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Article ; Online: Development of high affinity broadly reactive aptamers for spike protein of multiple SARS-CoV-2 variants.

Le, Thao T / Benton, Donald J / Wrobel, Antoni G / Gamblin, Steven J

RSC advances

2023 Volume 13, Issue 22, Page(s) 15322–15326

Abstract: We have developed broadly reactive aptamers against multiple variants by alternating the target between spike proteins from different SARS-CoV-2 variants during the selection process. In this process we have developed aptamers which can recognise all ... ...

Abstract	We have developed broadly reactive aptamers against multiple variants by alternating the target between spike proteins from different SARS-CoV-2 variants during the selection process. In this process we have developed aptamers which can recognise all variants, from the original wild-type 'Wuhan' strain to Omicron, with high affinity (
Language	English
Publishing date	2023-05-19
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d3ra01382k
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structural transitions in influenza haemagglutinin at membrane fusion pH.

Benton, Donald J / Gamblin, Steven J / Rosenthal, Peter B / Skehel, John J

Nature

2020 Volume 583, Issue 7814, Page(s) 150–153

Abstract: Infection by enveloped viruses involves fusion of their lipid envelopes with cellular membranes to release the viral genome into cells. For HIV, Ebola, influenza and numerous other viruses, envelope glycoproteins bind the infecting virion to cell-surface ...

Abstract	Infection by enveloped viruses involves fusion of their lipid envelopes with cellular membranes to release the viral genome into cells. For HIV, Ebola, influenza and numerous other viruses, envelope glycoproteins bind the infecting virion to cell-surface receptors and mediate membrane fusion. In the case of influenza, the receptor-binding glycoprotein is the haemagglutinin (HA), and following receptor-mediated uptake of the bound virus by endocytosis
MeSH term(s)	Cryoelectron Microscopy ; Endosomes/metabolism ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry ; Hemagglutinin Glycoproteins, Influenza Virus/metabolism ; Hemagglutinin Glycoproteins, Influenza Virus/ultrastructure ; Hydrogen-Ion Concentration ; Influenza A Virus, H3N2 Subtype/chemistry ; Influenza A Virus, H3N2 Subtype/metabolism ; Influenza A Virus, H3N2 Subtype/ultrastructure ; Membrane Fusion ; Models, Molecular ; Protein Conformation ; Time Factors
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus
Language	English
Publishing date	2020-05-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2333-6
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Article ; Online: Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein.

Calvaresi, Valeria / Wrobel, Antoni G / Toporowska, Joanna / Hammerschmid, Dietmar / Doores, Katie J / Bradshaw, Richard T / Parsons, Ricardo B / Benton, Donald J / Roustan, Chloë / Reading, Eamonn / Malim, Michael H / Gamblin, Steve J / Politis, Argyris

Nature communications

2023 Volume 14, Issue 1, Page(s) 1421

Abstract: SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 receptor, and an open state that does so but displays more exposed antigenic ... ...

Abstract	SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 receptor, and an open state that does so but displays more exposed antigenic surface. Spikes of variants of concern (VOCs) acquired amino acid changes linked to increased virulence and immune evasion. Here, using HDX-MS, we identified changes in spike dynamics that we associate with the transition from closed to open conformations, to ACE2 binding, and to specific mutations in VOCs. We show that the RBD-associated subdomain plays a role in spike opening, whereas the NTD acts as a hotspot of conformational divergence of VOC spikes driving immune evasion. Alpha, beta and delta spikes assume predominantly open conformations and ACE2 binding increases the dynamics of their core helices, priming spikes for fusion. Conversely, substitutions in omicron spike lead to predominantly closed conformations, presumably enabling it to escape antibodies. At the same time, its core helices show characteristics of being pre-primed for fusion even in the absence of ACE2. These data inform on SARS-CoV-2 evolution and omicron variant emergence.
MeSH term(s)	Humans ; Spike Glycoprotein, Coronavirus/genetics ; Angiotensin-Converting Enzyme 2 ; COVID-19 ; SARS-CoV-2/genetics ; Mutation
Chemical Substances	spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2023-03-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36745-0
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Article ; Online: Genetic determinants of receptor-binding preference and zoonotic potential of H9N2 avian influenza viruses.

Peacock, Thomas P / Sealy, Joshua E / Harvey, William T / Benton, Donald J / Reeve, Richard / Iqbal, Munir

Journal of virology

2020 Volume 95, Issue 5

Abstract: Receptor recognition and binding is the first step of viral infection and a key determinant of host specificity. The inability of avian influenza viruses to effectively bind human-like sialylated receptors is a major impediment to their efficient ... ...

Abstract	Receptor recognition and binding is the first step of viral infection and a key determinant of host specificity. The inability of avian influenza viruses to effectively bind human-like sialylated receptors is a major impediment to their efficient transmission in humans and pandemic capacity. Influenza H9N2 viruses are endemic in poultry across Asia and parts of Africa where they occasionally infect humans and are therefore considered viruses with zoonotic potential. We previously described H9N2 viruses, including several isolated from human zoonotic cases, showing a preference for human-like receptors. Here we take a mutagenesis approach, making viruses with single or multiple substitutions in H9 haemagglutinin and test binding to avian and human receptor analogues using biolayer interferometry. We determine the genetic basis of preferences for alternative avian receptors and for human-like receptors, describing amino acid motifs at positions 190, 226 and 227 that play a major role in determining receptor specificity, and several other residues such as 159, 188, 193, 196, 198 and 225 that play a smaller role. Furthermore, we show changes at residues 135, 137, 147, 157, 158, 184, 188, and 192 can also modulate virus receptor avidity and that substitutions that increased or decreased the net positive charge around the haemagglutinin receptor-binding site show increases and decreases in avidity, respectively. The motifs we identify as increasing preference for the human-receptor will help guide future H9N2 surveillance efforts and facilitate our understanding of the emergence of influenza viruses with increased zoonotic potential.
Language	English
Publishing date	2020-12-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.01651-20
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Article ; Online: Author Correction: SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects.

Wrobel, Antoni G / Benton, Donald J / Xu, Pengqi / Roustan, Chloë / Martin, Stephen R / Rosenthal, Peter B / Skehel, John J / Gamblin, Steven J

Nature structural & molecular biology

2020 Volume 27, Issue 10, Page(s) 1001

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Keywords	covid19
Language	English
Publishing date	2020-08-14
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-020-0509-2
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Article ; Online: Multi-locus homozygosity promotes actuarial senescence in a wild mammal.

Hudson, Dave W / McKinley, Trevelyan J / Benton, Clare H / Delahay, Richard / McDonald, Robbie A / Hodgson, Dave J

The Journal of animal ecology

2023 Volume 92, Issue 9, Page(s) 1881–1892

Abstract: Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will ...

Abstract	Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will filter out negative impacts on younger individuals with greater reproductive value. Here we infer associations between multi-locus homozygosity (MLH), sex, disease and age-dependent mortality risks using Bayesian analysis of the life histories of wild European badgers Meles meles in a population naturally infected with Mycobacterium bovis (the causative agent of bovine tuberculosis [bTB]). We find important effects of MLH on all parameters of the Gompertz-Makeham mortality hazard function, but particularly in later life. Our findings confirm the predicted association between genomic homozygosity and actuarial senescence. Increased homozygosity is particularly associated with an earlier onset, and greater rates of actuarial senescence, regardless of sex. The association between homozygosity and actuarial senescence is further amplified among badgers putatively infected with bTB. These results recommend further investigation into the ecological and behavioural processes that result in genome-wide homozygosity, and focused work on whether homozygosity is harmful or beneficial during early life-stages.
MeSH term(s)	Animals ; Cattle ; Bayes Theorem ; Mycobacterium bovis ; Tuberculosis, Bovine/epidemiology ; Mustelidae ; Cattle Diseases
Language	English
Publishing date	2023-07-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3024-7
ISSN	1365-2656 ; 0021-8790
ISSN (online)	1365-2656
ISSN	0021-8790
DOI	10.1111/1365-2656.13979
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Article ; Online: Evolution of the SARS-CoV-2 spike protein in the human host

Antoni G. Wrobel / Donald J. Benton / Chloë Roustan / Annabel Borg / Saira Hussain / Stephen R. Martin / Peter B. Rosenthal / John J. Skehel / Steven J. Gamblin

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 7

Abstract: The SARS-CoV-2 spike has been evolving in the human population. The variants of concern alpha and beta evolved to optimise spike openness and so ability to bind its receptor ACE2, the affinity towards the receptor, and stability upon receptor binding. ...

Abstract	The SARS-CoV-2 spike has been evolving in the human population. The variants of concern alpha and beta evolved to optimise spike openness and so ability to bind its receptor ACE2, the affinity towards the receptor, and stability upon receptor binding.
Keywords	Science ; Q
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evolution of the SARS-CoV-2 spike protein in the human host.

Wrobel, Antoni G / Benton, Donald J / Roustan, Chloë / Borg, Annabel / Hussain, Saira / Martin, Stephen R / Rosenthal, Peter B / Skehel, John J / Gamblin, Steven J

Nature communications

2022 Volume 13, Issue 1, Page(s) 1178

Abstract: Recently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have examined the structure and receptor binding properties ... ...

Abstract	Recently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have examined the structure and receptor binding properties of spike proteins from the B.1.1.7 (Alpha) and B.1.351 (Beta) variants to better understand the evolution of the virus in humans. Spikes of both variants have the same mutation, N501Y, in the receptor-binding domains. This substitution confers tighter ACE2 binding, dependent on the common earlier substitution, D614G. Each variant spike has acquired other key changes in structure that likely impact virus pathogenesis. The spike from the Alpha variant is more stable against disruption upon binding ACE2 receptor than all other spikes studied. This feature is linked to the acquisition of a more basic substitution at the S1-S2 furin site (also observed for the variants of concern Delta, Kappa, and Omicron) which allows for near-complete cleavage. In the Beta variant spike, the presence of a new substitution, K417N (also observed in the Omicron variant), in combination with the D614G, stabilises a more open spike trimer, a conformation required for receptor binding. Our observations suggest ways these viruses have evolved to achieve greater transmissibility in humans.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/metabolism ; Angiotensin-Converting Enzyme 2/ultrastructure ; Binding Sites/genetics ; COVID-19/metabolism ; COVID-19/transmission ; COVID-19/virology ; Cryoelectron Microscopy ; Cytopathogenic Effect, Viral/genetics ; Evolution, Molecular ; Host-Pathogen Interactions ; Humans ; Kinetics ; Models, Molecular ; Mutation, Missense ; Protein Binding ; Protein Domains ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; SARS-CoV-2/physiology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-03-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28768-w
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Article ; Online: Treatment of Severely Shortened or Comminuted Clavicular Fractures in Older Adolescent Athletes.

Spence, David D / Wilson, Philip L / Pennock, Andrew T / Nepple, Jeffrey J / Pandya, Nirav K / Perkins, Crystal A / Li, Ying / Ellis, Henry B / Sabatini, Coleen S / Edmonds, Eric W / Willimon, S Clifton / Bae, Donald S / Busch, Michael T / Kocher, Mininder / Heyworth, Benton E

The American journal of sports medicine

2024 Volume 52, Issue 2, Page(s) 423–430

Abstract: Background: Recent evidence suggests that for completely displaced midshaft clavicular fractures, surgery offers no clear benefit over nonoperative treatment in a general adolescent population from 10 to 18 years of age. However, the comparative ... ...

Abstract	Background: Recent evidence suggests that for completely displaced midshaft clavicular fractures, surgery offers no clear benefit over nonoperative treatment in a general adolescent population from 10 to 18 years of age. However, the comparative outcomes of comminuted and/or severely shortened clavicular fractures specifically in older adolescent athletes have not been explored in a focused, methodologically rigorous fashion. Hypothesis: The study hypothesis was that outcomes would be superior in older adolescent athletes who underwent operative treatment compared with nonoperative treatment for comminuted and/or severely shortened clavicular fractures. Study design: Cohort study; Level of evidence, 2. Methods: A level 2, multicenter, prospective cohort study investigating the outcomes of midshaft fractures in adolescents between 2013 and 2017 was filtered to analyze the subcohorts of athletes 14 to 18 years of age with either fracture comminution or fracture shortening of ≥25 mm or both. Patient characteristics, injury mechanisms, fracture characteristics, and treatments were compared. Complications, rates, timing of return to sports (RTS), and patient-reported outcomes (PROs) were analyzed. Results: The 2 treatment groups, which included 136 older adolescent athletes (69 nonoperative, 67 operative), showed similar distributions of primary sport type, competition level, comminution, shortening, and 2-year PRO response rate (n = 99; 73%). The operative group demonstrated 3 mm-greater mean superior displacement, which was therefore statistically controlled for as a confounder in the comparative PRO analysis. No 2-year differences in nonunion, delayed union, symptomatic malunion, refracture, clinically significant complications, or rates of RTS were detected between treatment groups. The difference in timing of RTS (operative, 10.3 weeks; nonoperative, 13.5 weeks) was statistically significant. After controlling for the minor difference in superior displacement, regression analysis and matched comparison cohorts demonstrated no differences between the nonoperative and operative groups in mean or dichotomized PRO scores. Conclusion: In this prospective, multicenter cohort study investigating older adolescent athletes with comminuted and/or severely shortened clavicular fractures, contrary to the study hypothesis, there were no differences in complications, RTS, or PROs between nonoperatively and operatively treated patients at 2 years. Comparably excellent outcomes of severe clavicular fractures in adolescent athletes can be achieved with nonoperative treatment.
MeSH term(s)	Humans ; Adolescent ; Aged ; Prospective Studies ; Cohort Studies ; Fracture Healing/physiology ; Treatment Outcome ; Fractures, Bone/surgery ; Fracture Fixation, Internal/adverse effects ; Athletes ; Clavicle/diagnostic imaging ; Clavicle/surgery ; Clavicle/injuries
Language	English
Publishing date	2024-01-18
Publishing country	United States
Document type	Multicenter Study ; Journal Article
ZDB-ID	197482-8
ISSN	1552-3365 ; 0363-5465
ISSN (online)	1552-3365
ISSN	0363-5465
DOI	10.1177/03635465231219248
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Article ; Online: Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.

Benton, Donald J / Wrobel, Antoni G / Xu, Pengqi / Roustan, Chloë / Martin, Stephen R / Rosenthal, Peter B / Skehel, John J / Gamblin, Steven J

Nature

2020 Volume 588, Issue 7837, Page(s) 327–330

Abstract: Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by virus binding to the ACE2 cell-surface ... ...

Abstract	Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by virus binding to the ACE2 cell-surface receptors
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/metabolism ; Angiotensin-Converting Enzyme 2/ultrastructure ; Cryoelectron Microscopy ; Furin/metabolism ; Humans ; Membrane Fusion/physiology ; Models, Molecular ; Protein Binding ; Protein Folding ; Protein Subunits/chemistry ; Protein Subunits/metabolism ; Proteolysis ; Receptors, Coronavirus/chemistry ; Receptors, Coronavirus/metabolism ; Receptors, Coronavirus/ultrastructure ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Spike Glycoprotein, Coronavirus/ultrastructure
Chemical Substances	Protein Subunits ; Receptors, Coronavirus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Furin (EC 3.4.21.75)
Keywords	covid19
Language	English
Publishing date	2020-09-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2772-0
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