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Article ; Online: Structural basis for broad coronavirus neutralization

Veesler, David

bioRxiv

Abstract: Three highly pathogenic β-coronaviruses crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. SARSCoV-2 has infected more than 64 million people worldwide, claimed over 1.4 million lives and is ... ...

Abstract	Three highly pathogenic β-coronaviruses crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. SARSCoV-2 has infected more than 64 million people worldwide, claimed over 1.4 million lives and is responsible for the ongoing COVID-19 pandemic. We isolated a monoclonal antibody, termed B6, cross-reacting with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses, and broadly inhibiting entry of pseudotyped viruses from two coronavirus lineages. Cryoelectron microscopy and X-ray crystallography characterization reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery and indicate that antibody binding sterically interferes with spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages along with proof-of-concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-coronavirus vaccine.
Keywords	covid19
Language	English
Publishing date	2020-12-29
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.12.29.424482
Database	COVID19

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Article ; Online: Virus structures and molecular biology exchange glances.

Roy, Polly / Veesler, David / Rey, Felix

Structure (London, England : 1993)

2023

Abstract: The definition of structure as the arrangement of and relations between the parts of something complex has always been a challenge in virology. The balance required for a virus to be sufficiently stable to allow transmission yet also be primed for ... ...

Abstract	The definition of structure as the arrangement of and relations between the parts of something complex has always been a challenge in virology. The balance required for a virus to be sufficiently stable to allow transmission yet also be primed for disassembly on contact with a permissive cell is precarious and seemingly difficult to attain. Add to this that virus structural components often have multiple functions such as receptor binding, fusion, and cleavage, and the puzzle deepens. It also has consequences: virus yields may be compromised, vaccine shelf-life may be limited, and the ability to quickly evolve away from an intervention may be underestimated. Progress in understanding virus structure and the ways in which it might be exploited were the subject of the latest International Virus Assembly Symposium. Whole viruses, individual components, and transient intermediates were revealed at sufficiently high resolution to deduce the mechanisms concerned.
Language	English
Publishing date	2023-02-11
Publishing country	United States
Document type	Clinical Conference
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2023.01.013
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Article ; Online: Structural insights into coronavirus entry.

Tortorici, M Alejandra / Veesler, David

Advances in virus research

2019 Volume 105, Page(s) 93–116

Abstract: Coronaviruses (CoVs) have caused outbreaks of deadly pneumonia in humans since the beginning of the 21st century. The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 and was responsible for an epidemic that spread to five ... ...

Abstract	Coronaviruses (CoVs) have caused outbreaks of deadly pneumonia in humans since the beginning of the 21st century. The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 and was responsible for an epidemic that spread to five continents with a fatality rate of 10% before being contained in 2003 (with additional cases reported in 2004). The Middle-East respiratory syndrome coronavirus (MERS-CoV) emerged in the Arabian Peninsula in 2012 and has caused recurrent outbreaks in humans with a fatality rate of 35%. SARS-CoV and MERS-CoV are zoonotic viruses that crossed the species barrier using bats/palm civets and dromedary camels, respectively. No specific treatments or vaccines have been approved against any of the six human coronaviruses, highlighting the need to investigate the principles governing viral entry and cross-species transmission as well as to prepare for zoonotic outbreaks which are likely to occur due to the large reservoir of CoVs found in mammals and birds. Here, we review our understanding of the infection mechanism used by coronaviruses derived from recent structural and biochemical studies.
MeSH term(s)	Animals ; Coronavirus/physiology ; Coronavirus/ultrastructure ; Host-Pathogen Interactions ; Humans ; Virion/ultrastructure ; Virus Internalization
Keywords	covid19
Language	English
Publishing date	2019-08-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	195-8
ISSN	1557-8399 ; 0065-3527
ISSN (online)	1557-8399
ISSN	0065-3527
DOI	10.1016/bs.aivir.2019.08.002
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Article ; Online: Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps.

Muenks, Andrew / Zepeda, Samantha / Zhou, Guangfeng / Veesler, David / DiMaio, Frank

Nature communications

2023 Volume 14, Issue 1, Page(s) 1164

Abstract: Advances in cryo-electron microscopy (cryoEM) and deep-learning guided protein structure prediction have expedited structural studies of protein complexes. However, methods for accurately determining ligand conformations are lacking. In this manuscript, ... ...

Abstract	Advances in cryo-electron microscopy (cryoEM) and deep-learning guided protein structure prediction have expedited structural studies of protein complexes. However, methods for accurately determining ligand conformations are lacking. In this manuscript, we develop EMERALD, a tool for automatically determining ligand structures guided by medium-resolution cryoEM density. We show this method is robust at predicting ligands along with surrounding side chains in maps as low as 4.5 Å local resolution. Combining this with a measure of placement confidence and running on all protein/ligand structures in the EMDB, we show that 57% of ligands replicate the deposited model, 16% confidently find alternate conformations, 22% have ambiguous density where multiple conformations might be present, and 5% are incorrectly placed. For five cases where our approach finds an alternate conformation with high confidence, high-resolution crystal structures validate our placement. EMERALD and the resulting analysis should prove critical in using cryoEM to solve protein-ligand complexes.
MeSH term(s)	Cryoelectron Microscopy ; Ligands ; Mental Processes ; Running
Chemical Substances	Ligands
Language	English
Publishing date	2023-03-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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/s41467-023-36732-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Functional and antigenic landscape of the Nipah virus receptor binding protein.

Larsen, Brendan B / McMahon, Teagan / Brown, Jack T / Wang, Zhaoqian / Radford, Caelan E / Crowe, James E / Veesler, David / Bloom, Jesse D

bioRxiv : the preprint server for biology

2024

Abstract: Nipah virus recurrently spills over to humans, causing fatal infections. The viral receptor-binding protein (RBP or G) attaches to host receptors and is a major target of neutralizing antibodies. Here we use deep mutational scanning to measure how all ... ...

Abstract	Nipah virus recurrently spills over to humans, causing fatal infections. The viral receptor-binding protein (RBP or G) attaches to host receptors and is a major target of neutralizing antibodies. Here we use deep mutational scanning to measure how all amino-acid mutations to the RBP affect cell entry, receptor binding, and escape from neutralizing antibodies. We identify functionally constrained regions of the RBP, including sites involved in oligomerization, along with mutations that differentially modulate RBP binding to its two ephrin receptors. We map escape mutations for six anti-RBP antibodies, and find that few antigenic mutations are present in natural Nipah strains. Our findings offer insights into the potential for functional and antigenic evolution of the RBP that can inform the development of antibody therapies and vaccines.
Language	English
Publishing date	2024-04-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.17.589977
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Article ; Online: Tackling COVID-19 with neutralizing monoclonal antibodies.

Corti, Davide / Purcell, Lisa A / Snell, Gyorgy / Veesler, David

Cell

2021 Volume 184, Issue 17, Page(s) 4593–4595

Language	English
Publishing date	2021-08-20
Publishing country	United States
Document type	Published Erratum
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.07.027
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Tackling COVID-19 with neutralizing monoclonal antibodies.

Corti, Davide / Purcell, Lisa A / Snell, Gyorgy / Veesler, David

Cell

2021 Volume 184, Issue 12, Page(s) 3086–3108

Abstract: Monoclonal antibodies (mAbs) have revolutionized the treatment of several human diseases, including cancer and autoimmunity and inflammatory conditions, and represent a new frontier for the treatment of infectious diseases. In the last 20 years, ... ...

Abstract	Monoclonal antibodies (mAbs) have revolutionized the treatment of several human diseases, including cancer and autoimmunity and inflammatory conditions, and represent a new frontier for the treatment of infectious diseases. In the last 20 years, innovative methods have allowed the rapid isolation of mAbs from convalescent subjects, humanized mice, or libraries assembled in vitro and have proven that mAbs can be effective countermeasures against emerging pathogens. During the past year, an unprecedentedly large number of mAbs have been developed to fight coronavirus disease 2019 (COVID-19). Lessons learned from this pandemic will pave the way for the development of more mAb-based therapeutics for other infectious diseases. Here, we provide an overview of SARS-CoV-2-neutralizing mAbs, including their origin, specificity, structure, antiviral and immunological mechanisms of action, and resistance to circulating variants, as well as a snapshot of the clinical trials of approved or late-stage mAb therapeutics.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/immunology ; Angiotensin-Converting Enzyme 2/metabolism ; Animals ; Antibodies, Monoclonal/chemistry ; Antibodies, Monoclonal/immunology ; Antibodies, Monoclonal/therapeutic use ; Antibodies, Neutralizing/chemistry ; Antibodies, Neutralizing/immunology ; Antibodies, Neutralizing/therapeutic use ; Antibodies, Viral/chemistry ; Antibodies, Viral/immunology ; Antibodies, Viral/therapeutic use ; COVID-19/pathology ; COVID-19/virology ; Humans ; SARS-CoV-2/immunology ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/immunology ; COVID-19 Drug Treatment
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-05-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.05.005
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article: Human coronavirus HKU1 recognition of the TMPRSS2 host receptor.

McCallum, Matthew / Park, Young-Jun / Stewart, Cameron / Sprouse, Kaitlin R / Brown, Jack / Tortorici, M Alejandra / Gibson, Cecily / Wong, Emily / Ieven, Margareta / Telenti, Amalio / Veesler, David

bioRxiv : the preprint server for biology

2024

Abstract: The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain ... ...

Abstract	The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. Here, we designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2 providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among human type 2 transmembrane serine proteases. We found that human, rat, hamster and camel TMPRSS2 promote HKU1 S-mediated entry into cells and identified key residues governing host receptor usage. Our data show that serum antibodies targeting the HKU1 RBD TMPRSS2 binding-site are key for neutralization and that HKU1 uses conformational masking and glycan shielding to balance immune evasion and receptor engagement.
Language	English
Publishing date	2024-01-09
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.09.574565
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Persistent immune imprinting occurs after vaccination with the COVID-19 XBB.1.5 mRNA booster in humans.

Tortorici, M Alejandra / Addetia, Amin / Seo, Albert J / Brown, Jack / Sprouse, Kaiti / Logue, Jenni / Clark, Erica / Franko, Nicholas / Chu, Helen / Veesler, David

Immunity

2024 Volume 57, Issue 4, Page(s) 904–911.e4

Abstract: Immune imprinting describes how the first exposure to a virus shapes immunological outcomes of subsequent exposures to antigenically related strains. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron breakthrough infections and ... ...

Abstract	Immune imprinting describes how the first exposure to a virus shapes immunological outcomes of subsequent exposures to antigenically related strains. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron breakthrough infections and bivalent COVID-19 vaccination primarily recall cross-reactive memory B cells induced by prior Wuhan-Hu-1 spike mRNA vaccination rather than priming Omicron-specific naive B cells. These findings indicate that immune imprinting occurs after repeated Wuhan-Hu-1 spike exposures, but whether it can be overcome remains unclear. To understand the persistence of immune imprinting, we investigated memory and plasma antibody responses after administration of the updated XBB.1.5 COVID-19 mRNA vaccine booster. We showed that the XBB.1.5 booster elicited neutralizing antibody responses against current variants that were dominated by recall of pre-existing memory B cells previously induced by the Wuhan-Hu-1 spike. Therefore, immune imprinting persists after multiple exposures to Omicron spikes through vaccination and infection, including post XBB.1.5 booster vaccination, which will need to be considered to guide future vaccination.
MeSH term(s)	Humans ; COVID-19 Vaccines ; COVID-19/prevention & control ; SARS-CoV-2 ; Antibodies, Neutralizing ; RNA, Messenger/genetics ; Vaccination ; Antibodies, Viral
Chemical Substances	COVID-19 Vaccines ; Antibodies, Neutralizing ; RNA, Messenger ; Antibodies, Viral
Language	English
Publishing date	2024-03-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	1217235-2
ISSN	1097-4180 ; 1074-7613
ISSN (online)	1097-4180
ISSN	1074-7613
DOI	10.1016/j.immuni.2024.02.016
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Article ; Online: Structure and design of Langya virus glycoprotein antigens.

Wang, Zhaoqian / McCallum, Matthew / Yan, Lianying / Gibson, Cecily A / Sharkey, William / Park, Young-Jun / Dang, Ha V / Amaya, Moushimi / Person, Ashley / Broder, Christopher C / Veesler, David

Proceedings of the National Academy of Sciences of the United States of America

2024 Volume 121, Issue 16, Page(s) e2314990121

Abstract: Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which are the main targets of neutralizing antibodies. We ... ...

Abstract	Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which are the main targets of neutralizing antibodies. We show here that the LayV F and G glycoproteins promote membrane fusion with human, mouse, and hamster target cells using a different, yet unknown, receptor than Nipah virus (NiV) and Hendra virus (HeV) and that NiV- and HeV-elicited monoclonal and polyclonal antibodies do not cross-react with LayV F and G. We determined cryoelectron microscopy structures of LayV F, in the prefusion and postfusion states, and of LayV G, revealing their conformational landscape and distinct antigenicity relative to NiV and HeV. We computationally designed stabilized LayV G constructs and demonstrate the generalizability of an HNV F prefusion-stabilization strategy. Our data will support the development of vaccines and therapeutics against LayV and closely related HNVs.
MeSH term(s)	Humans ; Animals ; Mice ; Cryoelectron Microscopy ; Nipah Virus ; Hendra Virus ; Glycoproteins ; Henipavirus Infections ; Virus Internalization ; Henipavirus
Chemical Substances	Glycoproteins
Language	English
Publishing date	2024-04-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2314990121
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