474 results on '"Stuart, DI"'
Search Results
2. An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status
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Lumley, SF, Rodger, G, Constantinides, B, Sanderson, N, Chau, KK, Street, TL, O'Donnell, D, Howarth, A, Hatch, SB, Marsden, BD, Cox, S, James, T, Warren, F, Peck, LJ, Ritter, TG, de Toledo, Z, Warren, L, Axten, D, Cornall, RJ, Jones, EY, Stuart, DI, Screaton, G, Ebner, D, Hoosdally, S, Chand, M, Crook, DW, O'Donnell, A-M, Conlon, CP, Pouwels, KB, Walker, AS, Peto, TEA, Hopkins, S, Walker, TM, Stoesser, NE, Matthews, PC, Jeffery, K, and Eyre, DW
- Abstract
Background Natural and vaccine-induced immunity will play a key role in controlling the SARS-CoV-2 pandemic. SARS-CoV-2 variants have the potential to evade natural and vaccine-induced immunity. Methods In a longitudinal cohort study of healthcare workers (HCWs) in Oxfordshire, UK, we investigated the protection from symptomatic and asymptomatic PCR-confirmed SARS-CoV-2 infection conferred by vaccination (Pfizer-BioNTech BNT162b2, Oxford-AstraZeneca ChAdOx1 nCOV-19) and prior infection (determined using anti-spike antibody status), using Poisson regression adjusted for age, sex, temporal changes in incidence and role. We estimated protection conferred after one versus two vaccinations and from infections with the B.1.1.7 variant identified using whole genome sequencing. Results 13,109 HCWs participated; 8285 received the Pfizer-BioNTech vaccine (1407 two doses) and 2738 the Oxford-AstraZeneca vaccine (49 two doses). Compared to unvaccinated seronegative HCWs, natural immunity and two vaccination doses provided similar protection against symptomatic infection: no HCW vaccinated twice had symptomatic infection, and incidence was 98% lower in seropositive HCWs (adjusted incidence rate ratio 0.02 [95%CI Conclusion Natural infection resulting in detectable anti-spike antibodies and two vaccine doses both provide robust protection against SARS-CoV-2 infection, including against the B.1.1.7 variant.
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- 2021
3. Differential occupational risks to healthcare workers from SARS-CoV-2 observed during a prospective observational study
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Eyre, DW, Lumley, SF, O'Donnell, D, Campbell, M, Sims, E, Lawson, E, Warren, F, James, T, Cox, S, Howarth, A, Doherty, G, Hatch, SB, Kavanagh, J, Chau, KK, Fowler, PW, Swann, J, Volk, D, Yang-Turner, F, Stoesser, N, Matthews, PC, Dudareva, M, Davies, T, Shaw, RH, Peto, L, Downs, LO, Vogt, A, Amini, A, Young, BC, Drennan, PG, Mentzer, AJ, Skelly, DT, Karpe, F, Neville, MJ, Andersson, M, Brent, AJ, Jones, N, Martins Ferreira, L, Christott, T, Marsden, BD, Hoosdally, S, Cornall, R, Crook, DW, Stuart, DI, Screaton, G, Group, Oxford University Hospitals Staff Testing, Watson, AJ, Taylor, A, Chetwynd, A, Grassam-Rowe, A, Mighiu, AS, Peck, LJ, Ebner, D, and Conlon, CP
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Male ,0301 basic medicine ,serology ,law.invention ,0302 clinical medicine ,law ,Surveys and Questionnaires ,Health care ,Epidemiology ,Medicine ,risk factors ,030212 general & internal medicine ,Young adult ,Biology (General) ,Asymptomatic Infections ,Incidence ,General Neuroscience ,Incidence (epidemiology) ,Age Factors ,General Medicine ,Middle Aged ,Intensive care unit ,Virus ,3. Good health ,Intensive Care Units ,Female ,medicine.symptom ,Coronavirus Infections ,Covid-19 ,Research Article ,Adult ,Risk ,medicine.medical_specialty ,Infectious Disease Transmission, Patient-to-Professional ,Adolescent ,QH301-705.5 ,Health Personnel ,Science ,Pneumonia, Viral ,030106 microbiology ,Asymptomatic ,General Biochemistry, Genetics and Molecular Biology ,Betacoronavirus ,Young Adult ,03 medical and health sciences ,Humans ,Hospitals, Teaching ,Pandemics ,Aged ,General Immunology and Microbiology ,business.industry ,SARS-CoV-2 ,healthcare workers ,Odds ratio ,United Kingdom ,Epidemiology and Global Health ,Family medicine ,symptoms ,Observational study ,business - Abstract
We conducted voluntary Covid-19 testing programmes for symptomatic and asymptomatic staff at a UK teaching hospital using naso-/oro-pharyngeal PCR testing and immunoassays for IgG antibodies. 1128/10,034 (11.2%) staff had evidence of Covid-19 at some time. Using questionnaire data provided on potential risk-factors, staff with a confirmed household contact were at greatest risk (adjusted odds ratio [aOR] 4.82 [95%CI 3.45–6.72]). Higher rates of Covid-19 were seen in staff working in Covid-19-facing areas (22.6% vs. 8.6% elsewhere) (aOR 2.47 [1.99–3.08]). Controlling for Covid-19-facing status, risks were heterogenous across the hospital, with higher rates in acute medicine (1.52 [1.07–2.16]) and sporadic outbreaks in areas with few or no Covid-19 patients. Covid-19 intensive care unit staff were relatively protected (0.44 [0.28–0.69]), likely by a bundle of PPE-related measures. Positive results were more likely in Black (1.66 [1.25–2.21]) and Asian (1.51 [1.28–1.77]) staff, independent of role or working location, and in porters and cleaners (2.06 [1.34–3.15]).
- Published
- 2020
4. Recovery of data from perfectly twinned virus crystals revisited
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Ginn, HM and Stuart, DI
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Models, Molecular ,noncrystallographic symmetry ,Crystallography ,Foot-and-Mouth Disease Virus ,Foot-and-Mouth Disease ,perfect merohedral twinning ,Animals ,Crystallization ,Research Papers ,virus crystals ,Software - Abstract
An iterative method of map recovery for perfectly merohedrally twinned crystals in the presence of noncrystallographic symmetry is reimplemented and released and an independent metric of success is provided., Perfect merohedral twinning of crystals is not uncommon and complicates structural analysis. An iterative method for the deconvolution of data from perfectly merohedrally twinned crystals in the presence of noncrystallographic symmetry (NCS) has been reimplemented. It is shown that the method recovers the data effectively using test data, and an independent metric of success, based on special classes of reflections that are unaffected by the twin operator, is now provided. The method was applied to a real problem with fivefold NCS and rather poor-quality diffraction data, and it was found that even in these circumstances the method appears to recover most of the information. The software has been made available in a form that can be applied to other crystal systems.
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- 2016
5. Incorporation of tetanus-epitope into virus-like particles achieves vaccine responses even in older recipients in models of psoriasis, Alzheimer’s and cat allergy
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Zeltins, A, West, J, Zabel, F, El-Turabi, A, Balke, I, Haas, S, Maudrich, M, Storni, F, Engernoff, P, Jennings, GT, Kotecha, A, Stuart, DI, Foerster, J, and Bachmann, M
- Abstract
Monoclonal antibodies are widely used to treat non-infectious conditions but are costly. Vaccines could offer a cost-effective alternative but have been limited by sub-optimal T-cell stimulation and/or weak vaccine responses in recipients, for example, in elderly patients. We have previously shown that the repetitive structure of virus-like-particles (VLPs) can effectively bypass self-tolerance in therapeutic vaccines. Their efficacy could be increased even further by the incorporation of an epitope stimulating T cell help. However, the self-assembly and stability of VLPs from envelope monomer proteins is sensitive to geometry, rendering the incorporation of foreign epitopes difficult. We here show that it is possible to engineer VLPs derived from a non human-pathogenic plant virus to incorporate a powerful T-cell-stimulatory epitope derived from Tetanus toxoid. These VLPs (termed CMVTT) retain self-assembly as well as long-term stability. Since Th cell memory to Tetanus is near universal in humans, CMVTT-based vaccines can deliver robust antibody-responses even under limiting conditions. By way of proof of concept, we tested a range of such vaccines against chronic inflammatory conditions (model: psoriasis, antigen: interleukin-17), neurodegenerative (Alzheimer’s, β-amyloid), and allergic disease (cat allergy, Fel-d1), respectively. Vaccine responses were uniformly strong, selective, efficient in vivo, observed even in old mice, and employing low vaccine doses. In addition, randomly ascertained human blood cells were reactive to CMVTT-VLPs, confirming recognition of the incorporated Tetanus epitope. The CMVTT-VLP platform is adaptable to almost any antigen and its features and performance are ideally suited for the design of vaccines delivering enhanced responsiveness in aging populations.
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- 2017
6. Structures of foot and mouth disease virus pentamers: Insight into capsid dissociation and unexpected pentamer reassociation
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Malik, N, Kotecha, A, Gold, S, Asfor, A, Ren, J, Huiskonen, JT, Tuthill, TJ, Fry, EE, Stuart, DI, and Tao, YJ
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viruses ,virus diseases ,biochemical phenomena, metabolism, and nutrition - Abstract
Foot-and-mouth disease virus (FMDV) belongs to the aphthovirus genus of the Picornaviridae, a family of small, icosahedral, non-enveloped, single-stranded RNA viruses. It is a highly infectious pathogen and is one of the biggest hindrances to the international trade of animals and animal products. FMDV capsids (which are unstable below pH6.5) release their genome into the host cell from an acidic compartment, such as that of an endosome, and in the process dissociate into pentamers. Whilst other members of the family (enteroviruses) have been visualized to form an expanded intermediate capsid with holes from which inner capsid proteins (VP4), N-termini (VP1) and RNA can be released, there has been no visualization of any such state for an aphthovirus, instead the capsid appears to simply dissociate into pentamers. Here we present the 8-Å resolution structure of isolated dissociated pentamers of FMDV, lacking VP4. We also found these pentamers to re-associate into a rigid, icosahedrally symmetric assembly, which enabled their structure to be solved at higher resolution (5.2 Å). In this assembly, the pentamers unexpectedly associate 'inside out', but still with their exposed hydrophobic edges buried. Stabilizing interactions occur between the HI loop of VP2 and its symmetry related partners at the icosahedral 3-fold axes, and between the BC and EF loops of VP3 with the VP2 βB-strand and the CD loop at the 2-fold axes. A relatively extensive but subtle structural rearrangement towards the periphery of the dissociated pentamer compared to that in the mature virus provides insight into the mechanism of dissociation of FMDV and the marked difference in antigenicity.
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- 2017
7. On the release of cppxfel for processing X-ray free-electron laser images
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Ginn, HM, Evans, G, Sauter, NK, and Stuart, DI
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serial femtosecond crystallography ,XFELS ,Engineering ,data analysis ,Physical Sciences ,X-ray free-electron lasers ,Inorganic & Nuclear Chemistry ,computer programs ,Mathematical Sciences - Abstract
© 2016 International Union of Crystallography. As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.
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- 2016
8. Phosphate-recognition sites in catalysis and control of glycogen phosphorylase b
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Johnson, LN, Acharya, KR, Stuart, DI, Barford, D, Oikonomakos, NG, Hajdu, J, and Varvill, KM
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- 2016
9. The structure of a cypovirus and the functional organization of dsRNA viruses
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Hill, CL, Booth, TF, Prasad, BV, Grimes, JM, Mertens, PP, Sutton, GC, and Stuart, DI
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viruses - Abstract
Cytoplasmic polyhedrosis virus (CPV) is unique among the double-stranded RNA viruses of the family Reoviridae in having a single capsid layer. Analysis by cryo-electron microscopy allows comparison of the single shelled CPV and orthoreovirus with the high resolution crystal structure of the inner shell of the bluetongue virus (BTV) core. This suggests that the novel arrangement identified in BTV, of 120 protein subunits in a so-called 'T=2' organization, is a characteristic of the Reoviridae and allows us to delineate structural similarities and differences between two subgroups of the family--the turreted and the smooth-core viruses. This in turn suggests a coherent picture of the structural organization of many dsRNA viruses.
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- 2016
10. Structure of a complex of CD47 and the paired receptor SIRP alpha reveals a mechanism for ligand discrimination
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Hatherley, D, Graham, SC, Turner, J, Harlos, K, Stuart, DI, and Barclay, AN
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- 2016
11. MACROMOLECULAR CRYSTALLOGRAPHY WITH SYNCHROTRON RADIATION .2. RESULTS
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Wilson, Ks, Enrico STURA, Wild, Dl, Todd, Rj, Stuart, Di, Babu, Ys, Jenkins, Ja, Standing, Ts, Johnson, Ln, Fourme, R., Kahn, R., Gadet, A., Bartels, Ks, and Bartunik, Hd
- Published
- 2016
12. Phenylethylthiazolylthiourea (PETT) non-nucleoside inhibitors of HIV-1 and HIV-2 reverse transcriptases. Structural and biochemical analyses
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Ren, J, Diprose, J, Warren, J, Esnouf, RM, Bird, LE, Ikemizu, S, Slater, M, Milton, J, Balzarini, J, Stuart, DI, and Stammers, DK
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virus diseases - Abstract
Most non-nucleoside reverse transcriptase (RT) inhibitors are specific for HIV-1 RT and demonstrate minimal inhibition of HIV-2 RT. However, we report that members of the phenylethylthiazolylthiourea (PETT) series of non-nucleoside reverse transcriptase inhibitors showing high potency against HIV-1 RT have varying abilities to inhibit HIV-2 RT. Thus, PETT-1 inhibits HIV-1 RT with an IC(50) of 6 nM but shows only weak inhibition of HIV-2 RT, whereas PETT-2 retains similar potency against HIV-1 RT (IC(50) of 5 nM) and also inhibits HIV-2 RT (IC(50) of 2.2 microM). X-ray crystallographic structure determinations of PETT-1 and PETT-2 in complexes with HIV-1 RT reveal the compounds bind in an overall similar conformation albeit with some differences in their interactions with the protein. To investigate whether PETT-2 could be acting at a different site on HIV-2 RT (e.g. the dNTP or template primer binding site), we compared modes of inhibition for PETT-2 against HIV-1 and HIV-2 RT. PETT-2 was a noncompetitive inhibitor with respect to the dGTP substrate for both HIV-1 and HIV-2 RTs. PETT-2 was also a noncompetitive inhibitor with respect to a poly(rC).(dG) template primer for HIV-2 RT. These results are consistent with PETT-2 binding in corresponding pockets in both HIV-1 and HIV-2 RT with amino acid sequence differences in HIV-2 RT affecting the binding of PETT-2 compared with PETT-1.
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- 2016
13. Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors
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Ren, J, Nichols, C, Bird, L, Chamberlain, P, Weaver, K, Short, S, Stuart, DI, and Stammers, DK
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Mutations at either Tyr181 or Tyr188 within HIV-1 reverse transcriptase (RT) give high level resistance to many first generation non-nucleoside inhibitors (NNRTIs) such as the anti-AIDS drug nevirapine. By comparison second generation inhibitors, for instance the drug efavirenz, show much greater resilience to these mutations. In order to understand the structural basis for these differences we have determined a series of seven crystal structures of mutant RTs in complexes with first and second generation NNRTIs as well as one example of an unliganded mutant RT. These are Tyr181Cys RT (TNK-651) to 2.4 A, Tyr181Cys RT (efavirenz) to 2.6 A, Tyr181Cys RT (nevirapine) to 3.0 A, Tyr181Cys RT (PETT-2) to 3.0 A, Tyr188Cys RT (nevirapine) to 2.6 A, Tyr188Cys RT (UC-781) to 2.6 A and Tyr188Cys RT (unliganded) to 2.8 A resolution. In the two previously published structures of HIV-1 reverse transcriptase with mutations at 181 or 188 no side-chain electron density was observed within the p66 subunit (which contains the inhibitor binding pocket) for the mutated residues. In contrast the mutated side-chains can be seen in the NNRTI pocket for all seven structures reported here, eliminating the possibility that disordering contributes to the mechanism of resistance. In the case of the second generation compounds efavirenz with Tyr181Cys RT and UC-781 with Tyr188Cys RT there are only small rearrangements of either inhibitor within the binding site compared to wild-type RT and also for the first generation compounds TNK-651, PETT-2 and nevirapine with Tyr181Cys RT. For nevirapine with the Tyr188Cys RT there is however a more substantial movement of the drug molecule. We conclude that protein conformational changes and rearrangements of drug molecules within the mutated sites are not general features of these particular inhibitor/mutant combinations. The main contribution to drug resistance for Tyr181Cys and Tyr188Cys RT mutations is the loss of aromatic ring stacking interactions for first generation compounds, providing a simple explanation for the resilience of second generation NNRTIs, as such interactions make much less significant contribution to their binding.
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- 2016
14. Dame Louise Napier Johnson (1940-2012) Obituary
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Wilson, KS and Stuart, DI
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- 2016
15. Structure of the TRAIL-DR5 complex reveals mechanisms conferring specificity in apoptotic initiation
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Mongkolsapaya, J, Grimes, JM, Chen, N, Xu, XN, Stuart, DI, Jones, EY, and Screaton, GR
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TRAIL, an apoptosis inducing ligand, has at least four cell surface receptors including the death receptor DR5. Here we report the crystal structure at 2.2 A resolution of a complex between TRAIL and the extracellular region of DR5. TRAIL forms a central homotrimer around which three DR5 molecules bind. Radical differences in the surface charge of the ligand, together with variation in the alignment of the two receptor domains confer specificity between members of these ligand and receptor families. The existence of a switch mechanism allowing variation in receptor domain alignment may mean that it is possible to engineer receptors with multiple specificities by exploiting contact positions unique to individual receptor-ligand pairs.
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- 2016
16. Crystal structure of the complex between CD8αα human and HLA-A2
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Gao, GF, Tormo, J, Gerth, UC, Wyer, JR, Mcmichael, AJ, Stuart, DI, Bell, JI, Jones, EY, and Jakobsen, BK
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chemical and pharmacologic phenomena - Abstract
The dimeric cell-surface glycoprotein CD8 is crucial to the positive selection of cytotoxic T cells in the thymus. The homodimer CD8αα or the heterodimer αβ stabilizes the interaction of the T-cell antigen receptor (TCR) with major histocompatibility complex (MHC) class l/peptide by binding to the class I molecule. Here we report the crystal structure at 2.7 Å resolution of a complex between CD8αα and the human MHC molecule HLA-A2, which is associated with peptide. CD8αα binds one HLA-A2/peptide molecule, interfacing with the α2 and α3 domains of HLA-A2 and also contacting β2- microglobulin. A flexible loop of the α3 domain (residues 223-229) is damped between the complementarity-determining region (CDR)-like loops of the two CD8 subunits in the classic manner of an antibody-antigen interaction, precluding the binding of a second MHC molecule. The position of the α3 domain is different from that in uncomplexed HLA-A2 (refs 3, 4), being most similar to that in the TCR/Tax/HLA-A2 complex, but no conformational change extends to the MHC/peptide surface presented for TCR recognition. Although these shifts in α3 may provide a synergistic modulation of affinity, the binding of CD8 to MHC is dearly consistent with an avidity-based contribution from CD8 to TCR-peptide-MHC interactions.
- Published
- 2016
17. Pushing the limits of sulfur SAD phasing: de novo structure solution of the N-terminal domain of the ectodomain of HCV E1
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El Omari, K, Iourin, O, Kadlec, J, Fearn, R, Hall, DR, Harlos, K, Grimes, JM, and Stuart, DI
- Abstract
Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by the paucity of the signal at the usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here, the data collection and structure solution of the N-terminal domain of the ectodomain of HCV E1 from crystals that diffracted very weakly is reported. By combining the data from 32 crystals, it was possible to solve the sulfur substructure and calculate initial maps at 7 Å resolution, and after density modication and phase extension using a higher resolution native data set to 3.5 Å resolution model building was achievable.
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- 2016
18. Modulation of apoptosis and pro-inflammatory signalling by vaccinia virus protein N1
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de Motes, M, Samantha, CC, Hongwei, R, Almeida, GMF, Keiran, M, Bahar, MW, Stuart, DI, Grimes, JM, Graham, SC, and Smith, GL
- Published
- 2016
19. TakeTwo: an indexing algorithm suited to still images with known crystal parameters
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Ginn, HM, Roedig, P, Kuo, A, Evans, G, Sauter, NK, Ernst, O, Meents, A, Mueller-Werkmeister, H, Miller, RJ, and Stuart, DI
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Crystallography ,Time Factors ,Protein Conformation ,Lasers ,X-Rays ,Proteins ,Electrons ,TakeTwo ,Crystallography, X-Ray ,Research Papers ,XFELs ,ddc:570 ,Computer Science::Computer Vision and Pattern Recognition ,X-Ray ,serial crystallography ,X-ray free-electron lasers ,Computer Science::Databases ,Algorithms ,Synchrotrons ,data processing - Abstract
A novel indexing method is presented that is well suited to the minimal information on a still image diffraction pattern and can achieve indexing rates of over one lattice per image., The indexing methods currently used for serial femtosecond crystallography were originally developed for experiments in which crystals are rotated in the X-ray beam, providing significant three-dimensional information. On the other hand, shots from both X-ray free-electron lasers and serial synchrotron crystallography experiments are still images, in which the few three-dimensional data available arise only from the curvature of the Ewald sphere. Traditional synchrotron crystallography methods are thus less well suited to still image data processing. Here, a new indexing method is presented with the aim of maximizing information use from a still image given the known unit-cell dimensions and space group. Efficacy for cubic, hexagonal and orthorhombic space groups is shown, and for those showing some evidence of diffraction the indexing rate ranged from 90% (hexagonal space group) to 151% (cubic space group). Here, the indexing rate refers to the number of lattices indexed per image.
- Published
- 2016
20. Application of in situ diffraction in high-throughput structure determination platforms
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Aller, P, Sanchez-Weatherby, J, Foadi, J, Winter, G, Lobley, CM, Axford, D, Ashton, AW, Bellini, D, Brandao-Neto, J, Culurgioni, S, Douangamath, A, Duman, R, Evans, G, Fisher, S, Flaig, R, Hall, DR, Lukacik, P, Mazzorana, M, McAuley, KE, Mykhaylyk, V, Owen, RL, Paterson, NG, Romano, P, Sandy, J, Sorensen, T, von Delft, F, Wagner, A, Warren, A, Williams, M, Stuart, DI, and Walsh, MA
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Automation, Laboratory ,Proteomics ,Macromolecular Substances ,Crystallography, X-Ray ,Software ,Synchrotrons - Abstract
Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.
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- 2014
21. The VIZIER project: Preparedness against pathogenic RNA viruses
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Coutard, B, Gorbalenya, AE, Snijder, EJ, Leontovich, AM, Poupon, A, De Lamballerie, X, Charrel, R, Gould, EA, Gunther, S, Norder, H, Klempa, B, Bourhy, H, Rohayem, J, L'hermite, E, Nordlund, P, Stuart, DI, Owens, RJ, Grimes, JM, Tucker, PA, and Bolognesi, M
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PROTEIN EXPRESSION ,ESCHERICHIA-COLI ,CRYSTAL-STRUCTURE ,CATALYTIC DOMAIN ,DENGUE VIRUS - Abstract
Life-threatening RNA viruses emerge regularly, and often in an unpredictable manner. Yet, the very few drugs available against known RNA viruses have sometimes required decades of research for development. Can we generate preparedness for outbreaks of the, as yet, unknown viruses? The VIZIER (VIral enZymes InvolvEd in Replication) (http://www.vizier-europe.org/) project has been set-up to develop the scientific foundations for countering this challenge to society. VIZIER studies the most conserved viral enzymes (that of the replication machinery, or replicases) that constitute attractive targets for drug-design. The aim of VIZIER is to determine as many replicase crystal structures as possible from a carefully selected list of viruses in order to comprehensively cover the diversity of the RNA virus universe, and generate critical knowledge that could be efficiently utilized to jump-start research on any emerging RNA virus. VIZIER is a multidisciplinary project involving (i) bioinformatics to define functional domains, (ii) viral genomics to increase the number of characterized viral genomes and prepare defined targets, (iii) proteomics to express, purify, and characterize targets, (iv) structural biology to solve their crystal structures, and (v) pre-lead discovery to propose active scaffolds of antiviral molecules. (C) 2007 Elsevier B.V. All rights reserved.
- Published
- 2008
22. Erratum: Application of the use of high-throughput technologies to the determination of protein structures of bacterial and viral pathogens (Acta Crystallographica Section D: Biological Crystallography (2006) D62 (1196-1207))
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Fogg, MJ, Alzari, P, Bahar, M, Bertini, I, Betton, J-M, Burmeister, WP, Cambillau, C, Canard, B, Carrondo, MA, Coll, M, Daenke, S, Dym, O, Egloff, M-P, Enguita, FJ, Geerlof, A, Haouz, A, Jones, TA, Ma, Q, Manicka, SN, Migliardi, M, Nordlund, P, Owens, RJ, Peleg, Y, Schneider, G, Schnell, R, Stuart, DI, Tarbouriech, N, Unge, T, Wilkinson, AJ, Wilmanns, M, Wilson, KS, Zimhony, O, and Grimes, JM
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- 2006
23. Application of the use of high-throughput technologies to the determination of protein structures of bacterial and viral pathogens (vol 62, pg 1196, 2006)
- Author
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Fogg, MJ, Alzari, P, Bahar, M, Bertini, I, Betton, J-M, Burmeister, WP, Cambillau, C, Canard, B, Carrondo, MA, Coll, M, Daenke, S, Dym, O, Egloff, M-P, Enguita, FJ, Geerlof, A, Haouz, A, Jones, TA, Ma, Q, Manicka, SN, Migliardi, M, Nordlund, P, Owens, RJ, Peleg, Y, Schneider, G, Schnell, R, Stuart, DI, Tarbouriech, N, Unge, T, Wilkinson, AJ, Wilmanns, M, Wilson, KS, Zimhony, O, and Grimes, JM
- Published
- 2006
24. Allosteric Inhibitors against HIV-1 Reverse Transcriptase: Design and Synthesis of MKC-442 Analogues Having an Ω-Functionalized Acyclic Structure
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Tanaka, H, primary, Walker, RT, additional, Hopkins, AL, additional, Ren, J, additional, Jones, EY, additional, Fujimoto, K, additional, Hayashi, M, additional, Miyasaka, T, additional, Baba, M, additional, Stammers, DK, additional, and Stuart, DI, additional
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- 1998
- Full Text
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25. STRUCTURE OF FOOT-AND-MOUTH-DISEASE VIRUS
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Acharya, R., Fry, E., Derek Logan, Stuart, Di, Fox, G., Rowlands, D., and Brown, F.
26. Epitope dominance studies with serotype O foot-and-mouth disease
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Borley, DW and Stuart, DI
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Vaccinology ,Viruses ,Immunology ,Infectious diseases ,Molecular biophysics (biochemistry) - Abstract
Foot-and-mouth disease virus (FMDV) is an economically devastating and highly contagious livestock pathogen. It exists as seven serotypes, comprising numerous antigenically distinct subtypes. The large amount of antigenic heterogeneity has confounded attempts at developing broadly reactive vaccines. In order to overcome this issue the fundamentals of the interactions between the virus and the host humoral immune response must first be understood. Previous work in this area using monoclonal antibody (mAb) escape mutants has identified five antigenic sites for the O serotype and efforts have been made to quantify their relative importance. However, this does not represent a complete picture of serotype O antigenicity. The work conducted in this thesis demonstrates the role of a limited number of dominant substitutions in mediating the antigenic diversity of serotype O Foot-and-Mouth disease virus. Two alternative but complementary methods for identifying epitopes were developed. The first used a mathematical model to analyse newly generated serological and sequence data from 105 viruses, cultured for this purpose (and cross-reacted to 5 reference antisera), in the context of an existing crystallographic structure to identify and quantify the antigenic importance of sites on the surface of the virus. The second approach was purely structural, using existing B cell epitope prediction tools to develop a method for predicting FMDV epitopes using existing crystallographic structures of FMDV. These techniques were validated by the use of reverse genetics, which confirmed the impact on cross reactivity of two predicted novel serotype O antigenic residues, with a further four novel residues identified by looking in depth at the interactions between two genetically close, but antigenically distant viruses. This increased knowledge of the antigenic composition of serotype O FMDV contributes to our understanding of the nature of vaccine efficacy and the breadth of protection, which, in the longer term, will aid in the goal of developing vaccines to better protect livestock from such a highly antigenically variable disease.
- Published
- 2016
27. Structure of the RNA-dependent RNA polymerase P2 from the cystovirus φ8.
- Author
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Latimer-Smith M, Salgado PS, Forsyth I, Makeyev E, Poranen MM, Stuart DI, Grimes JM, and El Omari K
- Subjects
- Models, Molecular, Crystallography, X-Ray, Viral Proteins chemistry, Viral Proteins genetics, Viral Proteins metabolism, RNA, Viral genetics, RNA, Viral chemistry, RNA, Viral metabolism, Protein Conformation, RNA-Dependent RNA Polymerase chemistry, RNA-Dependent RNA Polymerase metabolism, RNA-Dependent RNA Polymerase genetics, Cystoviridae genetics, Cystoviridae metabolism, Cystoviridae chemistry
- Abstract
The replication of RNA viruses relies on the activity of RNA-dependent RNA polymerases (RdRps). Despite large variations in their genomic sequences, viral RdRps share a common architecture generally known as a closed right hand. The P2 polymerase of cystovirus φ6 is currently among the best characterized viral RdRps. This polymerase is responsible for carrying out both replication and transcription of the viral double-stranded RNA genome using de novo initiation. Despite the extensive biochemical and structural studies conducted on φ6 P2, further structural information on other cystoviral RdRps is crucial to elucidate the structural and functional diversity of viral RdRps. Here, we have determined the atomic X-ray structure of the RdRp P2 from the φ6-related cystovirus φ8 at 3Å resolution. This structure completes the existing set of structural information on the φ8 polymerase complex and sheds light on the difference and similarities with related cystoviral RdRps., (© 2024. The Author(s).)
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- 2024
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28. Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike.
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Duyvesteyn HME, Dijokaite-Guraliuc A, Liu C, Supasa P, Kronsteiner B, Jeffery K, Stafford L, Klenerman P, Dunachie SJ, Mongkolsapaya J, Fry EE, Ren J, Stuart DI, and Screaton GR
- Subjects
- Humans, Models, Molecular, Epitopes chemistry, Epitopes immunology, Sequence Deletion, Antibodies, Viral immunology, Binding Sites, Protein Domains, Protein Binding, Spike Glycoprotein, Coronavirus chemistry, Spike Glycoprotein, Coronavirus genetics, Spike Glycoprotein, Coronavirus immunology, Spike Glycoprotein, Coronavirus metabolism, SARS-CoV-2 immunology, SARS-CoV-2 genetics, SARS-CoV-2 chemistry, Antibodies, Neutralizing immunology, COVID-19 immunology, COVID-19 virology
- 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., Competing Interests: Declaration of interests G.R.S. sits on the GSK Vaccines Scientific Advisory Board and is a founder member of RQ Biotechnology. D.I.S. consults for AstraZeneca. Oxford University holds intellectual property related to SARS-CoV-2 mAbs discovered in G.R.S.’s laboratory. S.J.D. is a Scientific Advisor to the Scottish Parliament on COVID-19., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2024
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29. A broadly reactive ultralong bovine antibody that can determine the integrity of foot-and-mouth disease virus capsids.
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Clarke JD, Duyvesteyn HME, Perez-Martin E, Latišenko U, Porta C, Humphreys KV, Hay AL, Ren J, Fry EE, van den Born E, Charleston B, Bonnet-Di Placido M, Owens RJ, Stuart DI, and Hammond JA
- Subjects
- Animals, Cattle, Foot-and-Mouth Disease immunology, Foot-and-Mouth Disease virology, Serogroup, Cross Reactions, Epitopes immunology, Foot-and-Mouth Disease Virus immunology, Antibodies, Viral immunology, Capsid immunology, Capsid Proteins immunology
- 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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- 2024
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30. Oligomerization-driven avidity correlates with SARS-CoV-2 cellular binding and inhibition.
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Asor R, Olerinyova A, Burnap SA, Kushwah MS, Soltermann F, Rudden LSP, Hensen M, Vasiljevic S, Brun J, Hill M, Chang L, Dejnirattisai W, Supasa P, Mongkolsapaya J, Zhou D, Stuart DI, Screaton GR, Degiacomi MT, Zitzmann N, Benesch JLP, Struwe WB, and Kukura P
- Subjects
- Humans, Virus Internalization drug effects, Antibodies, Viral immunology, Antibodies, Viral metabolism, Thermodynamics, SARS-CoV-2 metabolism, Angiotensin-Converting Enzyme 2 metabolism, Angiotensin-Converting Enzyme 2 chemistry, Spike Glycoprotein, Coronavirus metabolism, Spike Glycoprotein, Coronavirus chemistry, Protein Binding, COVID-19 virology, COVID-19 metabolism, COVID-19 immunology, Protein Multimerization
- Abstract
Cellular processes are controlled by the thermodynamics of the underlying biomolecular interactions. Frequently, structural investigations use one monomeric binding partner, while ensemble measurements of binding affinities generally yield one affinity representative of a 1:1 interaction, despite the majority of the proteome consisting of oligomeric proteins. For example, viral entry and inhibition in SARS-CoV-2 involve a trimeric spike surface protein, a dimeric angiotensin-converting enzyme 2 (ACE2) cell-surface receptor and dimeric antibodies. Here, we reveal that cooperativity correlates with infectivity and inhibition as opposed to 1:1 binding strength. We show that ACE2 oligomerizes spike more strongly for more infectious variants, while exhibiting weaker 1:1 affinity. Furthermore, we find that antibodies use induced oligomerization both as a primary inhibition mechanism and to enhance the effects of receptor-site blocking. Our results suggest that naive affinity measurements are poor predictors of potency, and introduce an antibody-based inhibition mechanism for oligomeric targets. More generally, they point toward a much broader role of induced oligomerization in controlling biomolecular interactions., Competing Interests: Competing interests statement:P.K. is a nonexecutive director, shareholder of and consultant to Refeyn Ltd., J.L.P.B. and W.B.S. are shareholders of and consultants to Refeyn Ltd. W.B.S. and P.K. received the University of Oxford’s COVID-19 Research Response Fund. P.K. has filed a patent for the contrast enhancement methodology and its application to mass measurement of single biomolecules. G.R.S. is on the GSK Vaccines Scientific Advisory Board, a founder shareholder of RQ biotechnology and Jenner investigator. Oxford University holds intellectual property related to the Oxford-AstraZeneca vaccine.
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- 2024
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31. Immunogenicity of Abdala COVID-19 vaccine in Vietnamese people after primary and booster vaccinations: A prospective observational study in Vietnam.
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Thanh TT, Tu NTK, Nguyet LA, Thuy CT, Thuan NLT, Ny NTH, Nhu LNT, Thanh LK, Hong NTT, Anh NT, Truong NT, Chau NVV, Yen LM, Van E P, Thuong NP, Van Truc N, Trung PH, Yap WC, Pandey R, Yee S, Weng R, Mongkolsapaya J, Dejnirattisai W, Hamers RL, Chantratita N, Screaton G, Dunachie SJ, Jones EY, Stuart DI, Dung NT, Thwaites G, Wang LF, Tan CW, and Tan LV
- Subjects
- Humans, Vietnam, Adult, Prospective Studies, Female, Male, Middle Aged, Young Adult, Immunogenicity, Vaccine, ChAdOx1 nCoV-19 immunology, Spike Glycoprotein, Coronavirus immunology, Vaccination, Southeast Asian People, Immunization, Secondary, Antibodies, Neutralizing blood, SARS-CoV-2 immunology, COVID-19 prevention & control, COVID-19 immunology, COVID-19 epidemiology, Antibodies, Viral blood, COVID-19 Vaccines immunology, COVID-19 Vaccines administration & dosage
- Abstract
Objectives: We studied the immunogenicity after primary and booster vaccinations of the Abdala COVID-19 vaccine, a receptor-binding domain protein subunit vaccine, in Vietnamese people by determining the level of neutralization and cross-neutralization activities against the ancestral SARS-CoV-2 and its variants and SARS-CoV-1., Methods: We performed a prospective observational study, enrolling adults aged 19-59 years in Dong Thap province, southern Vietnam, and collected blood samples from baseline until 4 weeks after the booster dose. We measured anti-nucleocapsid, anti-spike, and neutralizing antibodies against SARS-CoV-2 and assessed the cross-neutralization against 14 SARS-CoV-2 variants and SARS-CoV-1. Complementary antibody data came from Vietnamese health care workers fully vaccinated with ChAdOx1-S., Results: After primary vaccination, anti-spike antibody and neutralizing antibodies were detectable in 98.4% and 87% of 251 study participants, respectively, with neutralizing antibody titers similar to that induced by ChAdOx1-S vaccine. Antibody responses after a homologous (Abdala COVID-19) or heterologous (messenger RNA BNT162b2) booster could neutralize 14 SARS-CoV-2 variants (including Omicron) and SARS-CoV-1., Conclusions: Abdala COVID-19 vaccine is immunogenic in Vietnamese people. Enhanced antibody response after a booster dose could cross-neutralize 14 SARS-CoV-2 variants and SARS-CoV-1. Our results have added to the growing body of knowledge about the contribution of protein subunit vaccine platforms to pandemic control., Competing Interests: Declarations of competing interest The authors have no competing interests to declare., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2024
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32. The effect of pH on the structure of Bluetongue virus VP5.
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Zhang H, El Omari K, Sutton G, and Stuart DI
- Subjects
- Hydrogen-Ion Concentration, Virus Internalization, Animals, Protein Conformation, Bluetongue virus physiology, Bluetongue virus chemistry, Capsid Proteins chemistry, Capsid Proteins metabolism, Capsid Proteins genetics
- Abstract
The unenveloped Bluetongue virus capsid comprises several structural layers, the inner two comprising a core, which assembles before addition of the outer proteins, VP2 and VP5. Two symmetric trimers of VP5 fit like pegs into two distinct pits on the core and undergo pH conformational changes in the context of the virus, associated with cell entry. Here we show that in isolation VP5 alone undergoes essentially the same changes with pH and confirm a helical transition, indicating that VP5 is a motor during cell entry. In the absence of VP5 the two pits on the core differ from each other, presumably due to the asymmetric underlying structure of VP3, the innermost capsid protein. On insertion of VP5 these pits become closely similar and remain similar at low pH whilst VP5 is present. This natural asymmetry presumably destabilises the attachment of VP5, facilitating ejection upon low pH, membrane penetration and cell entry.
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- 2024
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33. The impact of exchanging the light and heavy chains on the structures of bovine ultralong antibodies.
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Clarke JD, Douangamath A, Mikolajek H, Bonnet-Di Placido M, Ren J, Fry EE, Stuart DI, Hammond JA, and Owens RJ
- Subjects
- Animals, Cattle, Crystallography, X-Ray, Amino Acid Sequence, Protein Conformation, Immunoglobulin Heavy Chains chemistry, Immunoglobulin Light Chains chemistry, Immunoglobulin Light Chains genetics, Complementarity Determining Regions chemistry, Immunoglobulin Fab Fragments chemistry, Models, Molecular
- 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., (open access.)
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- 2024
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34. Improving the representativeness of UK's national COVID-19 Infection Survey through spatio-temporal regression and post-stratification.
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Pouwels KB, Eyre DW, House T, Aspey B, Matthews PC, Stoesser N, Newton JN, Diamond I, Studley R, Taylor NGH, Bell JI, Farrar J, Kolenchery J, Marsden BD, Hoosdally S, Jones EY, Stuart DI, Crook DW, Peto TEA, and Walker AS
- Subjects
- Humans, United Kingdom epidemiology, Adult, Middle Aged, Aged, Adolescent, Young Adult, Child, Male, Female, Prevalence, Child, Preschool, Spatio-Temporal Analysis, Antibodies, Viral blood, Antibodies, Viral immunology, COVID-19 Vaccines administration & dosage, COVID-19 Vaccines immunology, Infant, Vaccination statistics & numerical data, Aged, 80 and over, COVID-19 epidemiology, COVID-19 prevention & control, COVID-19 virology, SARS-CoV-2 immunology, SARS-CoV-2 isolation & purification
- Abstract
Population-representative estimates of SARS-CoV-2 infection prevalence and antibody levels in specific geographic areas at different time points are needed to optimise policy responses. However, even population-wide surveys are potentially impacted by biases arising from differences in participation rates across key groups. Here, we used spatio-temporal regression and post-stratification models to UK's national COVID-19 Infection Survey (CIS) to obtain representative estimates of PCR positivity (6,496,052 tests) and antibody prevalence (1,941,333 tests) for different regions, ages and ethnicities (7-December-2020 to 4-May-2022). Not accounting for vaccination status through post-stratification led to small underestimation of PCR positivity, but more substantial overestimations of antibody levels in the population (up to 21 percentage points), particularly in groups with low vaccine uptake in the general population. There was marked variation in the relative contribution of different areas and age-groups to each wave. Future analyses of infectious disease surveys should take into account major drivers of outcomes of interest that may also influence participation, with vaccination being an important factor to consider., (© 2024. The Author(s).)
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- 2024
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35. A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
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Liu C, Zhou D, Dijokaite-Guraliuc A, Supasa P, Duyvesteyn HME, Ginn HM, Selvaraj M, Mentzer AJ, Das R, de Silva TI, Ritter TG, Plowright M, Newman TAH, Stafford L, Kronsteiner B, Temperton N, Lui Y, Fellermeyer M, Goulder P, Klenerman P, Dunachie SJ, Barton MI, Kutuzov MA, Dushek O, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, and Screaton GR
- Subjects
- Humans, Structure-Activity Relationship, Antibodies, Monoclonal immunology, Mutation genetics, Antibodies, Neutralizing immunology, Antibody Affinity, SARS-CoV-2 immunology, SARS-CoV-2 metabolism, SARS-CoV-2 genetics, Angiotensin-Converting Enzyme 2 metabolism, Angiotensin-Converting Enzyme 2 chemistry, COVID-19 immunology, COVID-19 virology, Antibodies, Viral immunology, Spike Glycoprotein, Coronavirus immunology, Spike Glycoprotein, Coronavirus genetics, Spike Glycoprotein, Coronavirus chemistry, Spike Glycoprotein, Coronavirus metabolism, Immune Evasion
- 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., Competing Interests: Declaration of interests G.R.S. sits on the GSK Vaccines Scientific Advisory Board, consults for AstraZeneca, and is a founder member of RQ Biotechnology. D.I.S. consults for AstraZeneca. Oxford University holds intellectual property related to SARS-CoV-2 mAbs discovered in G.R.S.’s laboratory. S.J.D. is a scientific advisor to the Scottish Parliament on COVID-19., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2024
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36. Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection.
- Author
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Liu C, Das R, Dijokaite-Guraliuc A, Zhou D, Mentzer AJ, Supasa P, Selvaraj M, Duyvesteyn HME, Ritter TG, Temperton N, Klenerman P, Dunachie SJ, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, and Screaton GR
- Subjects
- Humans, Mutation, SARS-CoV-2 genetics, Antibodies, Neutralizing, Antibodies, Viral, Antibodies, Monoclonal, Postoperative Complications
- 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., (© 2024. The Author(s).)
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- 2024
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37. Southeast Asia initiative to combat SARS-CoV-2 variants (SEACOVARIANTS) consortium.
- Author
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Nhu LNT, Chambers M, Chantratita N, Cheah PY, Day NPJ, Dejnirattisai W, Dunachie SJ, Grifoni A, Hamers RL, Hill J, Jones EY, Klenerman P, Mongkolsapaya J, Screaton G, Sette A, Stuart DI, Tan CW, Thwaites G, Thanh VD, Wang LF, and Tan LV
- Abstract
A strong and effective COVID-19 and future pandemic responses rely on global efforts to carry out surveillance of infections and emerging SARS-CoV-2 variants and to act accordingly in real time. Many countries in Southeast Asia lack capacity to determine the potential threat of new variants, or other emerging infections. Funded by Wellcome, the Southeast Asia initiative to combat SARS-CoV-2 variants (SEACOVARIANTS) consortium aims to develop and apply a multidisciplinary research platform in Southeast Asia (SEA) for rapid assessment of the biological significance of SARS-CoV-2 variants, thereby informing coordinated local, regional and global responses to the COVID-19 pandemic. Our proposal is delivered by the Vietnam and Thailand Wellcome Africa Asia Programmes, bringing together a multidisciplinary team in Indonesia, Thailand and Vietnam with partners in Singapore, the UK and the USA. Herein we outline five work packages to deliver strengthened regional scientific capacity that can be rapidly deployed for future outbreak responses., Competing Interests: Competing interests: L.V.T. received a consulting fee from MIMS Pte. Ltd. G.R.S. is in the GSK Vaccines Scientific Advisory Board, consults for AstraZeneca and is a founder member of RQ Biotechnology. No other competing interests were disclosed., (Copyright: © 2024 Nhu LNT et al.)
- Published
- 2024
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38. The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86.
- Author
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Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, and Screaton GR
- Subjects
- Humans, SARS-CoV-2 genetics, Antibodies, Monoclonal, Epitopes, Spike Glycoprotein, Coronavirus genetics, Antibodies, Viral, Antibodies, Neutralizing, COVID-19, Syndactyly
- 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., (© 2024. The Author(s).)
- Published
- 2024
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39. Structural comparison of typical and atypical E2 pestivirus glycoproteins.
- Author
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Aitkenhead H, Riedel C, Cowieson N, Rümenapf HT, Stuart DI, and El Omari K
- Subjects
- Swine, Animals, Rats, Glycoproteins, Antibodies, Neutralizing, Membrane Glycoproteins, Phylogeny, Pestivirus genetics
- Abstract
Pestiviruses, within the family Flaviviridae, are economically important viruses of livestock. In recent years, new pestiviruses have been reported in domestic animals and non-cloven-hoofed animals. Among them, atypical porcine pestivirus (APPV) and Norway rat pestivirus (NRPV) have relatively little sequence conservation in their surface glycoprotein E2. Despite E2 being the main target for neutralizing antibodies and necessary for cell attachment and viral fusion, the mechanism of viral entry remains elusive. To gain further insights into the pestivirus E2 mechanism of action and to assess its diversity within the genus, we report X-ray structures of the pestivirus E2 proteins from APPV and NRPV. Despite the highly divergent structures, both are able to dimerize through their C-terminal domain and contain a solvent-exposed β-hairpin reported to be involved in host receptor binding. Functional analysis of this β-hairpin in the context of BVDV revealed its ability to rescue viral infectivity., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2024
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40. COVID-19 therapeutics: stewardship in England and considerations for antimicrobial resistance.
- Author
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Bou-Antoun S, Rokadiya S, Ashiru-Oredope D, Demirjian A, Sherwood E, Ellaby N, Gerver S, Grossi C, Harman K, Hartman H, Lochen A, Ragonnet-Cronin M, Squire H, Sutton JM, Thelwall S, Tree J, Bahar MW, Stuart DI, Brown CS, Chand M, and Hopkins S
- Subjects
- Humans, SARS-CoV-2, Anti-Bacterial Agents therapeutic use, Pandemics prevention & control, Antiviral Agents therapeutic use, Antiviral Agents pharmacology, Drug Resistance, Bacterial, England epidemiology, COVID-19 epidemiology
- Abstract
The COVID-19 pandemic saw unprecedented resources and funds driven into research for the development, and subsequent rapid distribution, of vaccines, diagnostics and directly acting antivirals (DAAs). DAAs have undeniably prevented progression and life-threatening conditions in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, there are concerns of antimicrobial resistance (AMR), antiviral resistance specifically, for DAAs. To preserve activity of DAAs for COVID-19 therapy, as well as detect possible mutations conferring resistance, antimicrobial stewardship and surveillance were rapidly implemented in England. This paper expands on the ubiquitous ongoing public health activities carried out in England, including epidemiologic, virologic and genomic surveillance, to support the stewardship of DAAs and assess the deployment, safety, effectiveness and resistance potential of these novel and repurposed therapeutics., (© The Author(s) 2023. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)
- Published
- 2023
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41. Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
- Author
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El Omari K, Duman R, Mykhaylyk V, Orr CM, Latimer-Smith M, Winter G, Grama V, Qu F, Bountra K, Kwong HS, Romano M, Reis RI, Vogeley L, Vecchia L, Owen CD, Wittmann S, Renner M, Senda M, Matsugaki N, Kawano Y, Bowden TA, Moraes I, Grimes JM, Mancini EJ, Walsh MA, Guzzo CR, Owens RJ, Jones EY, Brown DG, Stuart DI, Beis K, and Wagner A
- Abstract
Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing., (© 2023. Springer Nature Limited.)
- Published
- 2023
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42. ChAdOx1 COVID vaccines express RBD open prefusion SARS-CoV-2 spikes on the cell surface.
- Author
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Ni T, Mendonça L, Zhu Y, Howe A, Radecke J, Shah PM, Sheng Y, Krebs AS, Duyvesteyn HME, Allen E, Lambe T, Bisset C, Spencer A, Morris S, Stuart DI, Gilbert S, and Zhang P
- Abstract
Vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been proven to be an effective means of decreasing COVID-19 mortality, hospitalization rates, and transmission. One of the vaccines deployed worldwide is ChAdOx1 nCoV-19, which uses an adenovirus vector to drive the expression of the original SARS-CoV-2 spike on the surface of transduced cells. Using cryo-electron tomography and subtomogram averaging, we determined the native structures of the vaccine product expressed on cell surfaces in situ . We show that ChAdOx1-vectored vaccines expressing the Beta SARS-CoV-2 variant produce abundant native prefusion spikes predominantly in one-RBD-up conformation. Furthermore, the ChAdOx1-vectored HexaPro-stabilized spike yields higher cell surface expression, enhanced RBD exposure, and reduced shedding of S1 compared to the wild type. We demonstrate in situ structure determination as a powerful means for studying antigen design options in future vaccine development against emerging novel SARS-CoV-2 variants and broadly against other infectious viruses., Competing Interests: The authors declare no competing interests., (© 2023 The Author(s).)
- Published
- 2023
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43. Broadly neutralizing antibodies against COVID-19.
- Author
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Zhou D, Ren J, Fry EE, and Stuart DI
- Subjects
- Humans, Broadly Neutralizing Antibodies, SARS-CoV-2 genetics, Pandemics, Antibodies, Neutralizing therapeutic use, Antibodies, Monoclonal therapeutic use, Antibodies, Viral therapeutic use, COVID-19
- 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., Competing Interests: Declaration of Competing Interest Oxford University holds intellectual property related to SARS-CoV-2 mAbs discovered in Gavin R Screaton’s laboratory and DIS consults for AstraZeneca, (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)
- Published
- 2023
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- View/download PDF
44. Structure of Bovine CD46 Ectodomain.
- Author
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Aitkenhead H, Stuart DI, and El Omari K
- Subjects
- Animals, Cattle, Humans, Complement Activation, Diarrhea, Membrane Cofactor Protein, Diarrhea Viruses, Bovine Viral
- Abstract
CD46, or membrane cofactor protein, is a type-one transmembrane protein from the complement regulatory protein family. Alongside its role in complement activation, CD46 is involved in many other processes, from T-cell activation to reproduction. It is also referred to as a pathogen magnet, because it is used as a receptor by multiple bacteria and viruses. Bovine CD46 (bovCD46) in particular is involved in bovine viral diarrhoea virus entry, an economically important disease in cattle industries. This study presents the X-ray crystallographic structure of the extracellular region of bovCD46, revealing a four-short-consensus-repeat (SCR) structure similar to that in human CD46. SCR1-3 are arranged linearly, while SCR 4 has a reduced interface angle, resulting in a hockey stick-like appearance. The structure also reveals the bovine viral diarrhoea virus interaction site in SCR1, which is likely to confer pestivirus specificity for their target host, CD46. Insights gained from the structural information on pestivirus receptors, such as CD46, could offer valuable guidance for future control strategies.
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- 2023
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45. Accelerating drug target inhibitor discovery with a deep generative foundation model.
- Author
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Chenthamarakshan V, Hoffman SC, Owen CD, Lukacik P, Strain-Damerell C, Fearon D, Malla TR, Tumber A, Schofield CJ, Duyvesteyn HME, Dejnirattisai W, Carrique L, Walter TS, Screaton GR, Matviiuk T, Mojsilovic A, Crain J, Walsh MA, Stuart DI, and Das P
- Subjects
- Humans, SARS-CoV-2 metabolism, Protein Binding, Amino Acid Sequence, Antibodies, Viral chemistry, COVID-19
- Abstract
Inhibitor discovery for emerging drug-target proteins is challenging, especially when target structure or active molecules are unknown. Here, we experimentally validate the broad utility of a deep generative framework trained at-scale on protein sequences, small molecules, and their mutual interactions-unbiased toward any specific target. We performed a protein sequence-conditioned sampling on the generative foundation model to design small-molecule inhibitors for two dissimilar targets: the spike protein receptor-binding domain (RBD) and the main protease from SARS-CoV-2. Despite using only the target sequence information during the model inference, micromolar-level inhibition was observed in vitro for two candidates out of four synthesized for each target. The most potent spike RBD inhibitor exhibited activity against several variants in live virus neutralization assays. These results establish that a single, broadly deployable generative foundation model for accelerated inhibitor discovery is effective and efficient, even in the absence of target structure or binder information.
- Published
- 2023
- Full Text
- View/download PDF
46. Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy.
- Author
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Ragonnet-Cronin M, Nutalai R, Huo J, Dijokaite-Guraliuc A, Das R, Tuekprakhon A, Supasa P, Liu C, Selvaraj M, Groves N, Hartman H, Ellaby N, Mark Sutton J, Bahar MW, Zhou D, Fry E, Ren J, Brown C, Klenerman P, Dunachie SJ, Mongkolsapaya J, Hopkins S, Chand M, Stuart DI, Screaton GR, and Rokadiya S
- Subjects
- Humans, Antibodies, Monoclonal therapeutic use, Immunotherapy, Mutation, Antibodies, Neutralizing, Antibodies, Viral, SARS-CoV-2 genetics, COVID-19
- Abstract
COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for antibodies targeting relatively conserved regions, individually e.g. sotrovimab. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively. Mutations occur within the antibody epitopes and for casirivimab+imdevimab multiple mutations are present on contiguous raw reads, simultaneously affecting both components. Using surface plasmon resonance and pseudoviral neutralisation assays we demonstrate these mutations reduce or completely abrogate antibody affinity and neutralising activity, suggesting they are driven by immune evasion. In addition, we show that some mutations also reduce the neutralising activity of vaccine-induced serum., (© 2023. The Author(s).)
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- 2023
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47. Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer.
- Author
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Pei X, Zhou L, Huang C, Boyce M, Kim JS, Liberti E, Hu Y, Sasaki T, Nellist PD, Zhang P, Stuart DI, Kirkland AI, and Wang P
- Abstract
Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible., (© 2023. The Author(s).)
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- 2023
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48. Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK.
- Author
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Wei J, Matthews PC, Stoesser N, Newton JN, Diamond I, Studley R, Taylor N, Bell JI, Farrar J, Kolenchery J, Marsden BD, Hoosdally S, Jones EY, Stuart DI, Crook DW, Peto TEA, Walker AS, Pouwels KB, and Eyre DW
- Subjects
- Adult, Humans, COVID-19 Vaccines, SARS-CoV-2, Antibodies, Viral, Reinfection, United Kingdom epidemiology, Vaccination, Breakthrough Infections, COVID-19 prevention & control
- Abstract
Following primary SARS-CoV-2 vaccination, whether boosters or breakthrough infections provide greater protection against SARS-CoV-2 infection is incompletely understood. Here we investigated SARS-CoV-2 antibody correlates of protection against new Omicron BA.4/5 (re-)infections and anti-spike IgG antibody trajectories after a third/booster vaccination or breakthrough infection following second vaccination in 154,149 adults ≥18 y from the United Kingdom general population. Higher antibody levels were associated with increased protection against Omicron BA.4/5 infection and breakthrough infections were associated with higher levels of protection at any given antibody level than boosters. Breakthrough infections generated similar antibody levels to boosters, and the subsequent antibody declines were slightly slower than after boosters. Together our findings show breakthrough infection provides longer-lasting protection against further infections than booster vaccinations. Our findings, considered alongside the risks of severe infection and long-term consequences of infection, have important implications for vaccine policy., (© 2023. The Author(s).)
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- 2023
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49. Investigation of the milling characteristics of different focused-ion-beam sources assessed by three-dimensional electron diffraction from crystal lamellae.
- Author
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Parkhurst JM, Crawshaw AD, Siebert CA, Dumoux M, Owen CD, Nunes P, Waterman D, Glen T, Stuart DI, Naismith JH, and Evans G
- Abstract
Three-dimensional electron diffraction (3DED) from nanocrystals of biological macromolecules requires the use of very small crystals. These are typically less than 300 nm-thick in the direction of the electron beam due to the strong interaction between electrons and matter. In recent years, focused-ion-beam (FIB) milling has been used in the preparation of thin samples for 3DED. These instruments typically use a gallium liquid metal ion source. Inductively coupled plasma (ICP) sources in principle offer faster milling rates. Little work has been done to quantify the damage these sources cause to delicate biological samples at cryogenic temperatures. Here, an analysis of the effect that milling with plasma FIB (pFIB) instrumentation has on lysozyme crystals is presented. This work evaluates both argon and xenon plasmas and compares them with crystals milled with a gallium source. A milling protocol was employed that utilizes an overtilt to produce wedge-shaped lamellae with a shallow thickness gradient which yielded very thin crystalline samples. 3DED data were then acquired and standard data-processing statistics were employed to assess the quality of the diffraction data. An upper bound to the depth of the pFIB-milling damage layer of between 42.5 and 50 nm is reported, corresponding to half the thickness of the thinnest lamellae that resulted in usable diffraction data. A lower bound of between 32.5 and 40 nm is also reported, based on a literature survey of the minimum amount of diffracting material required for 3DED., (open access.)
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- 2023
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50. Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.
- Author
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Dijokaite-Guraliuc A, Das R, Zhou D, Ginn HM, Liu C, Duyvesteyn HME, Huo J, Nutalai R, Supasa P, Selvaraj M, de Silva TI, Plowright M, Newman TAH, Hornsby H, Mentzer AJ, Skelly D, Ritter TG, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Roemer C, Peacock TP, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, and Screaton GR
- Subjects
- Humans, SARS-CoV-2, Amino Acid Substitution, Antibodies, Monoclonal, Antibodies, Viral, Antibodies, Neutralizing, Antibody Formation, COVID-19
- 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 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (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 titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum., Competing Interests: Declaration of interests G.R.S. sits on the GSK Vaccines Scientific Advisory Board, consults for AstraZeneca, and is a founding member of RQ Biotechnology. D.I.S. consults for AstraZeneca. Oxford University holds intellectual property related to SARS-CoV-2 mAbs discovered in G.R.S.’s laboratory. S.J.D. is a scientific advisor to the Scottish Parliament on COVID-19., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
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