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  • CORONAVIRUS Potent neutralizing antibodies from COVID-19 ...Andrew B.Ward3, Godelieve J. de Bree2†, Rogier W. Sanders1,9†, Marit J. van Gils1† The rapid spread of severe acute
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RESEARCH ARTICLE ◥ CORONAVIRUS Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability Philip J. M. Brouwer 1 * , Tom G. Caniels 1 * , Karlijn van der Straten 1,2 * , Jonne L. Snitselaar 1 , Yoann Aldon 1 , Sandhya Bangaru 3 , Jonathan L. Torres 3 , Nisreen M. A. Okba 4 , Mathieu Claireaux 1 , Gius Kerster 1 , Arthur E. H. Bentlage 5 , Marlies M. van Haaren 1 , Denise Guerra 1 , Judith A. Burger 1 , Edith E. Schermer 1 , Kirsten D. Verheul 1 , Niels van der Velde 6 , Alex van der Kooi 6 , Jelle van Schooten 1 , Mariëlle J. van Breemen 1 ,Tom P. L. Bijl 1 , Kwinten Sliepen 1 , Aafke Aartse 1,7 , Ronald Derking 1 , Ilja Bontjer 1 , Neeltje A. Kootstra 8 , W. Joost Wiersinga 2 , Gestur Vidarsson 5 , Bart L. Haagmans 4 , Andrew B. Ward 3 , Godelieve J. de Bree 2 †, Rogier W. Sanders 1,9 †, Marit J. van Gils 1 † 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. T he rapid emergence of three novel path- ogenic human coronaviruses in the past two decades has caused major concerns. The latest, severe acute respiratory syn- drome coronavirus 2 (SARS-CoV-2), is re- sponsible for >3 million infections and 230,000 deaths worldwide as of 1 May 2020 (1). Corona- virus disease 2019 (COVID-19), caused by SARS- CoV-2, is characterized by mild, flu-like symptoms in most patients. However, severe cases can present with bilateral pneumonia that may rapidly deteriorate into acute respiratory di- stress syndrome (2). With high transmission rates and no proven curative treatment available, health care systems are severely overwhelmed, and stringent public health measures are in place to prevent infection. Safe and effective treatment and prevention measures for COVID-19 are ur- gently needed. During the outbreak of the first severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle Eastern respiratory syndrome coronavirus (MERS-CoV), plasma of recovered patients containing neutralizing antibodies (NAbs) was used as a safe and effective treat- ment option to decrease viral load and to re- duce mortality in severe cases (3, 4). Recently, a small number of COVID-19 patients treated with convalescent plasma showed clinical im- provement and a decrease in viral load (5). An alternative treatment strategy would be to ad- minister purified monoclonal antibodies (mAbs) with neutralizing capacity. mAbs can be thor- oughly characterized in vitro and expressed in large quantities. In addition, because of the ability to control dosing and composition, mAb therapy has improved efficacy over convales- cent plasma treatment and prevents the poten- tial risks of antibody-dependent enhancement (ADE) from non-neutralizing or poorly neutral- izing Abs present in plasma that consists of a polyclonal mixture (6). Recent studies with pa- tients infected with the Ebola virus highlight the superiority of mAb treatment over conva- lescent plasma treatment (7, 8). Moreover, mAb therapy has been proven safe and effective against influenza virus, rabies virus, and res- piratory syncytial virus (RSV) (9–11). The main target for NAbs on coronaviruses is the spike (S) protein, a homotrimeric glyco- protein that is anchored in the viral mem- brane. Recent studies have shown that the S protein of SARS-CoV-2 bears considerable structural homology to that of SARS-CoV, con- sisting of two subdomains: the N-terminal S1 domain, which contains the N-terminal do- main (NTD) and the RBD for the host cell re- ceptor angiotensin-converting enzyme-2 (ACE2), and the S2 domain, which contains the fusion peptide ( 12, 13). Similar to other viruses contain- ing class 1 fusion proteins (e.g., HIV-1, RSV, and Lassa virus), the S protein undergoes a confor- mational change and proteolytic cleavage upon host cell receptor binding from a prefusion to a postfusion state, enabling merging of viral and target cell membranes (14, 15). When ex- pressed as recombinant soluble proteins, class 1 fusion proteins generally have the propensity to switch to a postfusion state. However, most NAb epitopes present in the prefusion confor- mation (16–18). The recent successes of isolat- ing potent NAbs against HIV-1 and RSV using stabilized prefusion glycoproteins reflect the importance of using the prefusion conforma- tion for isolating and mapping mAbs against SARS-CoV-2 (19, 20). Early efforts at obtaining NAbs focused on reevaluating SARS-CoV–specific mAbs iso- lated after the 2003 outbreak that might cross- neutralize SARS-CoV-2 (21, 22). Although two mAbs were described to cross-neutralize SARS- CoV-2, most SARS-CoV NAbs did not bind SARS- CoV-2 S protein or neutralize SARS-CoV-2 virus (12, 21–23). More recently, the focus has shifted from cross-neutralizing SARS-CoV NAbs to the isolation of new SARS-CoV-2 NAbs from recov- ered COVID-19 patients (24–28). S protein frag- ments containing the RBD have yielded multiple NAbs that can neutralize SARS-CoV-2 by tar- geting different RBD epitopes (24–28). In light of the rapid emergence of escape mutants in the RBD of SARS-CoV and MERS, monoclonal NAbs targeting epitopes other than the RBD are a valuable component of any therapeutic antibody cocktail (29, 30). Indeed, therapeutic antibody cocktails with a variety of specific- ities have been used successfully against Ebola virus disease (7) and are being tested widely in clinical trials for HIV-1 (31). NAbs target- ing non-RBD epitopes have been identified for SARS-CoV and MERS, supporting the rationale for sorting mAbs using the entire ectodomain of the SARS-CoV-2 S protein (32). In addition, considering the high sequence identity between the S2 subdomains of SARS-CoV-2 and SARS-CoV, using the complete S protein ectodomain instead of only the RBD may allow the isolation of mAbs that cross-neutralize different b-coronaviruses (33). In an attempt to obtain mAbs that target both RBD and non-RBD epitopes, we set out to isolate mAbs using the complete prefusion S protein ectodomain of SARS-CoV-2. RESEARCH Brouwer et al., Science 369, 643–650 (2020) 7 August 2020 1 of 8 1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands. 2 Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands. 3 Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. 4 Department of Viroscience, Erasmus Medical Center, Rotterdam, 3015GD, Netherlands. 5 Sanquin Research, Department of Experimental Immunohematology, Amsterdam, Netherlands and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1006AD Amsterdam, Netherlands. 6 IBIS Technologies BV, 7521PR Enschede, Netherlands. 7 Department of Virology, Biomedical Primate Research Centre, 2288GJ Rijswijk, Netherlands. 8 Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands. 9 Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA. *These authors contributed equally to this work. †Corresponding author. Email: [email protected] (M.J.v.G.); [email protected] (R.W.S.); g.j.debree@ amsterdamumc.nl (G.J.d.B.) on June 9, 2021 http://science.sciencemag.org/ Downloaded from

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  • RESEARCH ARTICLE◥

    CORONAVIRUS

    Potent neutralizing antibodies from COVID-19patients define multiple targets of vulnerabilityPhilip J. M. Brouwer1*, Tom G. Caniels1*, Karlijn van der Straten1,2*, Jonne L. Snitselaar1,Yoann Aldon1, Sandhya Bangaru3, Jonathan L. Torres3, Nisreen M. A. Okba4, Mathieu Claireaux1,Gius Kerster1, Arthur E. H. Bentlage5, Marlies M. van Haaren1, Denise Guerra1, Judith A. Burger1,Edith E. Schermer1, Kirsten D. Verheul1, Niels van der Velde6, Alex van der Kooi6, Jelle van Schooten1,Mariëlle J. van Breemen1, Tom P. L. Bijl1, Kwinten Sliepen1, Aafke Aartse1,7, Ronald Derking1,Ilja Bontjer1, Neeltje A. Kootstra8, W. Joost Wiersinga2, Gestur Vidarsson5, Bart L. Haagmans4,Andrew B. Ward3, Godelieve J. de Bree2†, Rogier W. Sanders1,9†, Marit J. van Gils1†

    The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a largeimpact on global health, travel, and economy. Therefore, preventative and therapeutic measuresare urgently needed. Here, we isolated monoclonal antibodies from three convalescent coronavirusdisease 2019 (COVID-19) patients using a SARS-CoV-2 stabilized prefusion spike protein. Theseantibodies 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-2infection at a concentration as low as 0.007 micrograms per milliliter. Competition and electronmicroscopy studies illustrate that the SARS-CoV-2 spike protein contains multiple distinct antigenicsites, including several receptor-binding domain (RBD) epitopes as well as non-RBD epitopes. In additionto providing guidance for vaccine design, the antibodies described here are promising candidatesfor COVID-19 treatment and prevention.

    The rapid emergence of three novel path-ogenic human coronaviruses in the pasttwo decades has caused major concerns.The latest, severe acute respiratory syn-drome coronavirus 2 (SARS-CoV-2), is re-

    sponsible for >3 million infections and 230,000deaths worldwide as of 1 May 2020 (1). Corona-virus disease 2019 (COVID-19), caused by SARS-CoV-2, is characterized bymild, flu-like symptomsin most patients. However, severe cases canpresent with bilateral pneumonia that mayrapidly deteriorate into acute respiratory di-stress syndrome (2). With high transmissionrates andno proven curative treatment available,

    health care systems are severely overwhelmed,and stringent public healthmeasures are in placeto prevent infection. Safe and effective treatmentand prevention measures for COVID-19 are ur-gently needed.During the outbreak of the first severe acute

    respiratory syndrome coronavirus (SARS-CoV)and Middle Eastern respiratory syndromecoronavirus (MERS-CoV), plasma of recoveredpatients containing neutralizing antibodies(NAbs) was used as a safe and effective treat-ment option to decrease viral load and to re-duce mortality in severe cases (3, 4). Recently,a small number of COVID-19 patients treatedwith convalescent plasma showed clinical im-provement and a decrease in viral load (5). Analternative treatment strategy would be to ad-minister purifiedmonoclonal antibodies (mAbs)with neutralizing capacity. mAbs can be thor-oughly characterized in vitro and expressed inlarge quantities. In addition, because of theability to control dosing and composition, mAbtherapy has improved efficacy over convales-cent plasma treatment and prevents the poten-tial risks of antibody-dependent enhancement(ADE) from non-neutralizing or poorly neutral-izing Abs present in plasma that consists of apolyclonal mixture (6). Recent studies with pa-tients infected with the Ebola virus highlightthe superiority of mAb treatment over conva-lescent plasma treatment (7, 8). Moreover, mAbtherapy has been proven safe and effectiveagainst influenza virus, rabies virus, and res-piratory syncytial virus (RSV) (9–11).

    The main target for NAbs on coronavirusesis the spike (S) protein, a homotrimeric glyco-protein that is anchored in the viral mem-brane. Recent studies have shown that the Sprotein of SARS-CoV-2 bears considerablestructural homology to that of SARS-CoV, con-sisting of two subdomains: the N-terminal S1domain, which contains the N-terminal do-main (NTD) and the RBD for the host cell re-ceptor angiotensin-converting enzyme-2 (ACE2),and the S2 domain, which contains the fusionpeptide (12, 13). Similar to other viruses contain-ing class 1 fusion proteins (e.g., HIV-1, RSV, andLassa virus), the S protein undergoes a confor-mational change and proteolytic cleavage uponhost cell receptor binding from a prefusion toa postfusion state, enabling merging of viraland target cell membranes (14, 15). When ex-pressed as recombinant soluble proteins, class 1fusion proteins generally have the propensityto switch to a postfusion state. However, mostNAb epitopes present in the prefusion confor-mation (16–18). The recent successes of isolat-ing potent NAbs against HIV-1 and RSV usingstabilized prefusion glycoproteins reflect theimportance of using the prefusion conforma-tion for isolating and mapping mAbs againstSARS-CoV-2 (19, 20).Early efforts at obtaining NAbs focused on

    reevaluating SARS-CoV–specific mAbs iso-lated after the 2003 outbreak that might cross-neutralize SARS-CoV-2 (21, 22). Although twomAbs were described to cross-neutralize SARS-CoV-2,most SARS-CoVNAbsdidnot bindSARS-CoV-2 S protein or neutralize SARS-CoV-2 virus(12, 21–23). More recently, the focus has shiftedfrom cross-neutralizing SARS-CoV NAbs to theisolation of new SARS-CoV-2 NAbs from recov-ered COVID-19 patients (24–28). S protein frag-ments containing the RBD have yieldedmultipleNAbs that can neutralize SARS-CoV-2 by tar-geting different RBD epitopes (24–28). In lightof the rapid emergence of escape mutants inthe RBD of SARS-CoV andMERS, monoclonalNAbs targeting epitopes other than the RBDare a valuable component of any therapeuticantibody cocktail (29, 30). Indeed, therapeuticantibody cocktails with a variety of specific-ities have been used successfully against Ebolavirus disease (7) and are being tested widelyin clinical trials for HIV-1 (31). NAbs target-ing non-RBD epitopes have been identified forSARS-CoV andMERS, supporting the rationalefor sorting mAbs using the entire ectodomainof the SARS-CoV-2 S protein (32). In addition,considering the high sequence identity betweentheS2 subdomainsofSARS-CoV-2andSARS-CoV,using the complete S protein ectodomain insteadof only the RBDmay allow the isolation of mAbsthat cross-neutralize different b-coronaviruses(33). In an attempt to obtain mAbs that targetboth RBD and non-RBD epitopes, we set outto isolate mAbs using the complete prefusionS protein ectodomain of SARS-CoV-2.

    RESEARCH

    Brouwer et al., Science 369, 643–650 (2020) 7 August 2020 1 of 8

    1Department of Medical Microbiology, Amsterdam UMC,University of Amsterdam, Amsterdam Institute for Infectionand Immunity, 1105AZ Amsterdam, Netherlands. 2Departmentof Internal Medicine, Amsterdam UMC, University ofAmsterdam, Amsterdam Institute for Infection and Immunity,1105AZ Amsterdam, Netherlands. 3Department of IntegrativeStructural and Computational Biology, The Scripps ResearchInstitute, La Jolla, CA 92037, USA. 4Department ofViroscience, Erasmus Medical Center, Rotterdam, 3015GD,Netherlands. 5Sanquin Research, Department of ExperimentalImmunohematology, Amsterdam, Netherlands andLandsteiner Laboratory, Amsterdam UMC, University ofAmsterdam, 1006AD Amsterdam, Netherlands. 6IBISTechnologies BV, 7521PR Enschede, Netherlands.7Department of Virology, Biomedical Primate ResearchCentre, 2288GJ Rijswijk, Netherlands. 8Department ofExperimental Immunology, Amsterdam UMC, University ofAmsterdam, Amsterdam Institute for Infection and Immunity,1105AZ Amsterdam, Netherlands. 9Department ofMicrobiology and Immunology, Weill Medical College ofCornell University, New York, NY 10021, USA.*These authors contributed equally to this work.†Corresponding author. Email: [email protected](M.J.v.G.); [email protected] (R.W.S.); [email protected] (G.J.d.B.)

    on June 9, 2021

    http://science.sciencemag.org/

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    nloaded from

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  • Phenotyping SARS-CoV-2–specificB cell subsetsWe collected a single blood sample from threepolymerase chain reaction–confirmed SARS-CoV-2–infected individuals (COSCA1, COSCA2,

    and COSCA3) ~4 weeks after symptom onset.COSCA1 (a 47-year-old male) and COSCA2 (a44-year-old female) showed symptoms of anupper respiratory tract infection andmild pneu-monia, respectively (Table 1). Both remained in

    home isolation during the course of COVID-19symptoms. COSCA3, a 69-year-oldmale, devel-oped a severe pneumonia and became respi-ratory insufficient 1.5 weeks after symptomonset, requiring admission to the intensive

    Brouwer et al., Science 369, 643–650 (2020) 7 August 2020 2 of 8

    Table 1. Patient characteristics, symptoms of COVID-19, treatment modalities, and sampling time points of three SARS-CoV-2–infected patients.

    COSCA1 COSCA2 COSCA3

    Patient characteristics.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Age (years) 47 44 69.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Gender Male Female Male.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Comorbidities None None None.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Symptoms, from onset to relief, days.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Fever (>38°C) 4–10 1–4 6–18.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Coughing 2–35 3–17 1–20.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Sputum production 2–35 No 1–20.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Dyspnea 4–24 No No.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Sore throat 1–5 5–17 No.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Rhinorrhea 2–34 5–17 No.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Anosmia No 5–17 No.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Myalgia No 1–4 6–18.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Headache No No 1–18.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Other No No Delirium.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Treatment modalities, treatment period, days.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Hospital admission No No 8–24.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    ICU admission No No 11–18.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Oxygen therapy No No 8–24.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Intubation No No 11–16.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Dialysis No No No.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Drug therapy.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Antiviral No No No.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Antibiotic No No Cefotaxime, 8–12 Ciprofloxacin, 8–11.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Immunomodulatory No No No.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    NSAIDs No No No.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Sampling time point, days after symptom onset 27 28 23.. .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .. ... ... .. ... .. ... ... .. ... ... .

    Fig. 1. Design of SARS-CoV-2 S protein andserology of COSCA1, COSCA2, and COSCA3.(A) (Top) Schematic overview of the authenticSARS-CoV-2 S protein with the signal peptide shownin blue and the S1 (red) and S2 (yellow) domainsseparated by a furin-cleavage site (RRAR; top).(Bottom) Schematic overview of the stabilizedprefusion SARS-CoV-2 S ectodomain, where thefurin cleavage site is replaced with a glycine linker(GGGG), two proline mutations are introduced(K986P and V987P), and a trimerization domain(cyan) preceded by a linker (GSGG) is attached.(B) Binding of sera from COSCA1, COSCA2, andCOSCA3 to prefusion SARS-CoV-2 S protein asdetermined by ELISA. The mean values andSDs of two technical replicates are shown.(C) Neutralization of SARS-CoV-2 pseudovirusby heat-inactivated sera from COSCA1, COSCA2,and COSCA3. The mean and SEM of at leastthree technical replicates are shown. The dottedline indicates 50% neutralization.

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  • care unit for mechanical ventilation. To iden-tify S protein–specific antibodies in the seraobtained from all three patients, we gener-ated soluble, prefusion-stabilized S proteinsof SARS-CoV-2 using stabilization strategiespreviously described for S proteins of SARS-CoV-2 and other b-coronaviruses (Fig. 1A) (12, 34).As demonstrated by the size-exclusion chro-matography trace, SDS–polyacrylamide gelelectrophoresis (PAGE), and blue native PAGE,the resulting trimeric SARS-CoV-2 S proteinswere of high purity (fig. S1, A and B). Serafrom all patients showed strong binding to theS protein of SARS-CoV-2 in an enzyme-linkedimmunosorbent assay (ELISA), with end-pointtiters of 13,637, 6133, and 48,120 for COSCA1,COSCA2, and COSCA3, respectively (Fig. 1B),and showed cross-reactivity to the S proteinof SARS-CoV (fig. S1C). COSCA1, COSCA2, andCOSCA3 had varying neutralizing poten-cies against SARS-CoV-2 pseudovirus, with50% inhibition of virus infection (ID50) val-ues of 383, 626, and 7645, respectively (Fig.1C), and similar activities against authenticvirus (fig. S1D). In addition, all sera showedcross-neutralization of SARS-CoV pseudovirusand authentic SARS-CoV virus, albeit withlow potency (fig. S1, E and F). The potent S

    protein–binding and -neutralizing responsesobserved for COSCA3 are consistent with earlierfindings showing that severe disease is asso-ciated with a strong humoral response (35). Onthe basis of these strong serum binding andneutralization titers, we sorted SARS-CoV-2 Sprotein–specific B cells for mAb isolation fromCOSCA1, COSCA2, and COSCA3.Peripheral blood mononuclear cells were

    stained dually with fluorescently labeled pre-fusion SARS-CoV-2 S proteins and analyzedfor the frequency and phenotype of specific Bcells by flow cytometry (Fig. 2A and fig S2).The analysis revealed a frequency rangingfrom 0.68 to 1.74% of S protein–specific B cells(S-AF647+, S-BV421+) among the total pool ofB cells (CD19+Via-CD3–CD14–CD16–), (Fig. 2B).These SARS-CoV-2 S protein–specific B cellsshowed a predominant memory (CD20+CD27+)and plasmablasts/plasma cells (PBs/PCs)(CD20–CD27+CD38+) phenotype. We observeda threefold higher percentage of PBs/PCs forSARS-CoV-2 S protein–specific B cells com-pared with total B cells (P = 0.034), indicatingan enrichment of specific B cells in this sub-population (Fig. 2C). COSCA3, who experi-enced severe symptoms, showed the highestfrequency of PBs/PCs in both total (34%) and

    specific (60%) B cells (Fig. 2C and fig. S2). Asexpected, the SARS-CoV-2 S protein–specificB cells were enriched in the immunoglobulinG–positive (IgG+) and IgM–/IgG– (most likelyrepresenting IgA+) B cell populations, althougha substantial portion of the specific B cells wereIgM+, particularly for COSCA3 (Fig. 2D).

    Genotypic signatures of the SARS-CoV-2–specific antibody response

    SARS-CoV-2 S protein–specific B cells weresubsequently single-cell sorted for sequenc-ing and mAb isolation. In total, 409 heavychain (HC) and light chain (LC) pairs wereobtained from the sorted B cells of the threepatients (137, 165, and 107 from COSCA1,COSCA2, and COSCA3, respectively), of which323 were unique clonotypes. Clonal expan-sion occurred in all three patients (Fig. 3A)but was strongest in COSCA3, where it wasdominated by HC variable (VH) regions VH3-7and VH4-39 (34 and 32% of SARS-CoV-2 Sprotein–specific sequences, respectively). Eventhough substantial clonal expansion occurredin COSCA3, the median somatic hypermu-tation (SHM) was 1.4%, with similar SHM inCOSCA1 and COSCA2 (2.1 and 1.4%, respec-tively) (Fig. 3B). These SHM levels are similar

    Brouwer et al., Science 369, 643–650 (2020) 7 August 2020 3 of 8

    Total Total0

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    Fig. 2. Characterization of SARS-CoV-2 S protein–specific B cells derivedfrom COSCA1, COSCA2, and COSCA3. (A) Representative gates of SARS-CoV-2S protein–specific B cells shown for a naïve donor (left panel) or COSCA1(middle left panel). Each dot represents a B cell. The gating strategy to identifyB cells is shown in fig. S2. From the total pool of SARS-CoV-2 S protein–specificB cells, CD27+CD38– memory B cells (Mem B cells; blue gate) and CD27+CD38+ B cellswere identified (middle panel). From the latter gate, PBs/PCs (CD20–; red gate)could be identified (middle right panel). SARS-CoV-2 S protein–specific B cellswere also analyzed for their IgG or IgM isotype (right panel). (B) Frequency of

    SARS-CoV-2 S protein–specific B cells in total B cells, Mem B cells, and PBs/PCs.Symbols represent individual patients, as shown in (D). (C) Comparison of thefrequency of Mem B cells (CD27+CD38–) and PB/PC cells (CD27+CD38+CD20–)between the specific (SARS-CoV2 S++) and nonspecific B cells (gating strategy isshown in fig. S2). Symbols represent individual patients, as shown in (D).Statistical differences between two groups were determined using paired t test(*P = 0.034). (D) Comparison of the frequency of IgM+, IgG+, and IgM–IgG– B cellsin specific and nonspecific compartments. Bars represent means; symbolsrepresent individual patients.

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  • to those observed in response to infectionwith other respiratory viruses (36).A hallmark of antibody diversity is the heavy

    chain complementarity-determining region 3(CDRH3). Because the CDRH3 is composedof V, D, and J gene segments, it is the mostvariable region of an antibody in terms of bothamino acid composition and length. The aver-age length of CDRH3 in the naïve human re-pertoire is 15 amino acids (37), but for a subsetof influenza virus and HIV-1 broadly neutral-izing antibodies, long CDRH3 regions of 20to 35 amino acids are crucial for high-affinity

    antigen–antibody interactions (38, 39). Eventhough the mean CDRH3 length of isolatedSARS-CoV-2 S protein–specific B cells did notdiffer substantially from that of a naïve pop-ulation (37), we observed a significant dif-ference in the distribution of CDRH3 length(two-sample Kolmogorov–Smirnov test, P =0.006) (Fig. 3C). This difference in CDRH3 dis-tribution can largely be attributed to an en-richment of longer (~20 amino acid) CDRH3s,leading to a bimodal distribution as opposed tothe bell-shaped distribution that was observedin the naïve repertoire (Fig. 3C and fig. S3).

    Next, to determine SARS-CoV-2–specific sig-natures in B cell receptor repertoire usage, wecompared ImmunoGenetics (IMGT) database–assigned unique germline V regions fromthe sorted SARS-CoV-2 S protein–specificB cells with the well-defined extensive germ-line repertoire in the naïve population (Fig.3D) (37). Multiple VH genes were enrichedin COSCA1, COSCA2, and COSCA3 comparedwith the naïve repertoire, including VH3-33(P = 0.009) and VH1-24 (P < 0.001) (Fig. 3D).Even though the enrichment of VH1-69 wasnot significant (P > 0.05), it should be noted

    Brouwer et al., Science 369, 643–650 (2020) 7 August 2020 4 of 8

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    e (%

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    Fig. 3. Genotypic characterization of SARS-CoV-2 S protein–specific B cellreceptors. (A) Maximum-likelihood phylogenetic tree of 409 isolated pairedB cell receptor HCs. Each color represents sequences isolated from differentpatients (COSCA1, COSCA2, and COSCA3). (B) Violin plot showing SHM levels(%; nucleotides) per patient. The dot represents the median SHM percentage.(C) Distribution of CDRH3 lengths in B cells from COSCA1, COSCA2, and COSCA3(purple, n = 323) versus a representative naïve population from three donors

    (cyan, n = 9.791.115) (37). (D) Bar graphs showing the mean (± SEM) VH geneusage (%) in COSCA1, COSCA2, and COSCA3 (purple, n = 323) versus arepresentative naïve population (cyan, n = 363,506,788). The error barsrepresent the variation between different patients (COSCA1, COSCA2, andCOSCA3) or naïve donors (37). Statistical differences between two groups weredetermined using unpaired t tests (with Holm–Sidak correction for multiplecomparisons, adjusted P values: *P < 0.05; **P < 0.01; ***P < 0.001).

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  • that an enrichment of VH1-69 has been shownin response to a number of other viral infec-tions, including influenza virus, hepatitis Cvirus, and rotavirus (40), and an enrichmentof VH3-33 was observed in response to mala-ria vaccination, whereas the enrichment ofVH1-24 appears to be specific for COVID-19(Fig. 3D) (41). By contrast, VH4-34 (P > 0.05)and VH3-23 (P = 0.018) were substantially un-derrepresented in SARS-CoV-2–specific se-quences compared with the naïve population.Although usage of most VH genes was con-sistent between COVID-19 patients, VH3-30-3andVH4-39 in particular showed considerablevariability. Thus, upon SARS-CoV-2 infection,the S protein recruits a subset of B cells fromthe naïve repertoire enriched in specific VHsegments and CDRH3 domains.

    Identification of unusually potentSARS-CoV-2–neutralizing antibodies

    Subsequently, all HC and LC pairs were tran-siently expressed in human embryonic kidney

    (HEK) 293T cells and screened for binding toSARS-CoV-2 S protein by ELISA. A total of84 mAbs that showed high-affinity bindingwere selected for small-scale expression inHEK 293F cells and purified (table S1). Weobtained few S protein–reactive mAbs fromCOSCA3, possibly because most B cells fromthis individual were IgM+, whereas cloning intoan IgG backbone nullified avidity contrib-utions to binding and neutralization presentin the serum. To gain insight in the immuno-dominance of the RBD as well as its ability tocross-react with SARS-CoV, we assessed thebinding capacity of these mAbs to the prefu-sion S proteins and the RBDs of SARS-CoV-2and SARS-CoV using ELISA. Of the 84 mAbstested, 32 (38%) bound to the SARS-CoV-2 RBD(Fig. 4, A and B), with sevenmAbs (22%) show-ing cross-binding to SARS-CoV RBD (fig. S4A).We also observed 33 mAbs (39%) that boundstrongly to SARS-CoV-2 S but did not bind theRBD, of which 10mAbs (30%) also bound to theS protein of SARS-CoV (Fig. 4, A andB). Notably,

    some mAbs that bound very weakly to solubleSARS-CoV-2 S protein in ELISA showed strongbinding to membrane-bound S protein, imply-ing that their epitopes are presented poorly onthe stabilized soluble S protein or that avidity isimportant for their binding (table S1). Surfaceplasmon resonance (SPR) assays confirmedbind-ing of 77 mAbs to S protein and 21 mAbs to theRBD with binding affinities in the nanomolarto picomolar range (table S1).All 84 mAbs were subsequently tested for

    their ability to block infection. A total of19 mAbs (23%) inhibited SARS-CoV-2 pseudo-virus infectionwith varying potencies (Fig. 4C)and, of these, 14 (74%) bound the RBD. Sevenof the 19 mAbs could be categorized as potentneutralizers [median inhibitory concentra-tion (IC50) < 0.1 mg/ml], six as moderate neu-tralizers (IC50 = 0.1 to 1 mg/mL), and six asweak neutralizers (IC50 = 1 to 10 mg/ml). Withan IC50 of 0.008 mg/ml, the RBD-targeting anti-bodies COVA1-18 and COVA2-15 in particularwere unusually potent. However, they were

    Brouwer et al., Science 369, 643–650 (2020) 7 August 2020 5 of 8

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    2-20 0.728 1.465

    Fig. 4. Phenotypic characterization of SARS-CoV-2 S protein–specificmAbs. (A) Bar graph depicting the binding of mAbs from COSCA1 (blue),COSCA2 (red), and COSCA3 (yellow) to SARS-CoV-2 S protein (dark shading)and SARS-CoV-2 RBD (light shading) as determined by ELISA. Each bar indicatesthe representative area under the curve (AUC) of the mAb indicated below fromtwo experiments. The gray area represents the cutoff for binding (AUC = 1). Themaximum concentration of mAb tested was 10 mg/ml. (B) Scatter plot depictingthe binding of mAbs from COSCA1, COSCA2, and COSCA3 [see (C) for colorcoding] to SARS-CoV-2 S protein and SARS-CoV-2 RBD as determined by ELISA.

    Each dot indicates the representative AUC of a mAb from two experiments.(C) Midpoint neutralization concentrations (IC50) of SARS-CoV-2 pseudovirus(left) or authentic SARS-CoV-2 virus (right). Each symbol represents the IC50 of asingle mAb. For comparability, the highest concentration was set to 10 mg/ml,although the actual start concentration for the authentic virus neutralizationassay was 20 mg/ml. The IC50s for pseudotyped and authentic SARS-CoV-2 virusof a selection of potently neutralizing RBD and non-RBD–specific mAbs (withasterisk) are shown in the adjacent table. Colored shading indicates the mostpotent mAbs from COSCA1, COSCA2, and COSCA3.

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    COVA2-16COVA2-36

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    COVA2-33COVA2-42COVA2-10COVA2-28COVA2-12COVA2-41COVA1-19COVA2-04COVA2-13

    COVA2-24COVA1-16COVA2-44COVA2-01COVA2-40COVA1-25COVA2-18COVA2-32COVA3-08COVA3-01COVA1-04COVA1-07COVA2-14COVA1-01COVA1-02COVA1-27COVA2-34COVA1-12COVA1-11COVA1-15COVA2-08COVA2-06COVA1-14

    COVA1-13COVA2-02COVA2-46COVA2-05

    COVA1-24

    COVA2-47COVA2-43COVA2-38COVA2-27COVA1-26COVA2-25COVA2-03COVA2-22COVA2-30

    COVA1-06COVA1-23COVA2-17COVA3-07COVA1-20COVA2-26COVA3-05

    COVA2-37

    COVA3-02COVA1-09

    COVA1-05COVA1-22

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    Fig. 5. Antigenic clustering of SARS-CoV-2 S protein–specific mAbs.(A) Dendrogram showing hierarchical clustering of the SPR-based cross-competitionheat map (table S2). Clusters are numbered I to XI and are depicted with colorshading. ELISA binding to SARS-CoV-2 S protein, SARS-CoV S protein,and SARS-CoV-2 RBD as presented by AUC and neutralization IC50 (mg/ml) ofSARS-CoV-2 is shown in the columns on the left. ELISA AUCs are shown in gray(AUC < 1) or blue (AUC > 1), and neutralization IC50 is shown in gray (>10 mg/ml),blue (1 to 10 mg/ml), violet (0.1 to 1 mg/ml), or purple (0.001 to 0.1 mg/ml).Asterisks indicate antibodies that cross-neutralize SARS-CoV pseudovirus.(B) Composite figure demonstrating binding of NTD-mAb COVA1-22 (blue) and

    RBD mAbs COVA2-07 (green), COVA2-39 (orange), COVA1-12 (yellow), COVA2-15(salmon), and COVA2-04 (purple) to SARS-CoV-2 spike (gray). The spike model(PDB 6VYB) is fit into the density. (C) Magnification of SARS-CoV-2 spike comparingepitopes of RBD mAbs with the ACE2-binding site (red) and the epitope of mAbCR3022 (blue). (D) Side (left) and top (right) views of the 3D reconstruction ofCOVA2-15 bound to SARS-CoV-2 S protein. COVA2-15 binds to both the down(magenta) and up (salmon) conformations of the RBD. The RBDs are colored blue inthe down conformation and black in the up conformation. The angle of approachfor COVA2-15 enables this broader recognition of the RBD while also partially over-lapping with the ACE2-binding site and therefore blocking receptor engagement.

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  • quite different in other aspects, such as theirHCV gene usage (VH3-66 versus VH3-23), LCusage (VL7-46 versus VK2-30), HC sequenceidentity (77%), and CDRH3 length (12 versus22 amino acids). Seventeen of the mAbs alsointeracted with the SARS-CoV S and RBDproteins and two of these cross-neutralizedthe SARS-CoV pseudovirus (IC50 = 2.5 mg/mlfor COVA1-16 and 0.61 mg/ml for COVA2-02;fig. S4B), with COVA2-02 being more potentagainst SARS-CoV than against SARS-CoV-2.Next, we assessed the ability of the 19 mAbsto block infection of authentic SARS-CoV-2virus (Fig. 4C and fig. S4C). Although pre-vious reports suggested a decrease in neu-tralization sensitivity of primary SARS-CoV-2compared with pseudovirus (25, 27, 28), weobserved very similar potencies for seven ofthe 19 NAbs, including the most potent NAbs(IC50 = 0.007 and 0.009 mg/ml for COVA1-18and COVA2-15, respectively; Fig. 4C). NAbsCOVA1-18, COVA2-04, COVA2-07, COVA2-15,and COVA2-39 also showed strong competitionwith ACE2 binding, illustrating that blockingACE2 binding is their likelymechanism of neu-tralization (fig. S4D). The RBD-targeting mAbCOVA2-17, however, showed incomplete com-petition with ACE2. This corroborates previousobservations that the RBD encompassesmulti-ple distinct antigenic sites, someofwhich donotinvolve blocking of ACE2 binding (23, 25, 26).The non-RBDNAbs all bear substantially longerCDRH3s compared with RBD NAbs (fig. S4E),suggesting a convergent, CDRH3-dependentcontact between antibody and epitope.

    Multiple targets of vulnerabilityon the SARS-CoV-2 S protein

    To identify and characterize the antigenic siteson the S protein and their interrelationships,we performed SPR-based cross-competitionassays using S protein, followed by clusteringanalysis. We note that competition clusters donot necessarily equal epitope clusters but theanalysis can provide clues as to the relation-ship between mAb epitopes. We identified 11competition clusters, of which nine containedmore than one mAb and two contained onlyone mAb (clusters X and XI; Fig. 5A and fig.S5). All nine multiple-mAb clusters includedmAbs from at least two of the three patients,emphasizing that these clusters represent com-mon epitopes targeted by the human humoralimmune response during SARS-CoV-2 infec-tion. Three clusters included predominantlyRBD-binding mAbs (clusters I, III, and VII),with cluster I forming two subclusters. Thesethree clusters were confirmed by performingcross-competition experiments with solubleRBD instead of complete S protein (fig. S5B).Four clusters (V, VI, XIII, and IX) included pre-dominantly mAbs that did not interact withRBD, and clusters II, IV, X, and XI consistedexclusively of non-RBD mAbs. mAbs with di-

    verse phenotypes (e.g., RBD and non-RBD–binding mAbs) merged together in multipleclusters, suggesting that these mAbs mighttarget epitopes bridging the RBD and non-RBD sites or that they sterically interfere witheach other’s binding as opposed to binding tooverlapping epitopes. Although clusters II, V, andVIII contained only mAbs incapable of neu-tralizing SARS-CoV-2, clusters I, III, IV, VI, andVII included both non-NAbs and NAbs. ClusterV was formed mostly by non-RBD–targetingmAbs that also bound to SARS-CoV. However,these mAbs were not able to neutralize eitherSARS-CoV-2 or SARS-CoV, suggesting that thesemAbs target a conserved non-neutralizing epi-tope on the S protein. Finally, the two non-RBDmAbs COVA1-03 and COVA1-21 formed single-mAb competition clusters (clusters X and XI, re-spectively) and showed anunusual competitionpattern, because binding of eithermAb blockedbinding by most of the other mAbs, but notvice versa (figs. S5 and S6 and table S2). Wehypothesize that these twomAbs allostericallyinterfere withmAb binding by causing confor-mational changes in the S protein that shieldor impair most other mAb epitopes. COVA1-21also efficiently blocked virus infection withoutblocking ACE2, suggesting an alternative mech-anism of neutralization than blocking ACE2 en-gagement (fig. S4C). The SPR-based clusteringwas corroborated using biolayer interferom-etry competition assays on a subset of NAbs(fig. S6). Overall, our data are consistent withthe previous identification of multiple anti-genic RBD sites for SARS-CoV-2 and additionalnon-RBD sites on the S protein, as described forSARS-CoV and MERS-CoV (32, 42).To visualize howselectedNAbsbound to their

    respective epitopes, we generated Fab–SARS-CoV-2 S complexes that were imaged by single-particle negative-stain electronmicroscopy (EM;Fig. 5, B and C, and fig. S7). We obtained low-resolution reconstruction with six Fabs, includ-ing five RBD-binding Fabs from three differentcompetitionclusters.COVA1-12overlappedhighlywith the epitope of COVA2-39, whereas COVA2-04 approached the RBD at a different anglesomewhat similar to that of the cross-bindingSARS-CoV–specific mAb CR3022 (42). The EMreconstructions confirmed the RBD as thetarget of these NAbs but revealed a diversityin approach angles (Fig. 5B). Furthermore,whereas four RBD NAbs interacted with astoichiometry of one Fab per trimer, consistentwith one RBD being exposed in the “up state”and two in the less accessible “down state”(13, 43), COVA2-15 boundwith a stoichiometryof three per trimer (fig. S7). COVA2-15was ableto bind RBD domains in both the up and downstate (Fig. 5D). In either conformation, theCOVA2-15 epitope partially overlapped withthe ACE2-binding site, and therefore the mAbblocks receptor engagement. The higher stoi-chiometry of this mAb may explain its un-

    usually strong neutralization potency. None ofthe epitopes of the five RBD Fabs overlappedwith that of CR3022, which is unable to neu-tralize SARS-CoV-2 (42), although COVA2-04does approach the RBD from a similar angleas CR3022. The sixth Fab for which we gener-ated a three-dimensional (3D) reconstructionwas from the non-RBDmAb COVA1-22 placedin competition cluster IX. EMdemonstrated thatthis mAb bound to the NTD of S1. Such NTDNAbs have also been found for MERS-CoV (44).

    Conclusions

    Convalescent COVID-19 patients showed stronganti–SARS-CoV-2 S protein–specific B cell re-sponses and developed memory and antibody-producing B cells that may have participated inthe control of infection and the establishmentof humoral immunity. We isolated 19 NAbsthat targeted a diverse range of antigenic siteson the S protein, of which two showed pico-molar neutralizing activities (IC50 = 0.007 and0.009 mg/ml or 47 and 60 pM, respectively)against authentic SARS-CoV-2 virus. This il-lustrates that SARS-CoV-2 infection elicits high-affinity and cross-reactive mAbs targetingthe RBD as well as other sites on the S protein.Several of the potent NAbs had VH segmentsvirtually identical to their germline origin,which holds promise for the induction of sim-ilar NAbs by vaccination because extensiveaffinity maturation does not appear to be arequirement for potent neutralization. Themost potent NAbs both targeted the RBD onthe S protein and fell within the same com-petition cluster, but were isolated from twodifferent individuals and bore little resem-blance genotypically. Although direct compar-isons are difficult, the neutralization potencyof these and several other mAbs exceeds thepotencies of the most advanced HIV-1 andEbola mAbs under clinical evaluation, as wellas the approved anti-RSV mAb palivizumab(45). Through large-scale SPR-based compe-tition assays, we defined NAbs that targetedmultiple sites of vulnerability on the RBD andthe additional previously undefined non-RBDepitopes on SARS-CoV-2. This is consistent withthe identification of multiple antigenic RBDsites for SARS-CoV-2 and the presence of ad-ditional non-RBD sites on the S protein ofSARS-CoV and MERS-CoV (32). Subsequentstructural characterization of these potentNAbs will guide vaccine design, and simul-taneous targeting of multiple non-RBD andRBD epitopes with mAb cocktails paves theway for safe and effective COVID-19 preven-tion and treatment.

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    ACKNOWLEDGMENTS

    We thank C. Russell and A. Han for helpful comments on themanuscript; J. Koopsen for help with the phylogenetic analyses;and H. Turner, B. Anderson, and C. Bowman for assistance with theEM studies. Funding: This work was supported by a NetherlandsOrganization for Scientific Research (NWO) Vici grant (to R.W.S.);by the Bill & Melinda Gates Foundation through the Collaborationfor AIDS Vaccine Discovery (CAVD) grants OPP1111923, OPP1132237,and INV-002022 to R.W.S. and grant OPP1170236 to A.B.W.; bythe Fondation Dormeur, Vaduz (to R.W.S. and to M.J.v.G.) andHealth Holland PPS-allowance LSHM20040 (to M.J.v.G.);and by the Netherlands Organisation for Health Research andDevelopment (ZONMW to B.L.H). M.J.v.G. is a recipient of an AMCFellowship from Amsterdam UMC and a COVID-19 grant fromthe Amsterdam Institute for Infection and Immunity. R.W.S andM.J.v.G. are recipients of support from the University of AmsterdamProof of Concept fund (contract no. 200421) as managed byInnovation Exchange Amsterdam (IXA). The funders had no role instudy design, data collection, data analysis, data interpretation,or data reporting. Author contributions: P.J.M.B., T.G.C., K.v.d.S.,

    G.V., B.H., A.B.W., G.J.d.B., R.W.S., and M.J.v.G. conceived anddesigned experiments. K.v.d.S., W.J.W., N.K., and G.d.B arrangedmedical ethical approval, recruitment of study participants,and collection of study material. P.J.M.B., T.G.C., J.L.S., Y.A., S.B.,J.L.T., N.M.A.O., G.K., A.E.H.B., M.M.v.H., D.G., J.A.B., E.E.S., K.D.V.,J.v.S., M.J.v.B., T.P.L.B., K.S., R.D., and I.B. performed theexperiments. P.J.M.B., T.G.C., M.C., and A.A. set up experimentalassays. P.J.M.B., T.G.C., K.v.d.S., N.v.d.V., A.v.d.K., R.W.S., andM.J.v.G. analyzed and interpreted data. P.J.M.B., T.G.C., K.v.d.S.,G.J.d.B., R.W.S., and M.J.v.G. wrote the manuscript with input fromall listed authors. Competing interests: Amsterdam UMC hasfiled a patent application concerning the SARS-CoV-2 mAbsdescribed here. Data and materials availability: Reagents andmaterials presented in this study are available from thecorresponding authors under a materials transfer agreementwith the Amsterdam UMC. Variable domain sequences of HC andLCs are available in table S1 and were uploaded on GenBankunder accession numbers MT599820 to MT599987. Thecoordinates of the negative stain electron microscopy reconstructionswere deposited in the Electron Microscopy Data Bank underaccession numbers EMD-22061 to EMD-22066. This work islicensed under a Creative Commons Attribution 4.0 International(CC BY 4.0) license, which permits unrestricted use, distribution,and reproduction in any medium, provided the original work isproperly cited. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/. This license does notapply to figures/photos/artwork or other content included in thearticle that is credited to a third party; obtain authorizationfrom the rights holder before using such material.

    SUPPLEMENTARY MATERIALS

    science.sciencemag.org/content/369/6504/643/suppl/DC1Materials and MethodsFigs. S1 to S5References (46–56)Tables S1 and S2MDAR Reproducibility Checklist

    View/request a protocol for this paper from Bio-protocol.

    4 May 2020; accepted 10 June 2020Published online 15 June 202010.1126/science.abc5902

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

    GilsWiersinga, Gestur Vidarsson, Bart L. Haagmans, Andrew B. Ward, Godelieve J. de Bree, Rogier W. Sanders and Marit J. van J. van Breemen, Tom P. L. Bijl, Kwinten Sliepen, Aafke Aartse, Ronald Derking, Ilja Bontjer, Neeltje A. Kootstra, W. JoostJudith A. Burger, Edith E. Schermer, Kirsten D. Verheul, Niels van der Velde, Alex van der Kooi, Jelle van Schooten, Mariëlle

    Guerra,L. Torres, Nisreen M. A. Okba, Mathieu Claireaux, Gius Kerster, Arthur E. H. Bentlage, Marlies M. van Haaren, Denise Philip J. M. Brouwer, Tom G. Caniels, Karlijn van der Straten, Jonne L. Snitselaar, Yoann Aldon, Sandhya Bangaru, Jonathan

    originally published online June 15, 2020DOI: 10.1126/science.abc5902 (6504), 643-650.369Science

    , this issue p. 643Sciencetwo most potent targeting the domain that binds the host receptor.Competition and electron microscopy studies showed that these antibodies target diverse epitopes on the spike, with the protein, a complex that binds to receptors on the host cell. A subset of antibodies was able to neutralize the virus.convalescent COVID-19 patients. They show that the patients had strong immune responses against the viral spike

    isolated 403 monoclonal antibodies from threeet al.tool in treating coronavirus disease 2019 (COVID-19). Brouwer Antibodies that neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be an important

    Sites of vulnerability in SARS-CoV-2

    ARTICLE TOOLS http://science.sciencemag.org/content/369/6504/643

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