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Instruments / Technical Area	Publication Details	Published
I03-Macromolecular Crystallography	Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine induced sera Daming Zhou , Wanwisa Dejnirattisai , Piyada Supasa , Chang Liu , Alexander J. Mentzer , Helen M. Ginn , Yuguang Zhao , Helen M. E. Duyvesteyn , Aekkachai Tuekprakhon , Rungtiwa Nutalai , Beibei Wang , Guido C. Paesen , Cesar Lopez-Camacho , Jose Slon-Campos , Bassam Hallis , Naomi Coombes , Kevin Bewley , Sue Charlton , Thomas S. Walter , Donal Skelly , Sheila F. Lumley , Christina Dold , Robert Levin , Tao Dong , Andrew J. Pollard , Julian C. Knight , Derrick Crook , Teresa Lambe , Elizabeth Clutterbuck , Sagida Bibi , Amy Flaxman , Mustapha Bittaye , Sandra Belij-Rammerstorfer , Sarah Gilbert , William James , Miles W. Carroll , Paul Klenerman , Eleanor Barnes , Susanna J. Dunachie , Elizabeth E. Fry , Juthathip Mongkolspaya , Jingshan Ren , David I. Stuart , Gavin R. Screaton Cell DOI: 10.1016/j.cell.2021.02.037 Diamond Proposal Number(s): [27009] Open Access Show Abstract ▼ Abstract: The race to produce vaccines against SARS-CoV-2 began when the first sequence was published, and this forms the basis for vaccines currently deployed globally. Independent lineages of SARS-CoV-2 have recently been reported: UK–B.1.1.7, South Africa–B.1.351 and Brazil–P.1. These variants have multiple changes in the immunodominant spike protein which facilitates viral cell entry via the Angiotensin converting enzyme-2 (ACE2) receptor. Mutations in the receptor recognition site on the spike are of great concern for their potential for immune escape. Here we describe a structure-function analysis of B.1.351 using a large cohort of convalescent and vaccinee serum samples. The receptor binding domain mutations provide tighter ACE2 binding and widespread escape from monoclonal antibody neutralization largely driven by E484K although K417N and N501Y act together against some important antibody classes. In a number of cases it would appear that convalescent and some vaccine serum offers limited protection against this variant.	Feb 2021
I03-Macromolecular Crystallography Krios I-Titan Krios I at Diamond	The antigenic anatomy of SARS-CoV-2 receptor binding domain Wanwisa Dejnirattisai , Daming Zhou , Helen M. Ginn , Helen M. E. Duyvesteyn , Piyada Supasa , James Brett Case , Yuguang Zhao , Thomas Walter , Alexander J. Mentzer , Chang Liu , Beibei Wang , Guido C. Paesen , Jose Slon-Campos , César López-Camacho , Natasha M. Kafai , Adam L. Bailey , Rita E. Chen , Baoling Ying , Craig Thompson , Jai Bolton , Alex Fyfe , Sunetra Gupta , Tiong Kit Tan , Javier Gilbert-Jaramillo , William James , Michael Knight , Miles W. Carroll , Donal Skelly , Christina Dold , Yanchun Peng , Robert Levin , Tao Dong , Andrew J. Pollard , Julian C. Knight , Paul Klenerman , Nigel Temperton , David R. Hall , Mark A. Williams , Neil G. Paterson , Felicity Bertram , C. Alistair Siebert , Daniel K. Clare , Andrew Howe , Julika Radecke , Yun Song , Alain R. Townsend , Kuan-Ying A. Huang , Elizabeth E. Fry , Juthathip Mongkolsapaya , Michael S. Diamond , Jingshan Ren , David I. Stuart , Gavin R. Screaton Cell DOI: 10.1016/j.cell.2021.02.032 Diamond Proposal Number(s): [27009, 26983] Open Access Show Abstract ▼ Abstract: Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike, and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC50<0.1μg/ml) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryo-electron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.	Feb 2021
I03-Macromolecular Crystallography	Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera Piyada Supasa , Daming Zhou , Wanwisa Dejnirattisai , Chang Liu , Alexander J. Mentzer , Helen M. Ginn , Yuguang Zhao , Helen M. E. Duyvesteyn , Rungtiwa Nutalai , Aekkachai Tuekprakhon , Beibei Wang , Guido Paesen , Jose Slon-Campos , César López-Camacho , Bassam Hallis , Naomi Coombes , Kevin Bewley , Sue Charlton , Thomas S. Walter , Eleanor Barnes , Susanna J. Dunachie , Donal Skelly , Sheila F. Lumley , Natalie Baker , Imam Shaik , Holly Humphries , Kerry Godwin , Nick Gent , Alex Sienkiewicz , Christina Dold , Robert Levin , Tao Dong , Andrew J. Pollard , Julian C. Knight , Paul Klenerman , Derrick Crook , Teresa Lambe , Elizabeth Clutterbuck , Sagida Bibi , Amy Flaxman , Mustapha Bittaye , Sandra Belij-Rammerstorfer , Sarah Gilbert , David R. Hall , Mark Williams , Neil G. Paterson , William James , Miles W. Carroll , Elizabeth E. Fry , Juthathip Mongkolsapaya , Jingshan Ren , David I. Stuart , Gavin R. Screaton Cell DOI: 10.1016/j.cell.2021.02.033 Diamond Proposal Number(s): [27009] Open Access Show Abstract ▼ Abstract: SARS-CoV-2 has caused over 2M deaths in little over a year. Vaccines are being deployed at scale, aiming to generate responses against the virus spike. The scale of the pandemic and error-prone virus replication is leading to the appearance of mutant viruses and potentially escape from antibody responses. Variant B.1.1.7, now dominant in the UK, with increased transmission, harbours 9 amino-acid changes in the spike, including N501Y in the ACE2 interacting-surface. We examine the ability of B.1.1.7 to evade antibody responses elicited by natural SARS-CoV-2 infection or vaccination. We map the impact of N501Y by structure/function analysis of a large panel of well-characterised monoclonal antibodies. B.1.1.7 is harder to neutralize than parental virus, compromising neutralization by some members of a major class of public antibodies through light chain contacts with residue 501. However, widespread escape from monoclonal antibodies or antibody responses generated by natural infection or vaccination was not observed.	Feb 2021
B07-C-Versatile Soft X-ray beamline: Ambient Pressure XPS and NEXAFS	Understanding metal organic chemical vapour deposition of monolayer WS2 : the enhancing role of Au substrate for simple organosulfur precursors Ye Fan , Kenichi Nakanishi , Vlad P. Veigang-Radulescu , Ryo Mizuta , J. Callum Stewart , Jack E. N. Swallow , Alice E. Dearle , Oliver J. Burton , Jack A. Alexander-Webber , Pilar Ferrer , Georg Held , Barry Brennan , Andrew J. Pollard , Robert S Weatherup , Stephan Hofmann Nanoscale 7 DOI: 10.1039/D0NR06459A Diamond Proposal Number(s): [22123] Open Access Show Abstract ▼ Abstract: We find that the use of Au substrate allows fast, self-limited WS2 monolayer growth using a simple sequential exposure pattern of low cost, low toxicity precursors, namely tungsten hexacarbonyl and dimethylsulfide (DMS). We use this model reaction system to fingerprint the technologically important metal organic chemical vapour deposition process by operando X-ray photoelectron spectroscopy (XPS) to address the current lack of understanding of the underlying fundamental growth mechanisms for WS2 and related transition metal dichalcogenides. Au effectively promotes the sulfidation of W with simple organosulfides, enabling WS2 growth with low DMS pressure (<1 mbar) and a suppression of carbon contamination of as-grown WS2, which to date has been a major challenge with this precursor chemistry. Full WS2 coverage can be achieved by one exposure cycle of 10 minutes at 700 °C. We discuss our findings in the wider context of previous literature on heterogeneous catalysis, 2D crystal growth, and overlapping process technologies such as atomic layer deposition (ALD) and direct metal conversion, linking to future integrated manufacturing processes for transition metal dichalcogenide layers.	Oct 2020
	Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel Emily R. Adams , Mark Ainsworth , Rekha Anand , Monique I. Andersson , Kathryn Auckland , J. Kenneth Baillie , Eleanor Barnes , Sally Beer , John I. Bell , Tamsin Berry , Sagida Bibi , Miles Carroll , Senthil K. Chinnakannan , Elizabeth Clutterbuck , Richard J. Cornall , Derrick W. Crook , Thushan De Silva , Wanwisa Dejnirattisai , Kate E. Dingle , Christina Dold , Alexis Espinosa , David W. Eyre , Helen Farmer , Maria Fernandez Mendoza , Dominique Georgiou , Sarah J. Hoosdally , Alastair Hunter , Katie Jefferey , Dominic F. Kelly , Paul Klenerman , Julian Knight , Clarice Knowles , Andrew J. Kwok , Ullrich Leuschner , Robert Levin , Chang Liu , César López-Camacho , Jose Martinez , Philippa C. Matthews , Hannah Mcgivern , Alexander J. Mentzer , Jonathan Milton , Juthathip Mongkolsapaya , Shona C. Moore , Marta S. Oliveira , Fiona Pereira , Elena Perez , Timothy Peto , Rutger J. Ploeg , Andrew Pollard , Tessa Prince , David J. Roberts , Justine K. Rudkin , Veronica Sanchez , Gavin R. Screaton , Malcolm G. Semple , Jose Slon-Campos , Donal T. Skelly , Elliot Nathan Smith , Alberto Sobrinodiaz , Julie Staves , David I. Stuart , Piyada Supasa , Tomas Surik , Hannah Thraves , Pat Tsang , Lance Turtle , A. Sarah Walker , Beibei Wang , Charlotte Washington , Nicholas Watkins , James Whitehouse Wellcome Open Research 5 DOI: 10.12688/wellcomeopenres.15927.1 Open Access Show Abstract ▼ Abstract: Background: The COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices. Methods: We tested plasma for COVID (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142). Results: ELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested ≥10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar. Conclusions: Currently available commercial LFIA devices do not perform sufficiently well for individual patient applications. However, ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.	Jun 2020
I05-ARPES	Reactive intercalation and oxidation at the buried graphene-germanium interface Philipp Braeuninger-Weimer , Oliver Burton , Robert S. Weatherup , Ruizhi Wang , Pavel Dudin , Barry Brennan , Andrew J. Pollard , Bernhard C. Bayer , Vlad P. Veigang-Radulescu , Jannik C. Meyer , Billy J. Murdoch , Peter J. Cumpson , Stephan Hofmann Apl Materials 7 DOI: 10.1063/1.5098351 Diamond Proposal Number(s): [17381] Open Access Show Abstract ▼ Abstract: We explore a number of different electrochemical, wet chemical, and gas phase approaches to study intercalation and oxidation at the buried graphene-Ge interface. While the previous literature focused on the passivation of the Ge surface by chemical vapor deposited graphene, we show that particularly via electrochemical intercalation in a 0.25 N solution of anhydrous sodium acetate in glacial acetic acid, this passivation can be overcome to grow GeO2 under graphene. Angle resolved photoemission spectroscopy, Raman spectroscopy, He ion microscopy, and time-of-flight secondary ion mass spectrometry show that the monolayer graphene remains undamaged and its intrinsic strain is released by the interface oxidation. Graphene acts as a protection layer for the as-grown Ge oxide, and we discuss how these insights can be utilized for new processing approaches.	Jul 2019

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