A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

Yuan, Meng; Wu, Nicholas C.; Zhu, Xueyong; Lee, Chang-Chun David; So, Ray T.Y.; Lv, Huibin; Mok, Chris Ka Pun; Wilson, Ian A.

doi:10.1126/science.abb7269

Cited by 1,466 publications

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“…The cross-reactivity of such mAbs with SARS-CoV-2 has been characterized, and it was found that many SARS-CoV-neutralizing mAbs exhibit no cross-neutralizing capacity ( 9, 31 ). For example, CR3022, a neutralizing antibody isolated from a convalescent SARS patient, cross-reacted with the RBD of SARS-CoV-2 but did not neutralize the virus ( 31, 32 ). Nonetheless, a new human anti-RBD mAb, 47D11, has just been isolated from transgenic mice immunized with a SARS-CoV S protein, which neutralizes both SARS-CoV-2 and SARS-CoV ( 33 ).…”

Section: Discussionmentioning

confidence: 99%

Cross-reactive neutralization of SARS-CoV-2 by serum antibodies from recovered SARS patients and immunized animals

Zhu

Han

et al. 2020

Preprint

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16The current COVID-19 pandemic, caused by a novel coronavirus SARS-CoV-2, poses serious 17 threats to public health and social stability, calling for urgent need for vaccines and 18 therapeutics. SARS-CoV-2 is genetically close to SARS-CoV, thus it is important to define 19 the between antigenic cross-reactivity and neutralization. In this study, we firstly analyzed 20 20 convalescent serum samples collected from SARS-CoV infected individuals during the 2003 21 SARS outbreak. All patient sera reacted strongly with the S1 subunit and receptor-binding 22 domain (RBD) of SARS-CoV, cross-reacted with the S ectodomain, S1, RBD, and S2 23 proteins of SARS-CoV-2, and neutralized both SARS-CoV and SARS-CoV-2 S 24 protein-driven infections. Multiple panels of antisera from mice and rabbits immunized with a 25 full-length S and RBD immunogens of SARS-CoV were also characterized, verifying the 26 cross-reactive neutralization against SARS-CoV-2. Interestingly, we found that a palm civet 27 SARS-CoV-derived RBD elicited more potent cross-neutralizing responses in immunized 28 animals than the RBD from a human SARS-CoV strain, informing a strategy to develop a 29 universe vaccine against emerging CoVs. 30 31 Summary 32 Serum antibodies from SARS-CoV infected patients and immunized animals cross-neutralize 33 SARS-CoV-2 suggests strategies for universe vaccines against emerging CoVs. acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is a new coronavirus (CoV) 37 genetically close to SARS-CoV emerged in 2002 (1-3). As of 20 April 2020, a total of 38 2,246,291 confirmed COVID-19 cases, including 152,707 deaths, have been reported from 39 213 countries or regions, and the numbers are growing rapidly (https://www.who.int). The 40 pandemic threatens to become one of the most difficult times faced by humans in modern 41 history. Unfortunately, even though 17 years passed, we have not developed effective 42 prophylactics and therapeutics in preparedness for the re-emergence of SARS or SARS-like 43 CoVs. A vaccine is urgently needed to prevent the human-to-human transmission of 44 SARS-CoV-2. 45Like SARS-CoV and many other CoVs, SARS-CoV-2 utilizes its surface spike (S) 46 glycoprotein to gain entry into host cells (4-6). Typically, the S protein forms a homotrimer 47 with each protomer consisting of S1 and S2 subunits. The N-terminal S1 subunit is 48 responsible for virus binding to the cellular receptor ACE2 through an internal 49 receptor-binding domain (RBD) that is capable of functional folding independently, whereas 50 the membrane-proximal S2 subunit mediates membrane fusion events. Very recently, the 51 prefusion structure of the SARS-CoV-2 S protein was determined by cryo-EM, which 52 revealed an overall similarity to that of SARS-CoV (4, 7); the crystal structure of the 53 SARS-CoV-2 RBD in complex with ACE2 was also determined by several independent 54 groups, and the residues or motifs critical for the higher-affinity RBD-ACE2 interaction were 55 identified (8-10).The S protein of CoVs is also a main target of ...

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Section: Discussionmentioning

confidence: 99%

Cross-reactive neutralization of SARS-CoV-2 by serum antibodies from recovered SARS patients and immunized animals

Zhu

Han

et al. 2020

Preprint

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“…(C) Spike expression on the surface of 293T cells transfected with the plasmids expressing our three Spike constructs was measured using flow cytometry 24 hours post-transfection. Spike expression was measured by staining with in-house produced CR3022 antibody [43][44][45] at a concentration of 10 µg/mL followed by staining with an anti-human Fc antibody conjugated to APC (Jackson Labs, 109-135-098) at a 1:100 dilution.…”

Section: General Approach For Pseudotyping Lentiviral Particles Withmentioning

confidence: 99%

Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays

Crawford

Eguia

Dingens

et al. 2020

Preprint

234

270

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AbstractSARS-CoV-2 enters cells using its Spike protein, which is also the main target of neutralizing antibodies. Therefore, assays to measure how antibodies and sera affect Spike-mediated viral infection are important for studying immunity. Because SARS-CoV-2 is a biosafety-level-3 virus, one way to simplify such assays is to pseudotype biosafety-level-2 viral particles with Spike. Such pseudotyping has now been described for single-cycle lentiviral, retroviral and VSV particles, but the reagents and protocols are not widely available. Here we detail how to effectively pseudotype lentiviral particles with SARS-CoV-2 Spike and infect 293T cells engineered to express the SARS-CoV-2 receptor, ACE2. We also make all the key experimental reagents available in the BEI Resources repository of ATCC and the NIH. Furthermore, we demonstrate how these pseudotyped lentiviral particles can be used to measure the neutralizing activity of human sera or plasma against SARS-CoV-2 in convenient luciferase-based assays, thereby providing a valuable complement to ELISA-based methods that measure antibody binding rather than neutralization.

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“…To the best of our knowledge, none of these neutralizing antibody sequences are publicly available. In another very encouraging study 17 , human antibody CR3022 (which is neutralizing against SARS-CoV-1 18 ) has been shown to bind to SARS-CoV-2 RBD in a cryptic epitope but without a neutralizing effect for SARS-CoV-2 in vitro. Moreover, we did not find any studies that performed guided design of high affinity antibodies against specific epitopes of SARS-CoV-2 proteins such as targeting the spike protein and subsequently prevent its binding with human ACE2.…”

Section: Mainmentioning

confidence: 99%

“…Figure 3b illustrates the trade-off between the Rosetta binding energy vs. H-score for the top 60 affinity matured variable region designs. Note that we calculated the H-score for the human CR3022 17 (anti-SARS-CoV-1 antibody) to be 667 which in the same range as our most human designs. We selected five designs that were on the Pareto optimum curve shown in Figure 3b.…”

Section: Mainmentioning

confidence: 99%

“…This implies that this design has the potential to competitively bind the RBD of the SARS-CoV-2 spike protein thus sequestering it from ACE2. In addition, we calculated the Rosetta binding energy between the human CR3022 17 (anti-SARS-CoV-1 antibody) and the SARS-CoV-2 spike protein RBD using complex structure (PDB-id:6W41) to be −48.83 kcal/mol and both our best binding designs P5.D1 and P5.D2 have better binding energies (~12 kcal/mol more negative) than CR3022. It is important to stress that our designs rely on the accuracy of the Rosetta energy function to recapitulate experimental affinities and that running experimental binding assays are needed to confirm or refute these findings.…”

Section: Mainmentioning

confidence: 99%

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De novo design of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike protein

Boorla

Chowdhury

Maranas

2020

Preprint

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1The emergence of SARS-CoV-2 is responsible for the pandemic of respiratory disease known as COVID-1 2 19, which emerged in the city of Wuhan, Hubei province, China in late 2019. Both vaccines and targeted 1 3 therapeutics for treatment of this disease are currently lacking. Viral entry requires binding of the viral 1 4 spike receptor binding domain (RBD) with the human angiotensin converting enzyme (ACE2). In an 1 5 3 1 (Cellex, GeneTex etc.) for the development of antibody-based tests for SARS-CoV-2 detection are 3 2 ongoing 8 . At the same time, significant progress towards the isolation and design of vaccines (mRNA-3 3 1273 vaccine © 2020 Moderna, Inc) and neutralizing antibodies 9 has been made. A computational study : bioRxiv preprint identified the structural basis for multi-epitope vaccines 10,11 whereas in another study, the glycosylation 3 5 patterns of the spike SARS-CoV-2 protein were computationally deduced 12 . In one study 13 , fully human 3 6 single domain anti-SARS-CoV-2 antibodies with sub-nanomolar affinities were identified from a phage-3 7 displayed single-domain antibody library by grafting naïve CDRs into framework regions of an identified 3 8 human germline IGHV allele using SARS-CoV-2 RBD and S1 protein as antigens. In another study 14 , a 3 9 human antibody 47D11 was identified to have cross neutralizing effect on SARS-CoV-2 by screening 4 0 through a library of SARS-Cov-1 antibodies. In two other studies, potent neutralizing antibodies were 4 1 isolated from the sera of convalescent COVID-19 patients 15,16 . To the best of our knowledge, none of 4 2 these neutralizing antibody sequences are publicly available. In another very encouraging study 17 , human 4 3 antibody CR3022 (which is neutralizing against SARS-CoV-1 18 ) has been shown to bind to SARS-CoV-2 4 4 RBD in a cryptic epitope but without a neutralizing effect for SARS-CoV-2 in vitro. Moreover, we did 4 5 not find any studies that performed guided design of high affinity antibodies against specific epitopes of 4 6 SARS-CoV-2 proteins such as targeting the spike protein and subsequently prevent its binding with 4 7 human ACE2. 8 9Motivated by these shortcomings, here we explore the de novo design of antibody variable regions For each one of the 3,234 spike poses, OptMAVEn-2.0 identified a variable region combination 9 3 composed of end-to-end joined V*, CDR3, and J* region parts that minimized the Rosetta binding energy 9 4 between the variable region and spike epitope formed by the seven residues. As part of OptMAVEn-2.0, 9 5 the combinatorial optimization problem was posed and solved as a mixed-integer linear programming 9 6 (MILP) problem using the cplex solver 26 . The solution of this problem identifies, for each one of the spike 9 7 poses, the complete design of the variable region using parts denoted as HV*, HCDR3, HJ* for the heavy 9 8 chain H and L/KV*, L/KCDR3 and L/KJ* for the light chain-L/K. Only 173 antigen-presenting poses out 9 9 of 3,234 explored, yielded non-clashing antigen-antibody complexes. These 173 poses ...

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A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

Cited by 1,466 publications

References 44 publications

Cross-reactive neutralization of SARS-CoV-2 by serum antibodies from recovered SARS patients and immunized animals

Cross-reactive neutralization of SARS-CoV-2 by serum antibodies from recovered SARS patients and immunized animals

Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays

De novo design of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike protein

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