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  1. Article: Structural diversity of the SARS-CoV-2 Omicron spike

    Gobeil, Sophie M.-C. / Henderson, Rory / Stalls, Victoria / Janowska, Katarzyna / Huang, Xiao / May, Aaron / Speakman, Micah / Beaudoin, Esther / Manne, Kartik / Li, Dapeng / Parks, Rob / Barr, Maggie / Deyton, Margaret / Martin, Mitchell / Mansouri, Katayoun / Edwards, Robert J. / Eaton, Amanda / Montefiori, David C. / Sempowski, Gregory D. /
    Saunders, Kevin O. / Wiehe, Kevin / Williams, Wilton / Korber, Bette / Haynes, Barton F. / Acharya, Priyamvada

    Molecular cell. 2022 Mar. 21,

    2022  

    Abstract: Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor-binding domain (RBD) and neutralizing ... ...

    Abstract Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor-binding domain (RBD) and neutralizing antibody epitope presentation, affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; crystallography ; epitopes ; immune evasion ; mutation ; peptides ; viruses
    Language English
    Dates of publication 2022-0321
    Publishing place Elsevier Inc.
    Document type Article
    Note Pre-press version
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2022.03.028
    Database NAL-Catalogue (AGRICOLA)

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  2. Article: Structural diversity of the SARS-CoV-2 Omicron spike.

    Gobeil, Sophie M-C / Henderson, Rory / Stalls, Victoria / Janowska, Katarzyna / Huang, Xiao / May, Aaron / Speakman, Micah / Beaudoin, Esther / Manne, Kartik / Li, Dapeng / Parks, Rob / Barr, Maggie / Deyton, Margaret / Martin, Mitchell / Mansouri, Katayoun / Edwards, Robert J / Sempowski, Gregory D / Saunders, Kevin O / Wiehe, Kevin /
    Williams, Wilton / Korber, Bette / Haynes, Barton F / Acharya, Priyamvada

    bioRxiv : the preprint server for biology

    2022  

    Abstract: Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor binding domain (RBD) and neutralizing ... ...

    Abstract Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor binding domain (RBD) and neutralizing antibody epitope presentation affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility.
    Language English
    Publishing date 2022-01-26
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2022.01.25.477784
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike.

    Stalls, Victoria / Lindenberger, Jared / Gobeil, Sophie M-C / Henderson, Rory / Parks, Rob / Barr, Maggie / Deyton, Margaret / Martin, Mitchell / Janowska, Katarzyna / Huang, Xiao / May, Aaron / Speakman, Micah / Beaudoin, Esther / Kraft, Bryan / Lu, Xiaozhi / Edwards, Robert J / Eaton, Amanda / Montefiori, David C / Williams, Wilton B /
    Saunders, Kevin O / Wiehe, Kevin / Haynes, Barton F / Acharya, Priyamvada

    Cell reports

    2022  Volume 39, Issue 13, Page(s) 111009

    Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sub-lineage has gained in proportion relative to BA.1. Because spike (S) protein variations may underlie differences in their pathobiology, here we determine cryoelectron ... ...

    Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sub-lineage has gained in proportion relative to BA.1. Because spike (S) protein variations may underlie differences in their pathobiology, here we determine cryoelectron microscopy (cryo-EM) structures of the BA.2 S ectodomain and compare these with previously determined BA.1 S structures. BA.2 receptor-binding domain (RBD) mutations induce remodeling of the RBD structure, resulting in tighter packing and improved thermostability. Interprotomer RBD interactions are enhanced in the closed (or 3-RBD-down) BA.2 S, while the fusion peptide is less accessible to antibodies than in BA.1. Binding and pseudovirus neutralization assays reveal extensive immune evasion while defining epitopes of two outer RBD face-binding antibodies, DH1044 and DH1193, that neutralize both BA.1 and BA.2. Taken together, our results indicate that stabilization of the closed state through interprotomer RBD-RBD packing is a hallmark of the Omicron variant and show differences in key functional regions in the BA.1 and BA.2 S proteins.
    MeSH term(s) Antibodies, Viral ; COVID-19 ; Cryoelectron Microscopy ; Humans ; Receptors, Virus/metabolism ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
    Chemical Substances Antibodies, Viral ; Receptors, Virus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2022-06-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; 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.2022.111009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Structural diversity of the SARS-CoV-2 Omicron spike.

    Gobeil, Sophie M-C / Henderson, Rory / Stalls, Victoria / Janowska, Katarzyna / Huang, Xiao / May, Aaron / Speakman, Micah / Beaudoin, Esther / Manne, Kartik / Li, Dapeng / Parks, Rob / Barr, Maggie / Deyton, Margaret / Martin, Mitchell / Mansouri, Katayoun / Edwards, Robert J / Eaton, Amanda / Montefiori, David C / Sempowski, Gregory D /
    Saunders, Kevin O / Wiehe, Kevin / Williams, Wilton / Korber, Bette / Haynes, Barton F / Acharya, Priyamvada

    Molecular cell

    2022  Volume 82, Issue 11, Page(s) 2050–2068.e6

    Abstract: Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor-binding domain (RBD) and neutralizing ... ...

    Abstract Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor-binding domain (RBD) and neutralizing antibody epitope presentation, affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility.
    MeSH term(s) Angiotensin-Converting Enzyme 2 ; COVID-19 ; Humans ; Mutation ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Language English
    Publishing date 2022-03-25
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2022.03.028
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5055: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice.

    Martinez, David R / Schäfer, Alexandra / Gobeil, Sophie / Li, Dapeng / De la Cruz, Gabriela / Parks, Robert / Lu, Xiaozhi / Barr, Maggie / Stalls, Victoria / Janowska, Katarzyna / Beaudoin, Esther / Manne, Kartik / Mansouri, Katayoun / Edwards, Robert J / Cronin, Kenneth / Yount, Boyd / Anasti, Kara / Montgomery, Stephanie A / Tang, Juanjie /
    Golding, Hana / Shen, Shaunna / Zhou, Tongqing / Kwong, Peter D / Graham, Barney S / Mascola, John R / Montefiori, David C / Alam, S Munir / Sempowski, Gregory / Sempowski, Gregory D / Khurana, Surender / Wiehe, Kevin / Saunders, Kevin O / Acharya, Priyamvada / Haynes, Barton F / Baric, Ralph S

    Science translational medicine

    2022  Volume 14, Issue 629, Page(s) eabj7125

    Abstract: Severe acute respiratory syndrome coronaviruses 1 (SARS-CoV) and 2 (SARS-CoV-2), including SARS-CoV-2 variants of concern, can cause deadly infections. The mortality associated with sarbecovirus infection underscores the importance of developing broadly ... ...

    Abstract Severe acute respiratory syndrome coronaviruses 1 (SARS-CoV) and 2 (SARS-CoV-2), including SARS-CoV-2 variants of concern, can cause deadly infections. The mortality associated with sarbecovirus infection underscores the importance of developing broadly effective countermeasures against them, which could be key in the prevention and mitigation of current and future zoonotic events. Here, we demonstrate the neutralization of SARS-CoV; bat coronaviruses WIV-1 and RsSHC014; and SARS-CoV-2 variants D614G, B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, B.1.617.1, and B.1.617.2 by a receptor binding domain (RBD)–specific human antibody, DH1047. Prophylactic and therapeutic treatment with DH1047 was protective against SARS-CoV, WIV-1, RsSHC014, and SARS-CoV-2 B.1.351 infection in mice. Binding and structural analysis showed high affinity binding of DH1047 to an epitope that is highly conserved among sarbecoviruses. Thus, DH1047 is a broadly protective antibody that can prevent infection and mitigate outbreaks caused by SARS-related strains and SARS-CoV-2 variants. Our results also suggest that the conserved RBD epitope bound by DH1047 is a rational target for a universal sarbecovirus vaccine.
    MeSH term(s) Animals ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 ; Humans ; Mice ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
    Chemical Substances Antibodies, Neutralizing ; Antibodies, Viral ; DH1047 ; Spike Glycoprotein, Coronavirus
    Language English
    Publishing date 2022-01-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.abj7125
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6941: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Structural diversity of the SARS-CoV-2 Omicron spike

    Gobeil, Sophie / Henderson, Rory / Stalls, Victoria / Janowska, Katarzyna / Huang, Xiao / May, Aaron / Speakman, Micah / Beaudoin, Esther / Manne, Kartik / Li, Dapeng / Parks, Rob / Barr, Maggie / Deyton, Margaret / Martin, Mitchell / Mansouri, Katayoun / Edwards, Robert J / Sempowski, Gregory D / Saunders, Kevin O'Neil / Wiehe, Kevin /
    Williams, Wilton / Korber, Bette / Haynes, Barton F / Acharya, Priyamvada

    bioRxiv

    Abstract: Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor binding domain (RBD) and neutralizing ... ...

    Abstract Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor binding domain (RBD) and neutralizing antibody epitope presentation affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility.
    Keywords covid19
    Language English
    Publishing date 2022-01-26
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2022.01.25.477784
    Database COVID19

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  7. Article ; Online: Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike

    Stalls, Victoria / Lindenberger, Jared / Gobeil, Sophie / Henderson, Rory / Parks, Rob / Barr, Maggie / Deyton, Margaret / Martin, Mitchell / Janowska, Katarzyna / Huang, Xiao / May, Aaron / Speakman, Micah / Beaudoin, Esther / Edwards, Robert J / Eaton, Amanda / Montefiori, David / Williams, Wilton / Saunders, Kevin O'Neil / Wiehe, Kevin /
    Haynes, Barton F / Acharya, Priyamvada

    bioRxiv

    Abstract: The BA.2 lineage of the SARS-CoV-2 Omicron variant has gained in proportion relative to BA.1. As differences in their spike (S) proteins may underlie differences in their pathobiology, here we determined cryo-EM structures of a BA.2 S protein ectodomain ... ...

    Abstract The BA.2 lineage of the SARS-CoV-2 Omicron variant has gained in proportion relative to BA.1. As differences in their spike (S) proteins may underlie differences in their pathobiology, here we determined cryo-EM structures of a BA.2 S protein ectodomain and compared these to previously determined BA.1 S structures. BA.2 Receptor Binding Domain (RBD) mutations induced remodeling of the internal RBD structure resulting in its improved thermostability and tighter packing within the 3-RBD-down spike. In the S2 subunit, the fusion peptide in the BA.2 was less accessible to antibodies than in BA.1. Pseudovirus neutralization and spike binding assays revealed extensive immune evasion while defining epitopes of two RBD-directed antibodies, DH1044 and DH1193, that bound the outer RBD face to neutralize both BA.1 and BA.2. Taken together, our results indicate that stabilization of the 3-RBD-down state through interprotomer RBD-RBD packing is a hallmark of the Omicron lineages, and reveal differences in key functional regions in the BA.1 and BA.2 S proteins.
    Keywords covid19
    Language English
    Publishing date 2022-04-08
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2022.04.07.487528
    Database COVID19

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