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  1. Article: Evolving spike-protein

    Baboo, Sabyasachi / Diedrich, Jolene K / Torres, Jonathan L / Copps, Jeffrey / Singh, Bhavya / Garrett, Patrick T / Ward, Andrew B / Paulson, James C / Yates, John R

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 ... ...

    Abstract Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily
    Language English
    Publishing date 2023-12-18
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.08.539897
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Repeat modules and N-linked glycans define structure and antigenicity of a critical enterotoxigenic

    Berndsen, Zachary T / Akhtar, Marjahan / Thapa, Mahima / Vickers, Tim / Schmitz, Aaron / Torres, Jonathan L / Baboo, Sabyasachi / Kumar, Pardeep / Khatoom, Nazia / Sheikh, Alaullah / Hamrick, Melissa / Diedrich, Jolene K / Martinez-Bartolome, Salvador / Garrett, Patrick T / Yates, John R / Turner, Jackson S / Laird, Renee M / Poly, Frédéric / Porter, Chad K /
    Copps, Jeffrey / Ellebedy, Ali H / Ward, Andrew B / Fleckenstein, James M

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Enterotoxigenic : Author summary: ... ...

    Abstract Enterotoxigenic
    Author summary: Enterotoxigenic
    Language English
    Publishing date 2024-05-08
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.05.08.593125
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimmers as HIV-1 vaccine candidates.

    Zhang, Yi-Nan / Paynter, Jennifer / Antanasijevic, Aleksandar / Allen, Joel D / Eldad, Mor / Lee, Yi-Zong / Copps, Jeffrey / Newby, Maddy L / He, Linling / Chavez, Deborah / Frost, Pat / Goodroe, Anna / Dutton, John / Lanford, Robert / Chen, Christopher / Wilson, Ian A / Crispin, Max / Ward, Andrew B / Zhu, Jiang

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 1985

    Abstract: Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native-like Env trimers as vaccine candidates. We characterize ... ...

    Abstract Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native-like Env trimers as vaccine candidates. We characterize the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. For 1c-SApNPs, glycan trimming improves recognition of the CD4 binding site without affecting broadly neutralizing antibodies (bNAbs) to major glycan epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increases the frequency of vaccine responders (FVR) and steers antibody responses away from immunodominant glycan holes and glycan patches. The mechanism of vaccine-induced immunity is examined in mice. Compared with the UFO trimer, the multilayered E2p and I3-01v9 1c-SApNPs show 420 times longer retention in lymph node follicles, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions. These findings can inform future HIV-1 vaccine development.
    MeSH term(s) Rabbits ; Animals ; Mice ; HIV Antibodies ; HIV-1 ; env Gene Products, Human Immunodeficiency Virus ; Antibodies, Neutralizing ; Vaccines/metabolism ; Polysaccharides/metabolism ; HIV Infections
    Chemical Substances HIV Antibodies ; env Gene Products, Human Immunodeficiency Virus ; Antibodies, Neutralizing ; Vaccines ; Polysaccharides
    Language English
    Publishing date 2023-04-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-37742-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Structural mapping of antibody landscapes to human betacoronavirus spike proteins.

    Bangaru, Sandhya / Antanasijevic, Aleksandar / Kose, Nurgun / Sewall, Leigh M / Jackson, Abigail M / Suryadevara, Naveenchandra / Zhan, Xiaoyan / Torres, Jonathan L / Copps, Jeffrey / de la Peña, Alba Torrents / Crowe, James E / Ward, Andrew B

    Science advances

    2022  Volume 8, Issue 18, Page(s) eabn2911

    Abstract: Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. We used electron microscopy-based ... ...

    Abstract Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. We used electron microscopy-based polyclonal epitope mapping (EMPEM) to characterize the antibody specificities against β-CoV spike proteins in prepandemic (PP) sera or SARS-CoV-2 convalescent (SC) sera. We observed that most PP sera had antibodies specific to seasonal human CoVs (HCoVs) OC43 and HKU1 spike proteins while the SC sera showed reactivity across all human β-CoVs. Detailed molecular mapping of spike-antibody complexes revealed epitopes that were differentially targeted by preexisting antibodies and SC serum antibodies. Our studies provide an antigenic landscape to β-HCoV spikes in the general population serving as a basis for cross-reactive epitope analyses in SARS-CoV-2-infected individuals.
    MeSH term(s) Antibodies, Viral ; COVID-19 ; Coronavirus OC43, Human ; Epitopes ; Humans ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
    Chemical Substances Antibodies, Viral ; Epitopes ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2022-05-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.abn2911
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Structural Basis of Pan-Ebolavirus Neutralization by an Antibody Targeting the Glycoprotein Fusion Loop.

    Murin, Charles D / Bruhn, Jessica F / Bornholdt, Zachary A / Copps, Jeffrey / Stanfield, Robyn / Ward, Andrew B

    Cell reports

    2018  Volume 24, Issue 10, Page(s) 2723–2732.e4

    Abstract: Monoclonal antibodies (mAbs) with pan-ebolavirus cross-reactivity are highly desirable, but development of such mAbs is limited by a lack of a molecular understanding of cross-reactive epitopes. The antibody ADI-15878 was previously identified from a ... ...

    Abstract Monoclonal antibodies (mAbs) with pan-ebolavirus cross-reactivity are highly desirable, but development of such mAbs is limited by a lack of a molecular understanding of cross-reactive epitopes. The antibody ADI-15878 was previously identified from a human survivor of Ebola virus Makona variant (EBOV/Mak) infection. This mAb demonstrated potent neutralizing activity against all known ebolaviruses and provided protection in rodent and ferret models against three ebolavirus species. Here, we describe the unliganded crystal structure of ADI-15878 as well as the cryo-EM structures of ADI-15878 in complex with the EBOV/Mak and Bundibugyo virus (BDBV) glycoproteins (GPs). ADI-15878 binds through an induced-fit mechanism by targeting highly conserved residues in the internal fusion loop (IFL), bridging across GP protomers via the heptad repeat 1 (HR1) region. Our structures provide a more complete description of the ebolavirus immunogenic landscape, as well as a molecular basis for how rare but potent antibodies target conserved filoviral fusion machinery.
    MeSH term(s) Antibodies, Neutralizing/genetics ; Antibodies, Neutralizing/immunology ; Antibodies, Neutralizing/metabolism ; Antibodies, Viral/immunology ; Antibodies, Viral/metabolism ; Cryoelectron Microscopy ; Crystallography ; Ebolavirus/genetics ; Ebolavirus/metabolism ; Filoviridae/genetics ; Filoviridae/metabolism ; Glycoproteins/genetics ; Glycoproteins/immunology ; Glycoproteins/metabolism ; Promoter Regions, Genetic/genetics ; Protein Structure, Secondary
    Chemical Substances Antibodies, Neutralizing ; Antibodies, Viral ; Glycoproteins
    Language English
    Publishing date 2018-09-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2018.08.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Evolving spike-protein N-glycosylation in SARS-CoV-2 variants

    Baboo, Sabyasachi / Diedrich, Jolene K. / Torres, Jonathan L. / Copps, Jeffrey / Singh, Bhavya / Garrett, Patrick T. / Ward, Andrew B. / Paulson, James C. / Yates, John R.

    bioRxiv

    Abstract: It has been three years since SARS-CoV-2 emerged and the world plunged into a "once in a century" pandemic. Since then, multiple waves of infection have swept through the human population, led by variants that were able to evade any acquired immunity. ... ...

    Abstract It has been three years since SARS-CoV-2 emerged and the world plunged into a "once in a century" pandemic. Since then, multiple waves of infection have swept through the human population, led by variants that were able to evade any acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune response, both of which are impacted by host-installed N-glycans. We compared the N-glycan landscape of recombinantly expressed, stabilized, soluble spike-protein trimers representing seven of the most prominent SARS-CoV-2 variants and found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.
    Keywords covid19
    Language English
    Publishing date 2023-05-09
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2023.05.08.539897
    Database COVID19

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  7. Article ; Online: Affinity-matured homotypic interactions induce spectrum of PfCSP structures that influence protection from malaria infection.

    Martin, Gregory M / Torres, Jonathan L / Pholcharee, Tossapol / Oyen, David / Flores-Garcia, Yevel / Gibson, Grace / Moskovitz, Re'em / Beutler, Nathan / Jung, Diana D / Copps, Jeffrey / Lee, Wen-Hsin / Gonzalez-Paez, Gonzalo / Emerling, Daniel / MacGill, Randall S / Locke, Emily / King, C Richter / Zavala, Fidel / Wilson, Ian A / Ward, Andrew B

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 4546

    Abstract: The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth ... ...

    Abstract The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by the immunoglobulin heavy chain variable (IGHV) gene IGHV3-33, which is among the most prevalent and potent antibody families induced in the anti-PfCSP immune response and targets the Asn-Ala-Asn-Pro (NANP) repeat region. Cryo-electron microscopy (cryo-EM) reveals a remarkable spectrum of helical antibody-PfCSP structures stabilized by homotypic interactions between tightly packed fragments antigen binding (Fabs), many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to PfCSP and in protection from Pf malaria infection. Together, these data emphasize the importance of anti-homotypic affinity maturation in the frequent selection of IGHV3-33 antibodies and highlight key features underlying the potent protection of this antibody family.
    MeSH term(s) Humans ; Cryoelectron Microscopy ; Plasmodium falciparum/genetics ; Malaria/prevention & control ; Malaria, Falciparum/prevention & control ; Protozoan Proteins/chemistry ; Malaria Vaccines ; Antibodies ; Antibodies, Protozoan
    Chemical Substances Protozoan Proteins ; Malaria Vaccines ; Antibodies ; Antibodies, Protozoan
    Language English
    Publishing date 2023-07-28
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-40151-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Mining HIV controllers for broad and functional antibodies to recognize and eliminate HIV-infected cells.

    Rossignol, Evan D / Dugast, Anne-Sophie / Compere, Hacheming / Cottrell, Christopher A / Copps, Jeffrey / Lin, Shu / Cizmeci, Deniz / Seaman, Michael S / Ackerman, Margaret E / Ward, Andrew B / Alter, Galit / Julg, Boris

    Cell reports

    2021  Volume 35, Issue 8, Page(s) 109167

    Abstract: HIV monoclonal antibodies for viral reservoir eradication strategies will likely need to recognize reactivated infected cells and potently drive Fc-mediated innate effector cell activity. We systematically characterize a library of 185 HIV-envelope- ... ...

    Abstract HIV monoclonal antibodies for viral reservoir eradication strategies will likely need to recognize reactivated infected cells and potently drive Fc-mediated innate effector cell activity. We systematically characterize a library of 185 HIV-envelope-specific antibodies derived from 15 spontaneous HIV controllers (HCs) that selectively exhibit robust serum Fc functionality and compared them to broadly neutralizing antibodies (bNAbs) in clinical development. Within the 10 antibodies with the broadest cell-recognition capability, seven originated from HCs and three were bNAbs. V3-loop-targeting antibodies are enriched among the top cell binders, suggesting the V3-loop may be selectively exposed and accessible on the cell surface. Fc functionality is more variable across antibodies, which is likely influenced by distinct binding topology and corresponding Fc accessibility, highlighting not only the importance of target-cell recognition but also the need to optimize for Fc-mediated elimination. Ultimately, our results demonstrate that this comprehensive selection process can identify monoclonal antibodies poised to eliminate infected cells.
    MeSH term(s) Adult ; Antibodies, Monoclonal/pharmacology ; Antibodies, Monoclonal/therapeutic use ; Female ; HIV Infections/drug therapy ; Humans ; Male ; Middle Aged
    Chemical Substances Antibodies, Monoclonal
    Language English
    Publishing date 2021-06-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2021.109167
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles.

    Kumar, Sonu / Lin, Xiaohe / Ngo, Timothy / Shapero, Benjamin / Sou, Cindy / Allen, Joel D / Copps, Jeffrey / Zhang, Lei / Ozorowski, Gabriel / He, Linling / Crispin, Max / Ward, Andrew B / Wilson, Ian A / Zhu, Jiang

    mBio

    2021  Volume 12, Issue 3, Page(s) e0042921

    Abstract: The immunogenicity of gp41-stabilized HIV-1 BG505 envelope (Env) trimers and nanoparticles (NPs) was recently assessed in mice and rabbits. Here, we combined Env-specific B-cell sorting and repertoire sequencing to identify neutralizing antibodies (NAbs) ...

    Abstract The immunogenicity of gp41-stabilized HIV-1 BG505 envelope (Env) trimers and nanoparticles (NPs) was recently assessed in mice and rabbits. Here, we combined Env-specific B-cell sorting and repertoire sequencing to identify neutralizing antibodies (NAbs) from immunized animals. A panel of mouse NAbs was isolated from mice immunized with a 60-meric I3-01 NP presenting 20 stabilized trimers. Three mouse NAbs potently neutralized BG505.T332N by recognizing a glycan epitope centered in the C3/V4 region on BG505 Env, as revealed by electron microscopy (EM), X-ray crystallography, and epitope mapping. A set of rabbit NAbs was isolated from rabbits immunized with a soluble trimer and a 24-meric ferritin NP presenting 8 trimers. Neutralization assays against BG505.T332N variants confirmed that potent rabbit NAbs targeted previously described glycan holes on BG505 Env and accounted for a significant portion of the autologous NAb response in both the trimer and ferritin NP groups. Last, we examined NAb responses that were induced by non-BG505 Env immunogens. We determined a 3.4-Å-resolution crystal structure for the clade C transmitted/founder (T/F) Du172.17 Env with a redesigned heptad repeat 1 (HR1) bend in gp41. This clade C Env, in a soluble trimer form and in a multivalent form with 8 trimers attached to ferritin NP, and the gp41-stabilized clade A Q482-d12 Env trimer elicited distinct NAb responses in rabbits, with notable differences in neutralization breadth. Although eliciting a broad NAb response remains a major challenge, our study provides valuable information on an HIV-1 vaccine design strategy that combines gp41 stabilization and NP display.
    MeSH term(s) Animals ; Antibodies, Neutralizing/immunology ; Antigens, Viral/immunology ; B-Lymphocytes/immunology ; Epitope Mapping ; Epitopes/immunology ; Female ; HEK293 Cells ; HIV Antibodies/immunology ; HIV Envelope Protein gp41/administration & dosage ; HIV Envelope Protein gp41/chemistry ; HIV Envelope Protein gp41/immunology ; Humans ; Immunization ; Immunogenicity, Vaccine ; Mice ; Nanoparticles/administration & dosage ; Nanoparticles/chemistry ; Rabbits
    Chemical Substances Antibodies, Neutralizing ; Antigens, Viral ; Epitopes ; HIV Antibodies ; HIV Envelope Protein gp41
    Language English
    Publishing date 2021-06-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mBio.00429-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies.

    Murin, Charles D / Gilchuk, Pavlo / Ilinykh, Philipp A / Huang, Kai / Kuzmina, Natalia / Shen, Xiaoli / Bruhn, Jessica F / Bryan, Aubrey L / Davidson, Edgar / Doranz, Benjamin J / Williamson, Lauren E / Copps, Jeffrey / Alkutkar, Tanwee / Flyak, Andrew I / Bukreyev, Alexander / Crowe, James E / Ward, Andrew B

    Cell reports

    2021  Volume 35, Issue 2, Page(s) 108984

    Abstract: Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization are not well ... ...

    Abstract Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization are not well understood. Here, we present cryoelectron microscopy (cryo-EM) structures of diverse glycan cap antibodies that variably synergize with GP base-binding antibodies. These structures describe a conserved site of vulnerability that anchors the mucin-like domains (MLDs) to the glycan cap, which we call the MLD anchor and cradle. Antibodies that bind to the MLD cradle share common features, including use of IGHV1-69 and IGHJ6 germline genes, which exploit hydrophobic residues and form β-hairpin structures to mimic the MLD anchor, disrupt MLD attachment, destabilize GP quaternary structure, and block cleavage events required for receptor binding. Our results provide a molecular basis for ebolavirus neutralization by broadly reactive glycan cap antibodies.
    MeSH term(s) Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/chemistry ; Antibodies, Monoclonal/metabolism ; Antibodies, Monoclonal/pharmacology ; Antibodies, Neutralizing/chemistry ; Antibodies, Neutralizing/metabolism ; Antibodies, Neutralizing/pharmacology ; Antibodies, Viral/chemistry ; Antibodies, Viral/metabolism ; Antibodies, Viral/pharmacology ; Antibody Specificity ; Binding Sites ; Cryoelectron Microscopy ; Ebolavirus/drug effects ; Ebolavirus/growth & development ; Ebolavirus/immunology ; Ebolavirus/pathogenicity ; Epitopes/chemistry ; Epitopes/immunology ; Female ; HEK293 Cells ; HeLa Cells ; Hemorrhagic Fever, Ebola/drug therapy ; Hemorrhagic Fever, Ebola/immunology ; Hemorrhagic Fever, Ebola/pathology ; Hemorrhagic Fever, Ebola/virology ; Humans ; Jurkat Cells ; Mice ; Models, Molecular ; Polysaccharides/chemistry ; Polysaccharides/immunology ; Protein Binding ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Sequence Alignment ; Sequence Homology, Amino Acid ; Viral Envelope Proteins/antagonists & inhibitors ; Viral Envelope Proteins/chemistry ; Viral Envelope Proteins/genetics ; Viral Envelope Proteins/metabolism
    Chemical Substances Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Epitopes ; Polysaccharides ; Viral Envelope Proteins
    Language English
    Publishing date 2021-04-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2021.108984
    Database MEDical Literature Analysis and Retrieval System OnLINE

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