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Yanjun
Zhang
,
Yan
Wu
,
Meng-Qian
Zhang
,
Haiyue
Rao
,
Zhaoyong
Zhang
,
Xiangyue
He
,
Yiwen
Liang
,
Raoqing
Guo
,
Yaochang
Yuan
,
Jing
Sun
,
Helen M. E.
Duyvesteyn
,
Elizabeth E.
Fry
,
David I.
Stuart
,
Jingxian
Zhao
,
Xiaoyan
Pan
,
Shu-Lin
Liu
,
Jincun
Zhao
,
Jiandong
Huo
Open Access
Abstract: Current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are effective against severe disease and death, but do not prevent viral infections, probably due to the limited mucosal immunity induced by intramuscular administration of the vaccine. Fusion of SARS-CoV-2 subunit immunogens with a human IgG Fc backbone can be used as a mucosal vaccine but its effectiveness in delivery in animal models, and its immunogenicity and the vaccine-induced protection against viral infections requires further studies. Here we investigate a bivalent RBD-Fc vaccine that includes the spike receptor-binding domains (RBDs) of the ancestral and BQ.1.1 variant of SARS-CoV-2. Ex vivo fluorescent imaging demonstrates that this vaccine can be effectively delivered to the lungs of mice through intranasal administration, with enhancement of retention in the nasal cavity and lung parenchyma. In mice, the vaccine elicited potent and broad-spectrum antibody responses against different variants including KP.3 which could persist for at least 3 months after booster. Importantly, it was able to induce RBD-specific mucosal IgA responses. Further, heterologous intranasal immunisation with adeno-vectored Chadv1 and RBD-Fc elicited both potent neutralising antibody and T cell responses. Immunised BALB/c and K18-hACE2-transgenic mice were also protected against viral challenge of XBB.1 and viral transmission was effectively limited in hamsters through intranasal immunisation. This work thus demonstrates the potential of RBD-Fc antigens as mucosal vaccines for prevention of breakthrough infections and onward transmission. Moreover, Fc-fusion proteins can be used as an effective mucosal vaccine strategy which can be used either alone or in combination with other vaccine technology to constitute heterologous immunisations, enabling strong protection against SARS-CoV-2 and other respiratory viruses.
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May 2025
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Krios I-Titan Krios I at Diamond
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Lee
Sherry
,
Mohammad W.
Bahar
,
Claudine
Porta
,
Helen
Fox
,
Keith
Grehan
,
Veronica
Nasta
,
Helen M. E.
Duyvesteyn
,
Luigi
De Colibus
,
Johanna
Marsian
,
Inga
Murdoch
,
Daniel
Ponndorf
,
Seong-Ryong
Kim
,
Sachin
Shah
,
Sarah
Carlyle
,
Jessica J.
Swanson
,
Sue
Matthews
,
Clare
Nicol
,
George P.
Lomonossoff
,
Andrew J.
Macadam
,
Elizabeth E.
Fry
,
David I.
Stuart
,
Nicola J.
Stonehouse
,
David J.
Rowlands
Diamond Proposal Number(s):
[14856, 20223]
Open Access
Abstract: Polioviruses have caused crippling disease in humans for centuries, prior to the successful development of vaccines in the mid-1900’s, which dramatically reduced disease prevalence. Continued use of these vaccines, however, threatens ultimate disease eradication and achievement of a polio-free world. Virus-like particles (VLPs) that lack a viral genome represent a safer potential vaccine, although they require particle stabilization. Using our previously established genetic techniques to stabilize the structural capsid proteins, we demonstrate production of poliovirus VLPs of all three serotypes, from four different recombinant expression systems. We compare the antigenicity, thermostability and immunogenicity of these stabilized VLPs against the current inactivated polio vaccine, demonstrating equivalent or superior immunogenicity in female Wistar rats. Structural analyses of these recombinant VLPs provide a rational understanding of the stabilizing mutations and the role of potential excipients. Collectively, we have established these poliovirus stabilized VLPs as viable next-generation vaccine candidates for the future.
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Jan 2025
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John D.
Clarke
,
Helen M. E.
Duyvesteyn
,
Eva
Perez-Martin
,
Undīne
Latišenko
,
Claudine
Porta
,
Kathleen V.
Humphreys
,
Abigail L.
Hay
,
Jingshan
Ren
,
Elizabeth E.
Fry
,
Erwin
Van Den Born
,
Bryan
Charleston
,
Marie
Bonnet-Di Placido
,
Raymond J.
Owens
,
David I.
Stuart
,
John A.
Hammond
Open Access
Abstract: Foot-and-mouth disease vaccination using inactivated virus is suboptimal, as the icosahedral viral capsids often disassemble into antigenically distinct pentameric units during long-term storage, or exposure to elevated temperature or lowered pH, and thus raise a response that is no longer protective. Furthermore, as foot-and-mouth disease virus (FMDV)’s seven serotypes are antigenically diverse, cross-protection from a single serotype vaccine is limited, and most existing mouse and bovine antibodies and camelid single-domain heavy chain-only antibodies are serotype-specific. For quality control purposes, there is a real need for pan-serotype antibodies that clearly distinguish between pentamer (12S) and protective intact FMDV capsid. To date, few cross-serotype bovine-derived antibodies have been reported in the literature. We identify a bovine antibody with an ultralong CDR-H3, Ab117, whose structural analysis reveals that it binds to a deep, hydrophobic pocket on the interior surface of the capsid via the CDR-H3. Main-chain and hydrophobic interactions provide broad serotype specificity. ELISA analysis confirms that Ab117 is a novel pan-serotype and conformational epitope-specific 12S reagent, suitable for assessing capsid integrity.
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Oct 2024
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Helen M. E.
Duyvesteyn
,
Aiste
Dijokaite-Guraliuc
,
Chang
Liu
,
Piyada
Supasa
,
Barbara
Kronsteiner
,
Katie
Jeffery
,
Lizzie
Stafford
,
Paul
Klenerman
,
Susanna J.
Dunachie
,
Juthathip
Mongkolsapaya
,
Elizabeth
Fry
,
Jingshan
Ren
,
David I.
Stuart
,
Gavin R.
Screaton
Abstract: BA.2.87.1 represents a major shift in the BA.2 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is unusual in having two lengthy deletions of polypeptide in the spike (S) protein, one of which removes a beta-strand. Here we investigate its neutralization by a variety of sera from infected and vaccinated individuals and determine its spike (S) ectodomain structure. The BA.2.87.1 receptor binding domain (RBD) is structurally conserved and the RBDs are tightly packed in an “all-down” conformation with a small rotation relative to the trimer axis as compared to the closest previously observed conformation. The N-terminal domain (NTD) maintains a remarkably similar structure overall; however, the rearrangements resulting from the deletions essentially destroy the so-called supersite epitope and eliminate one glycan site, while a mutation creates an additional glycan site, effectively shielding another NTD epitope. BA.2.87.1 is relatively easily neutralized but acquisition of additional mutations in the RBD could increase antibody escape allowing it to become a dominant sub-lineage.
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Aug 2024
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I04-Macromolecular Crystallography
VMXi-Versatile Macromolecular Crystallography in situ
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Diamond Proposal Number(s):
[19946, 23570]
Open Access
Abstract: The third complementary-determining regions of the heavy-chain (CDR3H) variable regions (VH) of some cattle antibodies are highly extended, consisting of 48 or more residues. These `ultralong' CDR3Hs form β-ribbon stalks that protrude from the surface of the antibody with a disulfide cross-linked knob region at their apex that dominates antigen interactions over the other CDR loops. The structure of the Fab fragment of a naturally paired bovine ultralong antibody (D08), identified by single B-cell sequencing, has been determined to 1.6 Å resolution. By swapping the D08 native light chain with that of an unrelated antigen-unknown ultralong antibody, it is shown that interactions between the CDR3s of the variable domains potentially affect the fine positioning of the ultralong CDR3H; however, comparison with other crystallographic structures shows that crystalline packing is also a major contributor. It is concluded that, on balance, the exact positioning of ultralong CDR3H loops is most likely to be due to the constraints of crystal packing.
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Jul 2024
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I03-Macromolecular Crystallography
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Chang
Liu
,
Daming
Zhou
,
Aiste
Dijokaite-Guraliuc
,
Piyada
Supasa
,
Helen M. E.
Duyvesteyn
,
Helen M.
Ginn
,
Muneeswaran
Selvaraj
,
Alexander J.
Mentzer
,
Raksha
Das
,
Thushan I.
De Silva
,
Thomas G.
Ritter
,
Megan
Plowright
,
Thomas A.h.
Newman
,
Lizzie
Stafford
,
Barbara
Kronsteiner
,
Nigel
Temperton
,
Yuan
Lui
,
Martin
Fellermeyer
,
Philip
Goulder
,
Paul
Klenerman
,
Susanna J.
Dunachie
,
Michael I.
Barton
,
Mikhail A.
Kutuzov
,
Omer
Dushek
,
Elizabeth E.
Fry
,
Juthathip
Mongkolsapaya
,
Jingshan
Ren
,
David I.
Stuart
,
Gavin R.
Screaton
Diamond Proposal Number(s):
[28534, 27009]
Open Access
Abstract: BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
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May 2024
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Chang
Liu
,
Raksha
Das
,
Aiste
Dijokaite-Guraliuc
,
Daming
Zhou
,
Alexander J.
Mentzer
,
Piyada
Supasa
,
Muneeswaran
Selvaraj
,
Helen M. E.
Duyvesteyn
,
Thomas G.
Ritter
,
Nigel
Temperton
,
Paul
Klenerman
,
Susanna J.
Dunachie
,
Neil G.
Paterson
,
Mark A.
Williams
,
David R.
Hall
,
Elizabeth E.
Fry
,
Juthathip
Mongkolsapaya
,
Jingshan
Ren
,
David I.
Stuart
,
Gavin R.
Screaton
Open Access
Abstract: The rapid evolution of SARS-CoV-2 is driven in part by a need to evade the antibody response in the face of high levels of immunity. Here, we isolate spike (S) binding monoclonal antibodies (mAbs) from vaccinees who suffered vaccine break-through infections with Omicron sub lineages BA.4 or BA.5. Twenty eight potent antibodies are isolated and characterised functionally, and in some cases structurally. Since the emergence of BA.4/5, SARS-CoV-2 has continued to accrue mutations in the S protein, to understand this we characterize neutralization of a large panel of variants and demonstrate a steady attrition of neutralization by the panel of BA.4/5 mAbs culminating in total loss of function with recent XBB.1.5.70 variants containing the so-called ‘FLip’ mutations at positions 455 and 456. Interestingly, activity of some mAbs is regained on the recently reported variant BA.2.86.
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Apr 2024
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Daming
Zhou
,
Piyada
Supasa
,
Chang
Liu
,
Aiste
Dijokaite-Guraliuc
,
Helen M. E.
Duyvesteyn
,
Muneeswaran
Selvaraj
,
Alexander J.
Mentzer
,
Raksha
Das
,
Wanwisa
Dejnirattisai
,
Nigel
Temperton
,
Paul
Klenerman
,
Susanna J.
Dunachie
,
Elizabeth E.
Fry
,
Juthathip
Mongkolsapaya
,
Jingshan
Ren
,
David I.
Stuart
,
Gavin R.
Screaton
Open Access
Abstract: Under pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response.
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Mar 2024
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Open Access
Abstract: The COVID-19 pandemic caused by SARS-CoV-2 has led to hundreds of millions of infections and millions of deaths, however, human monoclonal antibodies (mAbs) can be an effective treatment. Since SARS-CoV-2 emerged, a variety of strains have acquired increasing numbers of mutations to gain increased transmissibility and escape from the immune response. Most reported neutralizing human mAbs, including all approved therapeutic ones, have been knocked down or out by these mutations. Broadly neutralizing mAbs are therefore of great value, to treat current and possible future variants. Here, we review four types of neutralizing mAbs against the spike protein with broad potency against previously and currently circulating variants. These mAbs target the receptor-binding domain, the subdomain 1, the stem helix, or the fusion peptide. Understanding how these mAbs retain potency in the face of mutational change could guide future development of therapeutic antibodies and vaccines.
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Aug 2023
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Aiste
Dijokaite-Guraliuc
,
Raksha
Das
,
Daming
Zhou
,
Helen M.
Ginn
,
Chang
Liu
,
Helen M. E.
Duyvesteyn
,
Jiandong
Huo
,
Rungtiwa
Nutalai
,
Piyada
Supasa
,
Muneeswaran
Selvaraj
,
Thushan I.
De Silva
,
Megan
Plowright
,
Thomas A. H.
Newman
,
Hailey
Hornsby
,
Alexander J.
Mentzer
,
Donal
Skelly
,
Thomas G.
Ritter
,
Nigel
Temperton
,
Paul
Klenerman
,
Eleanor
Barnes
,
Susanna J.
Dunachie
,
Cornelius
Roemer
,
Thomas P.
Peacock
,
Neil G.
Paterson
,
Mark A.
Williams
,
David R.
Hall
,
Elizabeth E.
Fry
,
Juthathip
Mongkolsapaya
,
Jingshan
Ren
,
David I.
Stuart
,
Gavin R.
Screaton
Diamond Proposal Number(s):
[27009]
Open Access
Abstract: In November 2021 Omicron BA.1, containing a raft of new spike mutations emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or SARS-CoV-2 infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional RBD amino-acid substitutions compared to BA.2. We describe a panel of 25 potent mAbs generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titre of vaccine or BA.1, BA.2 or BA.4/5 immune serum.
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Mar 2023
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