. Brouwer ◽

Tom G. Caniels ◽

Karlijn van der Straten ◽

Jonne L. Snitselaar ◽

Yoann Aldon ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Somatic Hypermutation ◽

Spike Protein ◽

Receptor Binding Domain ◽

Treatment And Prevention ◽

Antigenic Sites ◽

Rapid Spread ◽

Gene Usage ◽

Therapeutic Measures ◽

Low Levels

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a large impact on global health, travel, and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated monoclonal antibodies from three convalescent coronavirus disease 2019 (COVID-19) patients using a SARS-CoV-2 stabilized prefusion spike protein. These antibodies had low levels of somatic hypermutation and showed a strong enrichment in VH1-69, VH3-30-3, and VH1-24 gene usage. A subset of the antibodies was able to potently inhibit authentic SARS-CoV-2 infection at a concentration as low as 0.007 micrograms per milliliter. Competition and electron microscopy studies illustrate that the SARS-CoV-2 spike protein contains multiple distinct antigenic sites, including several receptor-binding domain (RBD) epitopes as well as non-RBD epitopes. In addition to providing guidance for vaccine design, the antibodies described here are promising candidates for COVID-19 treatment and prevention.

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Stereotypic neutralizing VH antibodies against SARS-CoV-2 spike protein receptor binding domain in COVID-19 patients and healthy individuals

Science Translational Medicine ◽

10.1126/scitranslmed.abd6990 ◽

2021 ◽

pp. eabd6990

Author(s):

Sang Il Kim ◽

Jinsung Noh ◽

Sujeong Kim ◽

Younggeun Choi ◽

Duck Kyun Yoo ◽

...

Keyword(s):

B Cells ◽

Receptor Binding ◽

Neutralizing Antibodies ◽

De Novo ◽

Binding Domain ◽

Host Cells ◽

Spike Protein ◽

Receptor Binding Domain ◽

Healthy Individuals

Stereotypic antibody clonotypes exist in healthy individuals and may provide protective immunity against viral infections by neutralization. We observed that 13 out of 17 patients with COVID-19 had stereotypic variable heavy chain (VH) antibody clonotypes directed against the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. These antibody clonotypes were comprised of immunoglobulin heavy variable (IGHV)3-53 or IGHV3-66 and immunoglobulin heavy joining (IGHJ)6 genes. These clonotypes included IgM, IgG3, IgG1, IgA1, IgG2, and IgA2 subtypes and had minimal somatic mutations, which suggested swift class switching after SARS-CoV-2 infection. The different immunoglobulin heavy variable chains were paired with diverse light chains resulting in binding to the RBD of SARS-CoV-2 spike protein. Human antibodies specific for the RBD can neutralize SARS-CoV-2 by inhibiting entry into host cells. We observed that one of these stereotypic neutralizing antibodies could inhibit viral replication in vitro using a clinical isolate of SARS-CoV-2. We also found that these VH clonotypes existed in six out of 10 healthy individuals, with IgM isotypes predominating. These findings suggest that stereotypic clonotypes can develop de novo from naïve B cells and not from memory B cells established from prior exposure to similar viruses. The expeditious and stereotypic expansion of these clonotypes may have occurred in patients infected with SARS-CoV-2 because they were already present.

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Kinetics of Anti-SARS-CoV-2 Antibody Responses 3 Months Post Complete Vaccination with BNT162b2; A Prospective Study in 283 Health Workers

Cells ◽

10.3390/cells10081942 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1942

Author(s):

Evangelos Terpos ◽

Ioannis P. Trougakos ◽

Vangelis Karalis ◽

Ioannis Ntanasis-Stathopoulos ◽

Sentiljana Gumeni ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Health Workers ◽

Antibody Responses ◽

Healthy Individuals ◽

Younger Age ◽

Constant Rate ◽

Rate Of Decline ◽

A Prospective Study ◽

Kinetics Of ◽

Over Time

The aim of this study was to investigate the kinetics of neutralizing antibodies (NAbs) and anti-SARS-CoV-2 anti-S-RBD IgGs up to three months after the second vaccination dose with the BNT162b2 mRNA vaccine. NAbs and anti-S-RBD levels were measured on days 1 (before the first vaccine shot), 8, 22 (before the second shot), 36, 50, and three months after the second vaccination (D111) (NCT04743388). 283 health workers were included in this study. NAbs showed a rapid increase from D8 to D36 at a constant rate of about 3% per day and reached a median (SD) of 97.2% (4.7) at D36. From D36 to D50, a slight decrease in NAbs values was detected and it became more prominent between D50 and D111 when the rate of decline was determined at −0.11 per day. The median (SD) NAbs value at D111 was 92.7% (11.8). A similar pattern was also observed for anti-S-RBD antibodies. Anti-S-RBDs showed a steeper increase during D22–D36 and a lower decline rate during D36–D111. Prior COVID-19 infection and younger age were associated with superior antibody responses over time. In conclusion, we found a persistent but declining anti-SARS-CoV-2 humoral immunity at 3 months following full vaccination with BNT162b2 in healthy individuals.

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Dissecting Human Antibody Responses: Useful, Basic, and Surprising Findings

Blood ◽

10.1182/blood.v130.suppl_1.sci-49.sci-49 ◽

2017 ◽

Vol 130 (Suppl_1) ◽

pp. SCI-49-SCI-49

Author(s):

Antonio Lanzavecchia

Keyword(s):

B Cell ◽

Dna Sequences ◽

Neutralizing Antibodies ◽

Influenza A ◽

Somatic Mutations ◽

Vaccine Design ◽

Human Memory ◽

Affinity Maturation ◽

Effective Vaccine ◽

Human Antibody

Abstract We use cell culture-based high-throughput methods to interrogate human memory B cell and plasma cell repertoires and to isolate antibodies selected on the basis of their neutralizing potency and breadth. Relevant examples are antibodies that neutralize all influenza A viruses or even four paramyxoviruses. By targeting conserved structures, these broadly neutralizing antibodies are less prone to select escape mutants and are promising candidates for prophylaxis and therapy of infections, as well as tools for vaccine design. The value of a target-agnostic approach to vaccine design is illustrated by our discovery of extremely potent antibodies that neutralize human cytomegalovirus, which led to the identification of their viral ligand, a pentameric complex that was then produced and tested as an effective vaccine. By reconstructing the genealogy trees of specific B cell clones, we investigate the role of somatic mutations in affinity maturation and in generation of antibody variants with broader or different specificity. Somatic mutations can also generate autoantibodies, as found in patients with pemphigus and autoimmune pulmonary alveolar proteinosis. Recently, while searching for antibodies that broadly react with malaria variant antigens, we discovered a new mechanism of antibody diversification, which relies on templated insertions of genomic DNA sequences into immunoglobulin genes, followed by somatic mutations. Disclosures Lanzavecchia: Humabs SA: Equity Ownership, Research Funding.

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Longitudinal dynamics of clonal hematopoiesis identifies gene-specific fitness effects

10.1101/2021.05.27.446006 ◽

2021 ◽

Author(s):

Neil A Robertson ◽

Eric Latorre-Crespo ◽

Maria Terrada-Terradas ◽

Alison C Purcell ◽

Benjamin J Livesey ◽

...

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Somatic Mutations ◽

Growth Potential ◽

Healthy Individuals ◽

Sequencing Data ◽

Fitness Effects ◽

Increased Risk ◽

Neutral Mutations ◽

Proliferative Advantage

The prevalence of clonal haematopoiesis of indeterminate potential (CHIP) in healthy individuals increases rapidly from age 60 onwards and has been associated with increased risk for malignancy, heart disease and ischemic stroke. CHIP is driven by somatic mutations in stem cells that are also drivers of myeloid malignancies. Since mutations in stem cells often drive leukaemia, we hypothesised that stem cell fitness substantially contributes to transformation from CHIP to leukaemia. Stem cell fitness is defined as the proliferative advantage over cells carrying no or only neutral mutations. We set out to quantify the fitness effects of CHIP drivers over a 15 year timespan in older age, using longitudinal error-corrected sequencing data. It is currently unknown whether mutations in different CHIP genes lead to distinct fitness advantages that could form the basis for patient stratification. We developed a new method based on drift-induced fluctuation (DIF) filtering to extract fitness effects from longitudinal data, and thus quantify the growth potential of variants within each individual. Our approach discriminates naturally drifting populations of cells and faster growing clones, while taking into account individual mutational context. We show that gene-specific fitness differences can outweigh inter-individual variation and therefore could form the basis for personalised clinical management.

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How I use molecular genetic tests to evaluate patients who have or may have myelodysplastic syndromes

Blood ◽

10.1182/blood-2018-06-860882 ◽

2018 ◽

Vol 132 (16) ◽

pp. 1657-1663 ◽

Cited By ~ 15

Author(s):

David P. Steensma

Keyword(s):

Myelodysplastic Syndromes ◽

Somatic Mutations ◽

Confounding Factor ◽

Morphological Changes ◽

Molecular Genetic ◽

Healthy Individuals ◽

Provisional Diagnosis ◽

Driver Genes ◽

Diagnostic Uncertainty ◽

Morphological Findings

Abstract Myelodysplastic syndromes (MDS) can be difficult to diagnose, especially when morphological changes in blood and marrow cells are minimal, myeloblast proportion is not increased, and the karyotype is normal. The discovery of >40 genes that are recurrently somatically mutated in MDS patients raised hope that molecular genetic testing for these mutations might help clarify the diagnosis in ambiguous cases where patients present with cytopenias and nondiagnostic marrow morphological findings. However, many older healthy individuals also harbor somatic mutations in leukemia-associated driver genes, especially in DNMT3A, TET2, and ASXL1, and detection of common aging-associated mutations in a cytopenic patient can cause diagnostic uncertainty. Despite this potential confounding factor, certain somatic mutation patterns when observed in cytopenic patients confer a high likelihood of disease progression and may allow a provisional diagnosis of MDS even if morphologic dysplasia and other diagnostic criteria are absent. A subset of acquired mutations also influences risk stratification of patients with an established MDS diagnosis and can inform treatment selection. Many unanswered questions remain about the implications of specific mutations, and clinicians also vary widely in their comfort with interpreting sequencing results. Here, I review the use of molecular genetic assays in patients with possible MDS or diagnosed MDS.

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Neutralizing Antibodies Targeting HIV-1 gp41

Viruses ◽

10.3390/v12111210 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1210

Author(s):

Christophe Caillat ◽

Delphine Guilligay ◽

Guidenn Sulbaran ◽

Winfried Weissenhorn

Keyword(s):

Conformational Changes ◽

Neutralizing Antibodies ◽

Somatic Mutations ◽

Heptad Repeat ◽

Broadly Neutralizing Antibodies ◽

Vaccine Research ◽

Membrane Components ◽

And Function ◽

Hiv 1

HIV-1 vaccine research has obtained an enormous boost since the discovery of many broadly neutralizing antibodies (bnAbs) targeting all accessible sites on the HIV-1 envelope glycoprotein (Env). This in turn facilitated high-resolution structures of the Env glycoprotein in complex with bnAbs. Here we focus on gp41, its highly conserved heptad repeat region 1 (HR1), the fusion peptide (FP) and the membrane-proximal external region (MPER). Notably, the broadest neutralizing antibodies target MPER. Both gp41 HR1 and MPER are only fully accessible once receptor-induced conformational changes have taken place, although some studies suggest access to MPER in the close to native Env conformation. We summarize the data on the structure and function of neutralizing antibodies targeting gp41 HR1, FP and MPER and we review their access to Env and their complex formation with gp41 HR1, MPER peptides and FP within native Env. We further discuss MPER bnAb binding to lipids and the role of somatic mutations in recognizing a bipartite epitope composed of the conserved MPER sequence and membrane components. The problematic of gp41 HR1 access and MPER bnAb auto- and polyreactivity is developed in the light of inducing such antibodies by vaccination.

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Oligomeric state of the ZIKV E protein defines protective immune responses

Nature Communications ◽

10.1038/s41467-019-12677-6 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 9

Author(s):

Stefan W. Metz ◽

Ashlie Thomas ◽

Alex Brackbill ◽

John Forsberg ◽

Michael J. Miley ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Quaternary Structure ◽

Poor Performance ◽

Oligomeric State ◽

Subunit Vaccines ◽

Safety Issues ◽

E Protein ◽

Protective Antibodies ◽

Low Levels ◽

Domain Iii

Abstract The current leading Zika vaccine candidates in clinical testing are based on live or killed virus platforms, which have safety issues, especially in pregnant women. Zika subunit vaccines, however, have shown poor performance in preclinical studies, most likely because the antigens tested do not display critical quaternary structure epitopes present on Zika E protein homodimers that cover the surface of the virus. Here, we produce stable recombinant E protein homodimers that are recognized by strongly neutralizing Zika specific monoclonal antibodies. In mice, the dimeric antigen stimulate strongly neutralizing antibodies that target epitopes that are similar to epitopes recognized by human antibodies following natural Zika virus infection. The monomer antigen stimulates low levels of E-domain III targeting neutralizing antibodies. In a Zika challenge model, only E dimer antigen stimulates protective antibodies, not the monomer. These results highlight the importance of mimicking the highly structured flavivirus surface when designing subunit vaccines.

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Broadly neutralizing antibodies with few somatic mutations and hepatitis C virus clearance

JCI Insight ◽

10.1172/jci.insight.92872 ◽

2017 ◽

Vol 2 (9) ◽

Cited By ~ 54

Author(s):

Justin R. Bailey ◽

Andrew I. Flyak ◽

Valerie J. Cohen ◽

Hui Li ◽

Lisa N. Wasilewski ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Neutralizing Antibodies ◽

Somatic Mutations ◽

Broadly Neutralizing Antibodies ◽

Virus Clearance

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Couchsurfing as a virtual hospitality network and a type of sustainable youth tourism

E3S Web of Conferences ◽

10.1051/e3sconf/202016609005 ◽

2020 ◽

Vol 166 ◽

pp. 09005

Author(s):

Olena Hanchuk ◽

Olga Bondarenko ◽

Iryna Varfolomyeyeva ◽

Olena Pakhomova ◽

Tetyana Lohvynenko

Keyword(s):

World Economy ◽

Human Wellbeing ◽

Transcultural Communication ◽

The World ◽

New Varieties ◽

Low Levels ◽

Anglo American ◽

Comprehensive Classification ◽

Tourist Flow

The modern tourism diversity coursed by the emergence of its new varieties is sure to evolve with a view to the goals of sustainable future. The article is dedicated to couchsurfing, a kind of sustainable youth tourism, a global hospitality network, as an online service used for transcultural communication of tourists through the organization of various assistance during joint travel. It helps meet tourists’ recreational needs and travelling at no charge. The article considers the organizational structure of couchsurfing as a network managed by regional units. The authors identify the factors that influence the development of this type of tourism (globalization of the world economy, the development of the Internet, the growth of human wellbeing, democratization of society and etc.). They offer a comprehensive classification of types of couchsurfing by several criteria (age of tourists, number of participants, purpose of the trip and direction, length of stay, intensity of tourist flow). The regional peculiarities of the couchsurfing development are identified, and the regions with high (Europe, Anglo-American, Australia and New Zealand), middle (Asia and Latin America) and low levels of its development (Africa, Oceania and Central America) are distinguished. The map material illustrating the spread of couchsurfing around the world is created.

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