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Article ; Online: Single-molecule FRET for virology: 20 years of insight into protein structure and dynamics.

Groves, Danielle / Hepp, Christof / Kapanidis, Achillefs N / Robb, Nicole C

2023 Volume 56, Page(s) e3

Abstract: Although viral protein structure and replication mechanisms have been explored extensively with X-ray crystallography, cryo-electron microscopy, and population imaging studies, these methods are often not able to distinguish dynamic conformational ... ...

Abstract	Although viral protein structure and replication mechanisms have been explored extensively with X-ray crystallography, cryo-electron microscopy, and population imaging studies, these methods are often not able to distinguish dynamic conformational changes in real time. Single-molecule fluorescence resonance energy transfer (smFRET) offers unique insights into interactions and states that may be missed in ensemble studies, such as nucleic acid or protein structure, and conformational transitions during folding, receptor-ligand interactions, and fusion. We discuss the application of smFRET to the study of viral protein conformational dynamics, with a particular focus on viral glycoprotein dynamics, viral helicases, proteins involved in HIV reverse transcription, and the influenza RNA polymerase. smFRET experiments have played a crucial role in deciphering conformational changes in these processes, emphasising the importance of smFRET as a tool to help elucidate the life cycle of viral pathogens and identify key anti-viral targets.
MeSH term(s)	Fluorescence Resonance Energy Transfer/methods ; Cryoelectron Microscopy ; Protein Conformation ; Nucleic Acids ; Viral Proteins
Chemical Substances	Nucleic Acids ; Viral Proteins
Language	English
Publishing date	2023-05-18
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	209912-3
ISSN	1469-8994 ; 0033-5835
ISSN (online)	1469-8994
ISSN	0033-5835
DOI	10.1017/S0033583523000021
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Article ; Online: The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design.

Groves, Danielle C / Rowland-Jones, Sarah L / Angyal, Adrienn

Biochemical and biophysical research communications

2020 Volume 538, Page(s) 104–107

Abstract: The development of the SARS-CoV-2 pandemic has prompted an extensive worldwide sequencing effort to characterise the geographical spread and molecular evolution of the virus. A point mutation in the spike protein, D614G, emerged as the virus spread from ... ...

Abstract	The development of the SARS-CoV-2 pandemic has prompted an extensive worldwide sequencing effort to characterise the geographical spread and molecular evolution of the virus. A point mutation in the spike protein, D614G, emerged as the virus spread from Asia into Europe and the USA, and has rapidly become the dominant form worldwide. Here we review how the D614G variant was identified and discuss recent evidence about the effect of the mutation on the characteristics of the virus, clinical outcome of infection and host immune response.
MeSH term(s)	Amino Acid Substitution ; Aspartic Acid/genetics ; COVID-19/prevention & control ; COVID-19/virology ; COVID-19 Vaccines/genetics ; COVID-19 Vaccines/immunology ; Evolution, Molecular ; Glycine/genetics ; Humans ; Immunogenicity, Vaccine ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; Severity of Illness Index ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	COVID-19 Vaccines ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Aspartic Acid (30KYC7MIAI) ; Glycine (TE7660XO1C)
Keywords	covid19
Language	English
Publishing date	2020-11-05
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2020.10.109
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Article ; Online: High-throughput super-resolution analysis of influenza virus pleomorphism reveals insights into viral spatial organization.

McMahon, Andrew / Andrews, Rebecca / Groves, Danielle / Ghani, Sohail V / Cordes, Thorben / Kapanidis, Achillefs N / Robb, Nicole C

PLoS pathogens

2023 Volume 19, Issue 6, Page(s) e1011484

Abstract: Many viruses form highly pleomorphic particles. In influenza, virion structure is of interest not only in the context of virus assembly, but also because pleomorphic variations may correlate with infectivity and pathogenicity. We have used fluorescence ... ...

Abstract	Many viruses form highly pleomorphic particles. In influenza, virion structure is of interest not only in the context of virus assembly, but also because pleomorphic variations may correlate with infectivity and pathogenicity. We have used fluorescence super-resolution microscopy combined with a rapid automated analysis pipeline, a method well-suited to the study of large numbers of pleomorphic structures, to image many thousands of individual influenza virions; gaining information on their size, morphology and the distribution of membrane-embedded and internal proteins. We observed broad phenotypic variability in filament size, and Fourier transform analysis of super-resolution images demonstrated no generalized common spatial frequency patterning of HA or NA on the virion surface, suggesting a model of virus particle assembly where the release of progeny filaments from cells occurs in a stochastic way. We also showed that viral RNP complexes are located preferentially within Archetti bodies when these were observed at filament ends, suggesting that these structures may play a role in virus transmission. Our approach therefore offers exciting new insights into influenza virus morphology and represents a powerful technique that is easily extendable to the study of pleomorphism in other pathogenic viruses.
MeSH term(s)	Humans ; Influenza, Human ; Orthomyxoviridae ; Virus Assembly ; Virion
Language	English
Publishing date	2023-06-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1011484
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Article ; Online: The D614G mutations in the SARS-CoV-2 spike protein

Groves, Danielle C. / Rowland-Jones, Sarah L. / Angyal, Adrienn

Biochemical and Biophysical Research Communications ; ISSN 0006-291X

Implications for viral infectivity, disease severity and vaccine design

2020

Keywords	Biophysics ; Cell Biology ; Biochemistry ; Molecular Biology ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
DOI	10.1016/j.bbrc.2020.10.109
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design

Groves, Danielle C / Rowland-Jones, Sarah L / Angyal, Adrienn

Biochem. biophys. res. commun

Abstract	The development of the SARS-CoV-2 pandemic has prompted an extensive worldwide sequencing effort to characterise the geographical spread and molecular evolution of the virus. A point mutation in the spike protein, D614G, emerged as the virus spread from Asia into Europe and the USA, and has rapidly become the dominant form worldwide. Here we review how the D614G variant was identified and discuss recent evidence about the effect of the mutation on the characteristics of the virus, clinical outcome of infection and host immune response.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #908990
Database	COVID19

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Article ; Online: Assessing Suicide Prevention Apps' Responsiveness to Help-Seeking Needs of Individuals Connected with Mental Health Services.

Kemp, Jessica / Shin, Hwayeon Danielle / Pape, Charlotte / Bennett-Poynter, Laura / Groves, Samantha / Lascelles, Karen / Strudwick, Gillian

Studies in health technology and informatics

2024 Volume 312, Page(s) 101–106

Abstract: This paper maps suicide help-seeking needs identified in the literature, on to the features and functionalities of suicide prevention mobile apps using the adapted ecological model, thereby revealing existing gaps between help-seeking needs and available ...

Abstract	This paper maps suicide help-seeking needs identified in the literature, on to the features and functionalities of suicide prevention mobile apps using the adapted ecological model, thereby revealing existing gaps between help-seeking needs and available apps. This paper builds upon previous work by our team, which includes 1) a rapid scoping review aimed at identifying barriers and facilitators of help-seeking related to suicide within psychiatric populations, and 2) a review of suicide prevention apps, including a content analysis of app features and functionalities.
MeSH term(s)	Humans ; Suicide Prevention ; Telemedicine ; Suicide/psychology ; Mobile Applications ; Mental Health Services
Language	English
Publishing date	2024-02-02
Publishing country	Netherlands
Document type	Review ; Journal Article
ISSN	1879-8365
ISSN (online)	1879-8365
DOI	10.3233/SHTI231321
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Article ; Online: Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data.

Parker, Matthew D / Lindsey, Benjamin B / Leary, Shay / Gaudieri, Silvana / Chopra, Abha / Wyles, Matthew / Angyal, Adrienn / Green, Luke R / Parsons, Paul / Tucker, Rachel M / Brown, Rebecca / Groves, Danielle / Johnson, Katie / Carrilero, Laura / Heffer, Joe / Partridge, David G / Evans, Cariad / Raza, Mohammad / Keeley, Alexander J /

Smith, Nikki / Filipe, Ana Da Silva / Shepherd, James G / Davis, Chris / Bennett, Sahan / Sreenu, Vattipally B / Kohl, Alain / Aranday-Cortes, Elihu / Tong, Lily / Nichols, Jenna / Thomson, Emma C / Wang, Dennis / Mallal, Simon / de Silva, Thushan I

Genome research

2021 Volume 31, Issue 4, Page(s) 645–658

Abstract: We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed " ... ...

Abstract	We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L, which is located in the 5' UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5' end of all sgRNA. We applied periscope to 1155 SARS-CoV-2 genomes from Sheffield, United Kingdom, and validated our findings using orthogonal data sets and in vitro cell systems. By using a simple local alignment to detect reads that contain the leader sequence, we were able to identify and quantify reads arising from canonical and noncanonical sgRNA. We were able to detect all canonical sgRNAs at the expected abundances, with the exception of ORF10. A number of recurrent noncanonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6
MeSH term(s)	Animals ; Base Sequence ; Chlorocebus aethiops ; Genome, Viral ; Humans ; Limit of Detection ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Sequence Analysis, RNA/methods ; Vero Cells
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-03-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.268110.120
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Zs.A 3729: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 8: Show issues

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Article ; Online: Streptococcus pyogenes Colonization in Children Aged 24-59 Months in the Gambia: Impact of Live Attenuated Influenza Vaccine and Associated Serological Responses.

The Journal of infectious diseases

2023 Volume 228, Issue 7, Page(s) 957–965

Abstract: Background: Immunity to Streptococcus pyogenes in high burden settings is poorly understood. We explored S. pyogenes nasopharyngeal colonization after intranasal live attenuated influenza vaccine (LAIV) among Gambian children aged 24-59 months, and ... ...

Abstract	Background: Immunity to Streptococcus pyogenes in high burden settings is poorly understood. We explored S. pyogenes nasopharyngeal colonization after intranasal live attenuated influenza vaccine (LAIV) among Gambian children aged 24-59 months, and resulting serological response to 7 antigens. Methods: A post hoc analysis was performed in 320 children randomized to receive LAIV at baseline (LAIV group) or not (control). S. pyogenes colonization was determined by quantitative polymerase chain reaction (qPCR) on nasopharyngeal swabs from baseline (day 0), day 7, and day 21. Anti-streptococcal IgG was quantified, including a subset with paired serum before/after S. pyogenes acquisition. Results: The point prevalence of S. pyogenes colonization was 7%-13%. In children negative at day 0, S. pyogenes was detected at day 7 or 21 in 18% of LAIV group and 11% of control group participants (P = .12). The odds ratio (OR) for colonization over time was significantly increased in the LAIV group (day 21 vs day 0 OR, 3.18; P = .003) but not in the control group (OR, 0.86; P = .79). The highest IgG increases following asymptomatic colonization were seen for M1 and SpyCEP proteins. Conclusions: Asymptomatic S. pyogenes colonization appears modestly increased by LAIV, and may be immunologically significant. LAIV could be used to study influenza-S. pyogenes interactions. Clinical Trials Registration. NCT02972957.
MeSH term(s)	Humans ; Child ; Influenza Vaccines ; Gambia/epidemiology ; Streptococcus pyogenes ; Influenza, Human/epidemiology ; Influenza, Human/prevention & control ; Vaccines, Attenuated ; Immunoglobulin G
Chemical Substances	Influenza Vaccines ; Vaccines, Attenuated ; Immunoglobulin G
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Randomized Controlled Trial ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiad153
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Article ; Online: Genomic Analysis and Surveillance of Respiratory Syncytial Virus (RSV) Using Wastewater-Based Epidemiology (WBE).

The Journal of infectious diseases

2024

Abstract: Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting in annual epidemics of respiratory disease. Currently, limited clinical surveillance and the lack of predictable seasonal dynamics ... ...

Abstract	Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting in annual epidemics of respiratory disease. Currently, limited clinical surveillance and the lack of predictable seasonal dynamics limits the public health response. Wastewater-based epidemiology (WBE) has recently been used globally as a key metric in determining prevalence of SARS-CoV-2 in the community but its application to other respiratory viruses is limited. In this study, we present an integrated genomic WBE approach, applying RT-qPCR and partial G-gene sequencing to track RSV levels and variants in the community. We report increasing detection of RSV in wastewater concomitant with increasing numbers of positive clinical cases. Analysis of wastewater-derived RSV sequences permitted identification of distinct circulating lineages within and between seasons. Altogether, our genomic WBE platform has the potential to complement ongoing global surveillance and aid the management of RSV by informing the timely deployment of pharmaceutical and non-pharmaceutical interventions.
Language	English
Publishing date	2024-04-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiae205
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Book ; Online: 2020-04-11/12 DAILY UNM GLOBAL HEALTH COVID-19 BRIEFING

Lambert, Christophe G / Stoicu, Shawn / Nestsiarovich, Anastasiya / Kumar, Praveen / Lauve, Nicolas / Anyona, Samuel / Raballah, Evans / Olewe, Perez / Groves, Hannah / Rivera, Danielle / Montanez, Estefania / King, Rachel D / Bologa, Cristian / Yang, Jeremy / Oprea, Tudor I / Myers, Orrin / Rowland, Andrew S / Perkins, Douglas J

HSC Covid 19 Briefings

2020

Abstract: ... newborns with mom. C-section protocol. Italian obstetrics. Pediatric cardiac catherization. Chinese ...

Abstract	Executive Summary: No NM church gatherings. NM a testing champ. Consolidation of elderly care. NM case update. 50-state disaster. Ventilator haggling. Economy reopening planning. PPE decontamination. Hospital ward contamination. Prolonged return to normal. FEMA projections. WHO tracking app. China SEIR model. Hubei epi. Mortality best measure. Covid-19 wave 2. Public should wear masks. Civil liberties. Safe grocery shopping. School closure impact. CDC caretaker guidelines. Psychiatric mobilization. Keep newborns with mom. C-section protocol. Italian obstetrics. Pediatric cardiac catherization. Chinese anesthesiology consensus. Cancer guidelines. Neuro-oncologic Tx. Radiology algorithm. Lung ultrasonography. ARF care. VTE common and predictable. Liver transplantation. Auto-immune treatments. Extracorporeal kidney involvement. Nutrition support. GI endoscopy. No stay-at-home for stroke. Intensive care collaboration. Supine swab collection. Lab tests for severity. Testing assay performance. False negative RT-PCR tests. IgM and IgG serum tests. FDA convalescent plasma. Blood purification device approval. Erythropoietin treatment. Tissue plasminogen activator. ECMO. Lopinavir/ritonavir study results. Immunotherapy review. Vaccine development. Hydroxychloroquine review. Candidates from in silico/virtual screening. Traditional Indian therapies. US trials update. Pathways and risk factors for death. ACE2 polymorphism. Severity in children. Lung tissue replication. Phylogenetic tracing. Text mining dataset. Risk by blood type.
Keywords	COVID-19 ; Coronavirus ; Coronavirus disease ; Coronavirus pandemic ; SARS-CoV-2 ; Epidemic ; Public Health ; covid19
Publishing date	2020-04-12T07:00:00Z
Publisher	UNM Digital Repository
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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