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Wademan DT, Saule Z, Marthinus A, Viljoen L, Nortier E, Hughes J, Courtney I, Palmer M, Garcia-Prats AJ, Hesseling AC, Hoddinott G. Acceptability of clofazimine capsules in children and adolescents with rifampicin-resistant TB. Int J Tuberc Lung Dis 2024; 28:256-258. [PMID: 38659140 DOI: 10.5588/ijtld.23.0517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Affiliation(s)
- D T Wademan
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Z Saule
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - A Marthinus
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - L Viljoen
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - E Nortier
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - J Hughes
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - I Courtney
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - M Palmer
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - A J Garcia-Prats
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa;, University of Wisconsin-Madison, School of Medicine and Public Health, Department of Pediatrics, Madison, WI, USA
| | - A C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - G Hoddinott
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa;, University of Wisconsin-Madison, School of Medicine and Public Health, Department of Pediatrics, Madison, WI, USA
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2
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Sampson FC, Hughes J, Long J, Buykx P, Goodacre SW, Snooks H, Edwards A, Evans B, Jones J, Moore C, Johnston S. Is a randomised controlled trial of take home naloxone distributed in emergency settings likely to be feasible and acceptable? Findings from a UK qualitative study exploring perspectives of people who use opioids and emergency services staff. BMC Emerg Med 2024; 24:75. [PMID: 38679713 PMCID: PMC11057101 DOI: 10.1186/s12873-024-00987-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
OBJECTIVE Distribution of take-home naloxone (THN) by emergency services may increase access to THN and reduce deaths and morbidity from opioid overdose. As part of a feasibility study for a randomised controlled trial (RCT) of distribution of THN kits and education within ambulance services and Emergency Departments (EDs), we used qualitative methods to explore key stakeholders' perceptions of feasibility and acceptability of delivering the trial. METHODS We undertook semi-structured interviews and focus groups with 26 people who use opioids and with 20 paramedics and ED staff from two intervention sites between 2019 and 2021. Interviews and focus groups were recorded, transcribed verbatim and analysed using Framework Analysis. RESULTS People using opioids reported high awareness of overdose management, including personal experience of THN use. Staff perceived emergency service provision of THN as a low-cost, low-risk intervention with potential to reduce mortality, morbidity and health service use. Staff understood the trial aims and considered it compatible with their work. All participants supported widening access to THN but reported limited trial recruitment opportunities partly due to difficulties in consenting patients during overdose. Procedural problems, restrictive recruitment protocols, limited staff buy-in and patients already owning THN limited trial recruitment. Determining trial effectiveness was challenging due to high levels of alternative community provision of THN. CONCLUSIONS Distribution of THN in emergency settings was considered feasible and acceptable for stakeholders but an RCT to establish the effectiveness of THN delivery is unlikely to generate further useful evidence due to difficulties in recruiting patients and assessing benefits.
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Affiliation(s)
- F C Sampson
- Division of Population Health, University of Sheffield, Sheffield, UK.
| | - J Hughes
- Division of Population Health, University of Sheffield, Sheffield, UK
| | - J Long
- Division of Population Health, University of Sheffield, Sheffield, UK
| | - P Buykx
- School of Humanities, Creative Industries and Social Sciences, University of Newcastle, Newcastle, Australia
| | - S W Goodacre
- Division of Population Health, University of Sheffield, Sheffield, UK
| | - H Snooks
- Department of Medicine, Swansea University, Swansea, UK
| | - A Edwards
- Division of Population Medicine, Cardiff University, Cardiff, UK
| | - Bridie Evans
- Department of Medicine, Swansea University, Swansea, UK
| | - Jenna Jones
- Department of Medicine, Swansea University, Swansea, UK
| | - Chris Moore
- Welsh Ambulance Service NHS Trust, Cardiff, UK
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3
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Barton E, Verduri A, Carter B, Hughes J, Hewitt J, Maskell NA. The association between frailty and survival in patients with pleural disease: a retrospective cohort study. BMC Pulm Med 2024; 24:180. [PMID: 38627673 PMCID: PMC11020337 DOI: 10.1186/s12890-024-02981-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND There are currently no data on the relationship between frailty and mortality in pleural disease. Understanding the relationship between frailty and outcomes is increasingly important for clinicians to guide decisions regarding investigation and management. This study aims to explore the relationship between all-cause mortality and frailty status in patients with pleural disease. METHODS In this retrospective analysis of a prospectively collected observational cohort study, outpatients presenting to the pleural service at a tertiary centre in Bristol, UK with a radiologically confirmed, undiagnosed pleural effusion underwent comprehensive assessment and were assigned a final diagnosis at 12 months. The modified frailty index (mFI) was calculated and participants classified as frail (mFI ≥ 0.4) or not frail (mFI ≤ 0.2). RESULTS 676 participants were included from 3rd March 2008 to 29th December 2020. The median time to mortality was 490 days (IQR 161-1595). A positive association was found between 12-month mortality and frailty (aHR = 1.72, 95% CI 1.02-2.76, p = 0.025) and age ≥ 80 (aHR = 1.80, 95% CI 1.24-2.62, p = 0.002). Subgroup analyses found a stronger association between 12-month mortality and frailty in benign disease (aHR = 4.36, 95% CI 2.17-8.77, p < 0.0001) than in all pleural disease. Malignancy irrespective of frailty status was associated with an increase in all-cause mortality (aHR = 10.40, 95% CI 6.01-18.01, p < 0.0001). CONCLUSION This is the first study evaluating the relationship between frailty and outcomes in pleural disease. Our data demonstrates a strong association between frailty and 12-month mortality in this cohort. A malignant diagnosis is an independent predictor of 12-month mortality, irrespective of frailty status. Frailty was also strongly associated with 12-month mortality in patients with a benign underlying cause for their pleural disease. This has clinical relevance for pleural physicians; evaluating patients' frailty status and its impact on mortality can guide clinicians in assessing suitability for invasive investigation and management. TRIAL REGISTRATION This study is registered with the Health Research Authority (REC reference 08/H0102/11) and the NIHR Portfolio (Study ID 8960).
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Affiliation(s)
- Eleanor Barton
- Academic Respiratory Unit, School of Clinical Sciences, University of Bristol, Bristol, UK.
| | - A Verduri
- Respiratory Unit, Department of Surgical and Medical Sciences, University of Modena and Reggio Emilia, Policlinico Modena, Italy
| | - B Carter
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK
- Department of Population Medicine, Cardiff University, Cardiff, UK
| | - J Hughes
- Academic Respiratory Unit, School of Clinical Sciences, University of Bristol, Bristol, UK
| | - J Hewitt
- Academic Respiratory Unit, School of Clinical Sciences, University of Bristol, Bristol, UK
| | - N A Maskell
- Academic Respiratory Unit, School of Clinical Sciences, University of Bristol, Bristol, UK
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4
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Gonzalo-Nadal V, Kohl A, Rocchi M, Brennan B, Hughes J, Nichols J, Da Silva Filipe A, Dunlop JI, Fares M, Clark JJ, Tandavanitj R, Patel AH, Cloquell-Miro A, Bongers J, Deacon J, Kaczmarska A, Stalin C, Liatis T, Irving J, Gutierrez-Quintana R. Suspected tick-borne flavivirus meningoencephalomyelitis in dogs from the UK: six cases (2021). J Small Anim Pract 2024; 65:132-143. [PMID: 37956993 DOI: 10.1111/jsap.13682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/30/2023] [Accepted: 10/01/2023] [Indexed: 11/21/2023]
Abstract
OBJECTIVES Tick-borne encephalitis virus and louping ill virus are neurotropic flaviviruses transmitted by ticks. Epidemiologically, tick-borne encephalitis is endemic in Europe whereas louping ill's predominant geographical distribution is the UK. Rarely, these flaviviruses affect dogs causing neurological signs. This case series aimed to describe the clinical, clinicopathological, and imaging findings, as well as the outcomes in six dogs with meningoencephalitis and/or meningomyelitis caused by a flavivirus in the UK in 2021. MATERIALS AND METHODS Observational retrospective case-series study. Clinical data were retrieved from medical records of dogs with positive serological or immunohistochemical results from three different institutions from spring to winter 2021. RESULTS Six dogs were included in the study. All dogs presented an initial phase of pyrexia and/or lethargy followed by progressive signs of spinal cord and/or intracranial disease. Magnetic resonance imaging showed bilateral and symmetrical lesions affecting the grey matter of the thalamus, pons, medulla oblongata, and thoracic or lumbar intumescences with none or mild parenchymal and meningeal contrast enhancement. Serology for tick-borne encephalitis virus was positive in five dogs with the presence of seroconversion in two dogs. The viral distinction between flaviviruses was not achieved. One dog with negative serology presented positive immunohistochemistry at post-mortem examination. Three dogs survived but presented neurological sequelae. Three dogs were euthanased due to the rapid progression of the clinical signs or static neurological signs. CLINICAL SIGNIFICANCE These cases raise awareness of the presence of tick-borne encephalitis as an emergent disease or the increased prevalence of louping ill virus affecting dogs in the UK.
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Affiliation(s)
- V Gonzalo-Nadal
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - A Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - M Rocchi
- Moredun Research Institute, Midlothian, UK
| | - B Brennan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - J Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - J Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - J I Dunlop
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - M Fares
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - J J Clark
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - R Tandavanitj
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - A H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - A Cloquell-Miro
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - J Bongers
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Moorview Vets, Cramlington, UK
| | | | - A Kaczmarska
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - C Stalin
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Moorview Vets, Cramlington, UK
| | - T Liatis
- Queen Mother Hospital for Animals, Royal Veterinary College, University of London, London, UK
| | - J Irving
- Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, Hertfordshire, UK
- Harper & Keele Veterinary School, Newport, Shropshire, UK
| | - R Gutierrez-Quintana
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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5
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Zhang K, Carrod AJ, Del Giorgio E, Hughes J, Rurack K, Bennet F, Hodoroaba VD, Harrad S, Pikramenou Z. Luminescence Lifetime-Based Sensing Platform Based on Cyclometalated Iridium(III) Complexes for the Detection of Perfluorooctanoic Acid in Aqueous Samples. Anal Chem 2024; 96:1565-1575. [PMID: 38226978 PMCID: PMC10831797 DOI: 10.1021/acs.analchem.3c04289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/17/2024]
Abstract
Luminescence lifetimes are an attractive analytical method for detection due to its high sensitivity and stability. Iridium probes exhibit luminescence with long excited-state lifetimes, which are sensitive to the local environment. Perfluorooctanoic acid (PFOA) is listed as a chemical of high concern regarding its toxicity and is classified as a "forever chemical". In addition to strict limits on the presence of PFOA in drinking water, environmental contamination from industrial effluent or chemical spills requires rapid, simple, accurate, and cost-effective analysis in order to aid containment. Herein, we report the fabrication and function of a novel and facile luminescence sensor for PFOA based on iridium modified on gold surfaces. These surfaces were modified with lipophilic iridium complexes bearing alkyl chains, namely, IrC6 and IrC12, and Zonyl-FSA surfactant. Upon addition of PFOA, the modified surfaces IrC6-FSA@Au and IrC12-FSA @Au show the largest change in the red luminescence signal with changes in the luminescence lifetime that allow monitoring of PFOA concentrations in aqueous solutions. The platform was tested for the measurement of PFOA in aqueous samples spiked with known concentrations of PFOA and demonstrated the capacity to determine PFOA at concentrations >100 μg/L (240 nM).
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Affiliation(s)
- Kun Zhang
- School
of Chemistry, University of Birmingham, Birmingham B15 2TT, U.K.
- School
of Geography, Earth & Environmental Sciences, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Andrew J. Carrod
- School
of Chemistry, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Elena Del Giorgio
- School
of Chemistry, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Joseph Hughes
- School
of Chemistry, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Knut Rurack
- Chemical
and Optical Sensing Division, Federal Institute
for Materials Research and Testing (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Francesca Bennet
- Surface
Analysis and Interfacial Chemistry Division, Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Vasile-Dan Hodoroaba
- Surface
Analysis and Interfacial Chemistry Division, Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Stuart Harrad
- School
of Geography, Earth & Environmental Sciences, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Zoe Pikramenou
- School
of Chemistry, University of Birmingham, Birmingham B15 2TT, U.K.
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Waltzek TB, Subramaniam K, Doszpoly A, Hughes J, Vučak M, Davison AJ. Genome sequence of white sturgeon herpesvirus 1 isolated from farmed white sturgeon ( Acipenser transmontanus). Microbiol Resour Announc 2023; 12:e0057123. [PMID: 37916837 PMCID: PMC10720441 DOI: 10.1128/mra.00571-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
The genome sequence of white sturgeon herpesvirus 1, which was isolated from farmed white sturgeon (Acipenser transmontanus), was determined. Comparative analyses suggest the classification of this virus as a new species in a new genus in the family Alloherpesviridae.
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Affiliation(s)
- Thomas B. Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Andor Doszpoly
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Matej Vučak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Andrew J. Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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7
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Vlachava VM, Seirafian S, Fielding CA, Kollnberger S, Aicheler RJ, Hughes J, Baker A, Weekes MP, Forbes S, Wilkinson GWG, Wang ECY, Stanton RJ. HCMV-secreted glycoprotein gpUL4 inhibits TRAIL-mediated apoptosis and NK cell activation. Proc Natl Acad Sci U S A 2023; 120:e2309077120. [PMID: 38011551 PMCID: PMC10710050 DOI: 10.1073/pnas.2309077120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/07/2023] [Indexed: 11/29/2023] Open
Abstract
Human cytomegalovirus (HCMV) is a paradigm of pathogen immune evasion and sustains lifelong persistent infection in the face of exceptionally powerful host immune responses through the concerted action of multiple immune-evasins. These reduce NK cell activation by inhibiting ligands for activating receptors, expressing ligands for inhibitory receptors, or inhibiting synapse formation. However, these functions only inhibit direct interactions with the infected cell. To determine whether the virus also expresses soluble factors that could modulate NK function at a distance, we systematically screened all 170 HCMV canonical protein-coding genes. This revealed that UL4 encodes a secreted and heavily glycosylated protein (gpUL4) that is expressed with late-phase kinetics and is capable of inhibiting NK cell degranulation. Analyses of gpUL4 binding partners by mass spectrometry identified an interaction with TRAIL. gpUL4 bound TRAIL with picomolar affinity and prevented TRAIL from binding its receptor, thus acting as a TRAIL decoy receptor. TRAIL is found in both soluble and membrane-bound forms, with expression of the membrane-bound form strongly up-regulated on NK cells in response to interferon. gpUL4 inhibited apoptosis induced by soluble TRAIL, while also binding to the NK cell surface in a TRAIL-dependent manner, where it blocked NK cell degranulation and cytokine secretion. gpUL4 therefore acts as an immune-evasin by inhibiting both soluble and membrane-bound TRAIL and is a viral-encoded TRAIL decoy receptor. Interestingly, gpUL4 could also suppress NK responses to heterologous viruses, suggesting that it may act as a systemic virally encoded immunosuppressive agent.
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Affiliation(s)
- Virginia-Maria Vlachava
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Sepehr Seirafian
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Ceri A Fielding
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Simon Kollnberger
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Rebecca J Aicheler
- Department of Biomedical Sciences, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff CF5 2YB, United Kingdom
| | - Joseph Hughes
- Centre for Virus Research, School of Infection & Immunity, Glasgow University, Glasgow G61 1QH, United Kingdom
| | - Alexander Baker
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Michael P Weekes
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Simone Forbes
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Gavin W G Wilkinson
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Eddie C Y Wang
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Richard J Stanton
- Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
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8
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Lytras S, Wickenhagen A, Sugrue E, Stewart DG, Swingler S, Sims A, Jackson Ireland H, Davies EL, Ludlam EM, Li Z, Hughes J, Wilson SJ. Resurrection of 2'-5'-oligoadenylate synthetase 1 (OAS1) from the ancestor of modern horseshoe bats blocks SARS-CoV-2 replication. PLoS Biol 2023; 21:e3002398. [PMID: 38015855 PMCID: PMC10683996 DOI: 10.1371/journal.pbio.3002398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023] Open
Abstract
The prenylated form of the human 2'-5'-oligoadenylate synthetase 1 (OAS1) protein has been shown to potently inhibit the replication of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. However, the OAS1 orthologue in the horseshoe bats (superfamily Rhinolophoidea), the reservoir host of SARS-related coronaviruses (SARSr-CoVs), has lost the prenylation signal required for this antiviral activity. Herein, we used an ancestral state reconstruction approach to predict and reconstitute in vitro, the most likely OAS1 protein sequence expressed by the Rhinolophoidea common ancestor prior to its prenylation loss (RhinoCA OAS1). We exogenously expressed the ancient bat protein in vitro to show that, unlike its non-prenylated horseshoe bat descendants, RhinoCA OAS1 successfully blocks SARS-CoV-2 replication. Using protein structure predictions in combination with evolutionary hypothesis testing methods, we highlight sites under unique diversifying selection specific to OAS1's evolution in the Rhinolophoidea. These sites are located near the RNA-binding region and the C-terminal end of the protein where the prenylation signal would have been. Our results confirm that OAS1 prenylation loss at the base of the Rhinolophoidea clade ablated the ability of OAS1 to restrict SARSr-CoV replication and that subsequent evolution of the gene in these bats likely favoured an alternative function. These findings can advance our understanding of the tightly linked association between SARSr-CoVs and horseshoe bats.
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Affiliation(s)
- Spyros Lytras
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Elena Sugrue
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Douglas G. Stewart
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Simon Swingler
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Anna Sims
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Hollie Jackson Ireland
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Emma L. Davies
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Eliza M. Ludlam
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Zhuonan Li
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Sam J. Wilson
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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9
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Busch CA, Wiesenthal NJ, Mohammed TF, Anderson S, Barstow M, Custalow C, Gajewski J, Garcia K, Gilabert CK, Hughes J, Jenkins A, Johnson M, Kasper C, Perez I, Robnett B, Tillett K, Tsefrekas L, Goodwin EC, Cooper KM. The Disproportionate Impact of Fear of Negative Evaluation on First-Generation College Students, LGBTQ+ Students, and Students with Disabilities in College Science Courses. CBE Life Sci Educ 2023; 22:ar31. [PMID: 37347813 PMCID: PMC10424224 DOI: 10.1187/cbe.22-10-0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/05/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
Fear of negative evaluation (FNE), defined as a sense of dread associated with being negatively judged in a social situation, has been identified as the primary factor underlying undergraduate anxiety in active-learning science courses. However, no quantitative studies have examined the extent to which science undergraduates experience FNE and how they are impacted by FNE in college science courses. To address this gap, we surveyed 566 undergraduates from one university in the U.S. Southwest who were enrolled in life sciences courses where they had opportunities to speak in front of the whole class. Participants were asked a suite of questions regarding their experiences with FNE in large-enrollment college science courses. We found that first-generation college students, LGBTQ+ students, and students with disabilities reported disproportionately high levels of FNE compared with their counterparts. Additionally, students reported that FNE can cause them to overthink their responses and participate less in class. Participants rated being cold called and presenting alone as forms of whole-class participation that elicit the highest levels of FNE. This research highlights the impact of FNE on undergraduates and provides student-generated recommendations to reduce FNE in active-learning science courses.
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Affiliation(s)
- Carly A. Busch
- Research for Inclusive STEM Education Center, Arizona State University, Tempe, AZ 85287
| | | | - Tasneem F. Mohammed
- Research for Inclusive STEM Education Center, Arizona State University, Tempe, AZ 85287
| | - Shauna Anderson
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Margaret Barstow
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Cydney Custalow
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Jas Gajewski
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Kristin Garcia
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Cynthia K. Gilabert
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Joseph Hughes
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Aliyah Jenkins
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Miajah Johnson
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Cait Kasper
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Israel Perez
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Brieana Robnett
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Kaytlin Tillett
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Lauren Tsefrekas
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Emma C. Goodwin
- Research for Inclusive STEM Education Center, Arizona State University, Tempe, AZ 85287
| | - Katelyn M. Cooper
- Research for Inclusive STEM Education Center, Arizona State University, Tempe, AZ 85287
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10
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Ribaud M, Gabriel E, Hughes J, Soubeyrand S. Identifying potential significant factors impacting zero-inflated proportion data. Stat Med 2023; 42:3467-3486. [PMID: 37290435 DOI: 10.1002/sim.9814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 04/03/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
Classical supervised methods like linear regression and decision trees are not completely adapted for identifying impacting factors on a response variable corresponding to zero-inflated proportion data (ZIPD) that are dependent, continuous and bounded. In this article we propose a within-block permutation-based methodology to identify factors (discrete or continuous) that are significantly correlated with ZIPD, we propose a performance indicator quantifying the percentage of correlation explained by the subset of significant factors, and we show how to predict the ranks of the response variables conditionally on the observation of these factors. The methodology is illustrated on simulated data and on two real data sets dealing with epidemiology. In the first data set, ZIPD correspond to probabilities of transmission of Influenza between horses. In the second data set, ZIPD correspond to probabilities that geographic entities (eg, states and countries) have the same COVID-19 mortality dynamics.
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Affiliation(s)
| | | | - Joseph Hughes
- Centre for Virus Research, MRC-University of Glasgow, Glasgow, UK
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11
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Pascall DJ, Vink E, Blacow R, Bulteel N, Campbell A, Campbell R, Clifford S, Davis C, da Silva Filipe A, El Sakka N, Fjodorova L, Forrest R, Goldstein E, Gunson R, Haughney J, Holden MTG, Honour P, Hughes J, James E, Lewis T, MacLean O, McHugh M, Mollett G, Nyberg T, Onishi Y, Parcell B, Ray S, Robertson DL, Seaman SR, Shabaan S, Shepherd JG, Smollett K, Templeton K, Wastnedge E, Wilkie C, Williams T, Thomson EC. Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. J Infect 2023; 87:128-135. [PMID: 37270070 PMCID: PMC10234362 DOI: 10.1016/j.jinf.2023.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/27/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023]
Abstract
OBJECTIVES To determine how the intrinsic severity of successively dominant SARS-CoV-2 variants changed over the course of the pandemic. METHODS A retrospective cohort analysis in the NHS Greater Glasgow and Clyde (NHS GGC) Health Board. All sequenced non-nosocomial adult COVID-19 cases in NHS GGC with relevant SARS-CoV-2 lineages (B.1.177/Alpha, Alpha/Delta, AY.4.2 Delta/non-AY.4.2 Delta, non-AY.4.2 Delta/Omicron, and BA.1 Omicron/BA.2 Omicron) during analysis periods were included. Outcome measures were hospital admission, ICU admission, or death within 28 days of positive COVID-19 test. We report the cumulative odds ratio; the ratio of the odds that an individual experiences a severity event of a given level vs all lower severity levels for the resident and the replacement variant after adjustment. RESULTS After adjustment for covariates, the cumulative odds ratio was 1.51 (95% CI: 1.08-2.11) for Alpha versus B.1.177, 2.09 (95% CI: 1.42-3.08) for Delta versus Alpha, 0.99 (95% CI: 0.76-1.27) for AY.4.2 Delta versus non-AY.4.2 Delta, 0.49 (95% CI: 0.22-1.06) for Omicron versus non-AY.4.2 Delta, and 0.86 (95% CI: 0.68-1.09) for BA.2 Omicron versus BA.1 Omicron. CONCLUSIONS The direction of change in intrinsic severity between successively emerging SARS-CoV-2 variants was inconsistent, reminding us that the intrinsic severity of future SARS-CoV-2 variants remains uncertain.
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Affiliation(s)
- David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom; Joint Universities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom.
| | - Elen Vink
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Lothian, Edinburgh EH1 3EG, United Kingdom.
| | - Rachel Blacow
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | | | | | | | | | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | | | | | - Emily Goldstein
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Rory Gunson
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - John Haughney
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Matthew T G Holden
- Public Health Scotland, Edinburgh EH12 9EB, United Kingdom; School of Medicine, University of St Andrews, St Andrews KY16 9TF, United Kingdom.
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | - Tim Lewis
- NHS Lothian, Edinburgh EH1 3EG, United Kingdom.
| | - Oscar MacLean
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | - Guy Mollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Tommy Nyberg
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom.
| | | | - Ben Parcell
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
| | - Surajit Ray
- School of Mathematics and Statistics, University of Glasgow, Glasgow G12 8TA, United Kingdom.
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Shaun R Seaman
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom.
| | - Sharif Shabaan
- Public Health Scotland, Edinburgh EH12 9EB, United Kingdom.
| | - James G Shepherd
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | | | - Craig Wilkie
- School of Mathematics and Statistics, University of Glasgow, Glasgow G12 8TA, United Kingdom.
| | - Thomas Williams
- NHS Lothian, Edinburgh EH1 3EG, United Kingdom; Royal Hospital for Children and Young People, University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom.
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom; London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.
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12
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Hansen F, Vučak M, Nichols J, Hughes J, Bane S, Camiolo S, da Silva Filipe A, Ostermann E, Staliunaite L, Chan B, Mauch T, Sogoba N, Streblow DN, Voigt S, Oestereich L, Ehlers B, Redwood AJ, Feldmann H, Brune W, Rosenke K, Jarvis MA, Davison AJ. Isolation and genome sequencing of cytomegaloviruses from Natal multimammate mice ( Mastomys natalensis). J Gen Virol 2023; 104:001873. [PMID: 37643006 PMCID: PMC10721045 DOI: 10.1099/jgv.0.001873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023] Open
Abstract
Distinct cytomegaloviruses (CMVs) are widely distributed across their mammalian hosts in a highly host species-restricted pattern. To date, evidence demonstrating this has been limited largely to PCR-based approaches targeting small, conserved genomic regions, and only a few complete genomes of isolated viruses representing distinct CMV species have been sequenced. We have now combined direct isolation of infectious viruses from tissues with complete genome sequencing to provide a view of CMV diversity in a wild animal population. We targeted Natal multimammate mice (Mastomys natalensis), which are common in sub-Saharan Africa, are known to carry a variety of zoonotic pathogens, and are regarded as the primary source of Lassa virus (LASV) spillover into humans. Using transformed epithelial cells prepared from M. natalensis kidneys, we isolated CMVs from the salivary gland tissue of 14 of 37 (36 %) animals from a field study site in Mali. Genome sequencing showed that these primary isolates represent three different M. natalensis CMVs (MnatCMVs: MnatCMV1, MnatCMV2 and MnatCMV3), with some animals carrying multiple MnatCMVs or multiple strains of a single MnatCMV presumably as a result of coinfection or superinfection. Including primary isolates and plaque-purified isolates, we sequenced and annotated the genomes of two MnatCMV1 strains (derived from sequencing 14 viruses), six MnatCMV2 strains (25 viruses) and ten MnatCMV3 strains (21 viruses), totalling 18 MnatCMV strains isolated as 60 infectious viruses. Phylogenetic analysis showed that these MnatCMVs group with other murid viruses in the genus Muromegalovirus (subfamily Betaherpesvirinae, family Orthoherpesviridae), and that MnatCMV1 and MnatCMV2 are more closely related to each other than to MnatCMV3. The availability of MnatCMV isolates and the characterization of their genomes will serve as the prelude to the generation of a MnatCMV-based vaccine to target LASV in the M. natalensis reservoir.
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Affiliation(s)
- Frederick Hansen
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
- Present address: School of Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Matej Vučak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sidy Bane
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Salvatore Camiolo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- Present address: BioSpyder Technologies Inc., Carlsbad, CA, USA
| | | | | | | | - Baca Chan
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Crawley, WA, Australia
| | | | - Nafomon Sogoba
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Daniel N. Streblow
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Sebastian Voigt
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lisa Oestereich
- Bernhard Nocht Institute for Tropical Medicine and German Center for Infectious Research (DZIF), Partner Sites Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany, Germany
| | - Bernhard Ehlers
- Division 12, Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients, Robert Koch Institute, Berlin, Germany
| | - Alec J. Redwood
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Crawley, WA, Australia
| | - Heinz Feldmann
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | | | - Kyle Rosenke
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Michael A. Jarvis
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
- The Vaccine Group Ltd, Plymouth, Devon, UK
- School of Biomedical Sciences, University of Plymouth, Plymouth, UK
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13
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Ladlow P, Suffield C, Greeves JP, Comfort P, Hughes J, Cassidy RP, Bennett AN, Coppack RJ. How 'STRONG' is the British Army? BMJ Mil Health 2023:e002508. [PMID: 37487657 DOI: 10.1136/military-2023-002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 07/26/2023]
Affiliation(s)
- Peter Ladlow
- Academic Department of Military Rehabilitation, Defence Medical Rehabilitation Centre, Loughborough, UK
| | - C Suffield
- Physical Development Branch, Royal Army Physical Training Corps, Tidworth, UK
| | - J P Greeves
- Department of Army Health and Physical Performance Research, United Kingdom Ministry of Defence, Andover, UK
| | - P Comfort
- School of Health and Society, University of Salford, Salford, UK
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - J Hughes
- Headquarters, Royal Army Physical Training Corps, Aldershot, UK
| | - R P Cassidy
- Academic Department of Military Rehabilitation, Defence Medical Rehabilitation Centre, Loughborough, UK
| | - A N Bennett
- Academic Department of Military Rehabilitation, Defence Medical Rehabilitation Centre, Loughborough, UK
| | - R J Coppack
- Academic Department of Military Rehabilitation, Defence Medical Rehabilitation Centre, Loughborough, UK
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14
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Pekar JE, Lytras S, Ghafari M, Magee AF, Parker E, Havens JL, Katzourakis A, Vasylyeva TI, Suchard MA, Hughes AC, Hughes J, Robertson DL, Dellicour S, Worobey M, Wertheim JO, Lemey P. The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2. bioRxiv 2023:2023.07.12.548617. [PMID: 37502985 PMCID: PMC10369958 DOI: 10.1101/2023.07.12.548617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 has led to increased sampling of related sarbecoviruses circulating primarily in horseshoe bats. These viruses undergo frequent recombination and exhibit spatial structuring across Asia. Employing recombination-aware phylogenetic inference on bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed just ~1-3 years prior to their emergence in humans. Phylogeographic analyses examining the movement of related sarbecoviruses demonstrate that they traveled at similar rates to their horseshoe bat hosts and have been circulating for thousands of years in Asia. The closest-inferred bat virus ancestor of SARS-CoV likely circulated in western China, and that of SARS-CoV-2 likely circulated in a region comprising southwest China and northern Laos, both a substantial distance from where they emerged. This distance and recency indicate that the direct ancestors of SARS-CoV and SARS-CoV-2 could not have reached their respective sites of emergence via the bat reservoir alone. Our recombination-aware dating and phylogeographic analyses reveal a more accurate inference of evolutionary history than performing only whole-genome or single gene analyses. These results can guide future sampling efforts and demonstrate that viral genomic fragments extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.
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Affiliation(s)
- Jonathan E Pekar
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 92093, USA
- These authors contributed equally
| | - Spyros Lytras
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
- These authors contributed equally
| | - Mahan Ghafari
- Department of Biology, University of Oxford, Oxford, UK
| | - Andrew F Magee
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jennifer L Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Tetyana I Vasylyeva
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Alice C Hughes
- School of Biological Sciences, University of Hong Kong, Hong Kong
- China Biodiversity Green Development Foundation, Beijing, China
| | - Joseph Hughes
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - David L Robertson
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
- These authors jointly supervised the work
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, 1050, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
- These authors jointly supervised the work
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- These authors jointly supervised the work
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- These authors jointly supervised the work
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
- These authors jointly supervised the work
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15
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Pinto RM, Bakshi S, Lytras S, Zakaria MK, Swingler S, Worrell JC, Herder V, Hargrave KE, Varjak M, Cameron-Ruiz N, Collados Rodriguez M, Varela M, Wickenhagen A, Loney C, Pei Y, Hughes J, Valette E, Turnbull ML, Furnon W, Gu Q, Orr L, Taggart A, Diebold O, Davis C, Boutell C, Grey F, Hutchinson E, Digard P, Monne I, Wootton SK, MacLeod MKL, Wilson SJ, Palmarini M. BTN3A3 evasion promotes the zoonotic potential of influenza A viruses. Nature 2023; 619:338-347. [PMID: 37380775 DOI: 10.1038/s41586-023-06261-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/25/2023] [Indexed: 06/30/2023]
Abstract
Spillover events of avian influenza A viruses (IAVs) to humans could represent the first step in a future pandemic1. Several factors that limit the transmission and replication of avian IAVs in mammals have been identified. There are several gaps in our understanding to predict which virus lineages are more likely to cross the species barrier and cause disease in humans1. Here, we identified human BTN3A3 (butyrophilin subfamily 3 member A3)2 as a potent inhibitor of avian IAVs but not human IAVs. We determined that BTN3A3 is expressed in human airways and its antiviral activity evolved in primates. We show that BTN3A3 restriction acts primarily at the early stages of the virus life cycle by inhibiting avian IAV RNA replication. We identified residue 313 in the viral nucleoprotein (NP) as the genetic determinant of BTN3A3 sensitivity (313F or, rarely, 313L in avian viruses) or evasion (313Y or 313V in human viruses). However, avian IAV serotypes, such as H7 and H9, that spilled over into humans also evade BTN3A3 restriction. In these cases, BTN3A3 evasion is due to substitutions (N, H or Q) in NP residue 52 that is adjacent to residue 313 in the NP structure3. Thus, sensitivity or resistance to BTN3A3 is another factor to consider in the risk assessment of the zoonotic potential of avian influenza viruses.
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Affiliation(s)
- Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Siddharth Bakshi
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Simon Swingler
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Julie C Worrell
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Kerrie E Hargrave
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Margus Varjak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- Faculty of Science and Technology, Institute of Technology, University of Tartu, Tartu, Estonia
| | | | | | - Mariana Varela
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Colin Loney
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Yanlong Pei
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Elise Valette
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Lauren Orr
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Aislynn Taggart
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Ola Diebold
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Finn Grey
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Paul Digard
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Sarah K Wootton
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Megan K L MacLeod
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Sam J Wilson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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16
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Iannucci S, Harvey WT, Hughes J, Robertson DL, Poyade M, Hutchinson E. The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern. J Vis Commun Med 2023; 46:122-132. [PMID: 37526402 PMCID: PMC10726978 DOI: 10.1080/17453054.2023.2237087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/23/2023] [Indexed: 08/02/2023]
Abstract
Due to the COVID-19 pandemic the virus responsible, SARS-CoV-2, became a source of intense interest for non-expert audiences. The viral spike protein gained particular public interest as the main target for protective immune responses, including those elicited by vaccines. The rapid evolution of SARS-CoV-2 resulted in variations in the spike that enhanced transmissibility or weakened vaccine protection. This created new variants of concern (VOCs). The emergence of VOCs was studied using viral sequence data which was shared through portals such as the online Mutation Explorer of the COVID-19 Genomics UK consortium (COG-UK/ME). This was designed for an expert audience, but the information it contained could be of general interest if suitably communicated. Visualisations, interactivity and animation can improve engagement and understanding of molecular biology topics, and so we developed a graphical educational resource, the SARS-CoV-2 Spike Protein Mutation Explorer (SSPME), which used interactive 3D molecular models and animations to explain the molecular biology underpinning VOCs. User testing showed that the SSPME had better usability and improved participant knowledge confidence and knowledge acquisition compared to COG-UK/ME. This demonstrates how interactive visualisations can be used for effective molecular biology communication, as well as improving the public understanding of SARS-CoV-2 VOCs.
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Affiliation(s)
- Sarah Iannucci
- School of Simulation and Visualisation, The Glasgow School of Art, Glasgow, UK
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Matthieu Poyade
- School of Simulation and Visualisation, The Glasgow School of Art, Glasgow, UK
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17
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Chau KK, Goodall T, Bowes M, Easterbrook K, Brett H, Hughes J, Crook DW, Read DS, Walker AS, Stoesser N. High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent. Microb Genom 2023; 9. [PMID: 37145848 DOI: 10.1099/mgen.0.000983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Wastewater-based epidemiology (WBE) for population-level surveillance of antimicrobial resistance (AMR) is gaining significant traction, but the impact of wastewater sampling methods on results is unclear. In this study, we characterized taxonomic and resistome differences between single-timepoint-grab and 24 h composites of wastewater influent from a large UK-based wastewater treatment work [WWTW (population equivalent: 223 435)]. We autosampled hourly influent grab samples (n=72) over three consecutive weekdays, and prepared additional 24 h composites (n=3) from respective grabs. For taxonomic profiling, metagenomic DNA was extracted from all samples and 16S rRNA gene sequencing was performed. One composite and six grabs from day 1 underwent metagenomic sequencing for metagenomic dissimilarity estimation and resistome profiling. Taxonomic abundances of phyla varied significantly across hourly grab samples but followed a repeating diurnal pattern for all 3 days. Hierarchical clustering grouped grab samples into four time periods dissimilar in both 16S rRNA gene-based profiles and metagenomic distances. 24H-composites resembled mean daily phyla abundances and showed low variability of taxonomic profiles. Of the 122 AMR gene families (AGFs) identified across all day 1 samples, single grab samples identified a median of six (IQR: 5-8) AGFs not seen in the composite. However, 36/36 of these hits were at lateral coverage <0.5 (median: 0.19; interquartile range: 0.16-0.22) and potential false positives. Conversely, the 24H-composite identified three AGFs not seen in any grab with higher lateral coverage (0.82; 0.55-0.84). Additionally, several clinically significant human AGFs (bla VIM, bla IMP, bla KPC) were intermittently or completely missed by grab sampling but captured by the 24 h composite. Wastewater influent undergoes significant taxonomic and resistome changes on short timescales potentially affecting interpretation of results based on sampling strategy. Grab samples are more convenient and potentially capture low-prevalence/transient targets but are less comprehensive and temporally variable. Therefore, we recommend 24H-composite sampling where feasible. Further validation and optimization of WBE methods is vital for its development into a robust AMR surveillance approach.
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Affiliation(s)
- Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
| | - T Goodall
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - M Bowes
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - K Easterbrook
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - H Brett
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - J Hughes
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - D W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - D S Read
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - A S Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - N Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
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18
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Maugans C, Loveday M, Hlangu S, Waitt C, Van Schalkwyk M, van de Water B, Salazar-Austin N, McKenna L, Mathad JS, Kalk E, Hurtado R, Hughes J, Eke AC, Ahmed S, Furin J. Best practices for the care of pregnant people living with TB. Int J Tuberc Lung Dis 2023; 27:357-366. [PMID: 37143222 PMCID: PMC10171489 DOI: 10.5588/ijtld.23.0031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND: Each year more than 200,000 pregnant people become sick with TB, but little is known about how to optimize their diagnosis and therapy. Although there is a need for further research in this population, it is important to recognize that much can be done to improve the services they currently receive.METHODS: Following a systematic review of the literature and the input of a global team of health professionals, a series of best practices for the diagnosis, prevention and treatment of TB during pregnancy were developed.RESULTS: Best practices were developed for each of the following areas: 1) screening and diagnosis; 2) reproductive health services and family planning; 3) treatment of drug-susceptible TB; 4) treatment of rifampicin-resistant/multidrug-resistant TB; 5) compassionate infection control practices; 6) feeding considerations; 7) counseling and support; 8) treatment of TB infection/TB preventive therapy; and 9) research considerations.CONCLUSION: Effective strategies for the care of pregnant people across the TB spectrum are readily achievable and will greatly improve the lives and health of this under-served population.
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Affiliation(s)
- C Maugans
- Sentinel Project on Pediatric Drug Resistant Tuberculosis, Boston, MA, USA
| | - M Loveday
- HIV and other Infectious Diseases Research Unit (HIDRU), South African Medical Research Council, Durban, South Africa
| | - S Hlangu
- HIV and other Infectious Diseases Research Unit (HIDRU), South African Medical Research Council, Durban, South Africa
| | - C Waitt
- Department of Pharmacology and Therapeutics, University of Liverpool, UK, and the Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - M Van Schalkwyk
- Division of Adult Infectious Diseases, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - B van de Water
- Boston College Connell School of Nursing, Chestnut Hill, MA, USA
| | - N Salazar-Austin
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - L McKenna
- Treatment Action Group, New York, NY, USA
| | - J S Mathad
- Departments of Medicine and Obstetrics & Gynecology, Center for Global Health, Weill Cornell Medicine, New York, NY, USA
| | - E Kalk
- Centre for Infectious Disease Epidemiology & Research, School of Public Health, University of Cape Town, South Africa
| | - R Hurtado
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA, Global Health Committee, Boston, MA, USA
| | - J Hughes
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - A C Eke
- Division of Maternal Fetal Medicine, Department of Gynecology & Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Ahmed
- Interactive Research and Development, Karachi, Pakistan
| | - J Furin
- Harvard Medical School, Department of Global Health and Social Medicine, Boston, MA, USA
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19
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Pascall DJ, Vink E, Blacow R, Bulteel N, Campbell A, Campbell R, Clifford S, Davis C, da Silva Filipe A, El Sakka N, Fjodorova L, Forrest R, Goldstein E, Gunson R, Haughney J, Holden MTG, Honour P, Hughes J, James E, Lewis T, Lycett S, MacLean O, McHugh M, Mollett G, Onishi Y, Parcell B, Ray S, Robertson DL, Shabaan S, Shepherd JG, Smollett K, Templeton K, Wastnedge E, Wilkie C, Williams T, Thomson EC. The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis. PLoS One 2023; 18:e0284187. [PMID: 37053201 PMCID: PMC10101505 DOI: 10.1371/journal.pone.0284187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
OBJECTIVES The SARS-CoV-2 Alpha variant was associated with increased transmission relative to other variants present at the time of its emergence and several studies have shown an association between Alpha variant infection and increased hospitalisation and 28-day mortality. However, none have addressed the impact on maximum severity of illness in the general population classified by the level of respiratory support required, or death. We aimed to do this. METHODS In this retrospective multi-centre clinical cohort sub-study of the COG-UK consortium, 1475 samples from Scottish hospitalised and community cases collected between 1st November 2020 and 30th January 2021 were sequenced. We matched sequence data to clinical outcomes as the Alpha variant became dominant in Scotland and modelled the association between Alpha variant infection and severe disease using a 4-point scale of maximum severity by 28 days: 1. no respiratory support, 2. supplemental oxygen, 3. ventilation and 4. death. RESULTS Our cumulative generalised linear mixed model analyses found evidence (cumulative odds ratio: 1.40, 95% CI: 1.02, 1.93) of a positive association between increased clinical severity and lineage (Alpha variant versus pre-Alpha variants). CONCLUSIONS The Alpha variant was associated with more severe clinical disease in the Scottish population than co-circulating lineages.
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Affiliation(s)
- David J. Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom
| | - Elen Vink
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Lothian, Edinburgh, United Kingdom
| | - Rachel Blacow
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | | | | | | | | | - Chris Davis
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | | | | | | | - Rory Gunson
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - John Haughney
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Matthew T. G. Holden
- Public Health Scotland, Edinburgh, United Kingdom
- School of Medicine, University of St Andrews, St Andrews, Fife, United Kingdom
| | | | - Joseph Hughes
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Edward James
- NHS Borders, Melrose, Scottish Borders, United Kingdom
| | - Tim Lewis
- NHS Lothian, Edinburgh, United Kingdom
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Oscar MacLean
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - Guy Mollett
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | | | - Ben Parcell
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Surajit Ray
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - David L. Robertson
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - James G. Shepherd
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Katherine Smollett
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | | | - Craig Wilkie
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Thomas Williams
- NHS Lothian, Edinburgh, United Kingdom
- Royal Hospital for Children and Young People, University of Edinburgh, Edinburgh, United Kingdom
| | - Emma C. Thomson
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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20
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Alexander AJT, Salvemini M, Sreenu VB, Hughes J, Telleria EL, Ratinier M, Arnaud F, Volf P, Brennan B, Varjak M, Kohl A. Characterisation of the antiviral RNA interference response to Toscana virus in sand fly cells. PLoS Pathog 2023; 19:e1011283. [PMID: 36996243 PMCID: PMC10112792 DOI: 10.1371/journal.ppat.1011283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/18/2023] [Accepted: 03/09/2023] [Indexed: 04/01/2023] Open
Abstract
Toscana virus (TOSV) (Bunyavirales, Phenuiviridae, Phlebovirus, Toscana phlebovirus) and other related human pathogenic arboviruses are transmitted by phlebotomine sand flies. TOSV has been reported in nations bordering the Mediterranean Sea among other regions. Infection can result in febrile illness as well as meningitis and encephalitis. Understanding vector-arbovirus interactions is crucial to improving our knowledge of how arboviruses spread, and in this context, immune responses that control viral replication play a significant role. Extensive research has been conducted on mosquito vector immunity against arboviruses, with RNA interference (RNAi) and specifically the exogenous siRNA (exo-siRNA) pathway playing a critical role. However, the antiviral immunity of phlebotomine sand flies is less well understood. Here we were able to show that the exo-siRNA pathway is active in a Phlebotomus papatasi-derived cell line. Following TOSV infection, distinctive 21 nucleotide virus-derived small interfering RNAs (vsiRNAs) were detected. We also identified the exo-siRNA effector Ago2 in this cell line, and silencing its expression rendered the exo-siRNA pathway largely inactive. Thus, our data show that this pathway is active as an antiviral response against a sand fly transmitted bunyavirus, TOSV.
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Affiliation(s)
- Akira J T Alexander
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Marco Salvemini
- Department of Biology, University of Naples Federico II, Italy
| | - Vattipally B Sreenu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Erich L Telleria
- Department of Parasitology, Faculty of Science, Charles University, Prague,Czech Republic
| | - Maxime Ratinier
- IVPC UMR754, INRAE, Univ Lyon, Université Claude Bernard Lyon1, EPHE, PSL Research University, Lyon, France
| | - Frédérick Arnaud
- IVPC UMR754, INRAE, Univ Lyon, Université Claude Bernard Lyon1, EPHE, PSL Research University, Lyon, France
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague,Czech Republic
| | - Benjamin Brennan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Margus Varjak
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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21
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Howard C, Gorman I, Crushell E, Knerr I, Hughes J, Boruah R, O'Grady L, Elsammak MY, Brady JJ, Monavari AA. Medium Chain Acyl-CoA Dehydrogenase Deficiency: 3 years of Newborn Screening. Ir Med J 2023; 116:743. [PMID: 37010499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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22
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Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol 2023; 21:162-177. [PMID: 36653446 PMCID: PMC9847462 DOI: 10.1038/s41579-022-00841-7] [Citation(s) in RCA: 180] [Impact Index Per Article: 180.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/19/2023]
Abstract
In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited a major step change in its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates of transmission relative to previous variants and were termed 'variants of concern' (VOCs). Designated Alpha, Beta, Gamma, Delta and Omicron, the VOCs emerged independently from one another, and in turn each rapidly became dominant, regionally or globally, outcompeting previous variants. The success of each VOC relative to the previously dominant variant was enabled by altered intrinsic functional properties of the virus and, to various degrees, changes to virus antigenicity conferring the ability to evade a primed immune response. The increased virus fitness associated with VOCs is the result of a complex interplay of virus biology in the context of changing human immunity due to both vaccination and prior infection. In this Review, we summarize the literature on the relative transmissibility and antigenicity of SARS-CoV-2 variants, the role of mutations at the furin spike cleavage site and of non-spike proteins, the potential importance of recombination to virus success, and SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity. SARS-CoV-2 shows a complicated relationship among virus antigenicity, transmission and virulence, which has unpredictable implications for the future trajectory and disease burden of COVID-19.
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Affiliation(s)
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Wendy S Barclay
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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23
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Whitlock AOB, Bird BH, Ghersi B, Davison AJ, Hughes J, Nichols J, Vučak M, Amara E, Bangura J, Lavalie EG, Kanu MC, Kanu OT, Sjodin A, Remien CH, Nuismer SL. Identifying the genetic basis of viral spillover using Lassa virus as a test case. R Soc Open Sci 2023; 10:221503. [PMID: 36968239 PMCID: PMC10031424 DOI: 10.1098/rsos.221503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The rate at which zoonotic viruses spill over into the human population varies significantly over space and time. Remarkably, we do not yet know how much of this variation is attributable to genetic variation within viral populations. This gap in understanding arises because we lack methods of genetic analysis that can be easily applied to zoonotic viruses, where the number of available viral sequences is often limited, and opportunistic sampling introduces significant population stratification. Here, we explore the feasibility of using patterns of shared ancestry to correct for population stratification, enabling genome-wide association methods to identify genetic substitutions associated with spillover into the human population. Using a combination of phylogenetically structured simulations and Lassa virus sequences collected from humans and rodents in Sierra Leone, we demonstrate that existing methods do not fully correct for stratification, leading to elevated error rates. We also demonstrate, however, that the Type I error rate can be substantially reduced by confining the analysis to a less-stratified region of the phylogeny, even in an already-small dataset. Using this method, we detect two candidate single-nucleotide polymorphisms associated with spillover in the Lassa virus polymerase gene and provide generalized recommendations for the collection and analysis of zoonotic viruses.
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Affiliation(s)
| | - Brian H. Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Bruno Ghersi
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matej Vučak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Emmanuel Amara
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - James Bangura
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Edwin G. Lavalie
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Marilyn C. Kanu
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Osman T. Kanu
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Anna Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Christopher H. Remien
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, USA
| | - Scott L. Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
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24
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Cox M, Peacock TP, Harvey WT, Hughes J, Wright DW, Willett BJ, Thomson E, Gupta RK, Peacock SJ, Robertson DL, Carabelli AM. SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nat Rev Microbiol 2023; 21:112-124. [PMID: 36307535 PMCID: PMC9616429 DOI: 10.1038/s41579-022-00809-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2022] [Indexed: 01/20/2023]
Abstract
Monoclonal antibodies (mAbs) offer a treatment option for individuals with severe COVID-19 and are especially important in high-risk individuals where vaccination is not an option. Given the importance of understanding the evolution of resistance to mAbs by SARS-CoV-2, we reviewed the available in vitro neutralization data for mAbs against live variants and viral constructs containing spike mutations of interest. Unfortunately, evasion of mAb-induced protection is being reported with new SARS-CoV-2 variants. The magnitude of neutralization reduction varied greatly among mAb-variant pairs. For example, sotrovimab retained its neutralization capacity against Omicron BA.1 but showed reduced efficacy against BA.2, BA.4 and BA.5, and BA.2.12.1. At present, only bebtelovimab has been reported to retain its efficacy against all SARS-CoV-2 variants considered here. Resistance to mAb neutralization was dominated by the action of epitope single amino acid substitutions in the spike protein. Although not all observed epitope mutations result in increased mAb evasion, amino acid substitutions at non-epitope positions and combinations of mutations also contribute to evasion of neutralization. This Review highlights the implications for the rational design of viral genomic surveillance and factors to consider for the development of novel mAb therapies.
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Affiliation(s)
- MacGregor Cox
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Derek W Wright
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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25
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Carrozza ML, Niewiadomska AM, Mazzei M, Abi-Said MR, Hué S, Hughes J, Gatseva A, Gifford RJ. Emergence and pandemic spread of small ruminant lentiviruses. Virus Evol 2023; 9:vead005. [PMID: 36793939 PMCID: PMC9924038 DOI: 10.1093/ve/vead005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/02/2023] [Accepted: 01/17/2023] [Indexed: 01/19/2023] Open
Abstract
Small ruminant lentiviruses (SRLVs) cause chronic, persistent infections in populations of domestic sheep (Ovis aries) and goats (Capra hircus) worldwide. The vast majority of SRLV infections involve two genotypes (A and B) that spread in association with the emergence of global livestock trade. However, SRLVs have likely been present in Eurasian ruminant populations since at least the early Neolithic period. Here, we use phylogenetic and phylogeographic approaches to reconstruct the origin of pandemic SRLV strains and infer their historical pattern of global spread. We constructed an open computational resource ('Lentivirus-GLUE') via which an up-to-date database of published SRLV sequences, multiple sequence alignments (MSAs), and sequence-associated metadata can be maintained. We used data collated in Lentivirus-GLUE to perform a comprehensive phylogenetic investigation of global SRLV diversity. Phylogenies reconstructed from genome-length alignments reveal that the deep divisions in the SRLV phylogeny are consistent with an ancient split into Eastern (A-like) and Western (B-like) lineages as agricultural systems disseminated out of domestication centres during the Neolithic period. These findings are also consistent with historical and phylogeographic evidence linking the early 20th century emergence of SRLV-A to the international export of Central Asian Karakul sheep. Investigating the global diversity of SRLVs can help reveal how anthropogenic factors have impacted the ecology and evolution of livestock diseases. The open resources generated in our study can expedite these studies and can also serve more broadly to facilitate the use of genomic data in SRLV diagnostics and research.
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Affiliation(s)
| | - Anna-Maria Niewiadomska
- Virus Pathogen Resource, J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD 20850, USA
| | | | - Mounir R Abi-Said
- Faculty of Sciences II, Lebanese University, Campus Pierre Gemayel Fanar, Jdeidet 90656, Lebanon
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26
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Hughes J, McPhail N, Watkins P, Stark J, Warner RD. Increased light scattering in electrically stimulated beef longissimus muscle fibres contributes to the observed meat colour at grading. Anim Prod Sci 2023. [DOI: 10.1071/an22390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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27
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Cantoni D, Siracusano G, Mayora-Neto M, Pastori C, Fantoni T, Lytras S, Di Genova C, Hughes J, Lopalco L, Temperton N. Analysis of Antibody Neutralisation Activity against SARS-CoV-2 Variants and Seasonal Human Coronaviruses NL63, HKU1, and 229E Induced by Three Different COVID-19 Vaccine Platforms. Vaccines (Basel) 2022; 11:58. [PMID: 36679903 PMCID: PMC9864028 DOI: 10.3390/vaccines11010058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Coronaviruses infections, culminating in the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic beginning in 2019, have highlighted the importance of effective vaccines to induce an antibody response with cross-neutralizing activity. COVID-19 vaccines have been rapidly developed to reduce the burden of SARS-CoV-2 infections and disease severity. Cross-protection from seasonal human coronaviruses (hCoVs) infections has been hypothesized but is still controversial. Here, we investigated the neutralizing activity against ancestral SARS-CoV-2 and the variants of concern (VOCs) in individuals vaccinated with two doses of either BNT162b2, mRNA-1273, or AZD1222, with or without a history of SARS-CoV-2 infection. Antibody neutralizing activity to SARS-CoV-2 and the VOCs was higher in BNT162b2-vaccinated subjects who were previously infected with SARS-CoV-2 and conferred broad-spectrum protection. The Omicron BA.1 variant was the most resistant among the VOCs. COVID-19 vaccination did not confer protection against hCoV-HKU1. Conversely, antibodies induced by mRNA-1273 vaccination displayed a boosting in their neutralizing activity against hCoV-NL63, whereas AZD1222 vaccination increased antibody neutralization against hCoV-229E, suggesting potential differences in antigenicity and immunogenicity of the different spike constructs used between various vaccination platforms. These data would suggest that there may be shared epitopes between the HCoVs and SARS-CoV-2 spike proteins.
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Affiliation(s)
- Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham ME4 4TB, UK
| | - Gabriel Siracusano
- Division of Immunology, Transplantation and Infectious Disease, Immunobiology of HIV Group, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham ME4 4TB, UK
| | - Claudia Pastori
- Division of Immunology, Transplantation and Infectious Disease, Immunobiology of HIV Group, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Tobia Fantoni
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37129 Verona, Italy
| | - Spyros Lytras
- MRC-Centre for Virus Research, University of Glasgow, Glasgow G12 BQQ, UK
| | - Cecilia Di Genova
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham ME4 4TB, UK
| | - Joseph Hughes
- MRC-Centre for Virus Research, University of Glasgow, Glasgow G12 BQQ, UK
| | | | - Lucia Lopalco
- Division of Immunology, Transplantation and Infectious Disease, Immunobiology of HIV Group, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham ME4 4TB, UK
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Camiolo S, Hughes J, Baldanti F, Furione M, Lilleri D, Lombardi G, Angelini M, Gerna G, Zavattoni M, Davison AJ, Suárez NM. Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples. Virus Evol 2022; 8:veac114. [PMID: 37091479 PMCID: PMC10120596 DOI: 10.1093/ve/veac114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/27/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT
Understanding the intrahost evolution of viral populations has implications in pathogenesis, diagnosis and treatment, and has recently made impressive advances from developments in high-throughput sequencing. However, the underlying analyses are very sensitive to sources of bias, error and artefact in the data, and it is important that these are addressed adequately if robust conclusions are to be drawn. The key factors include: (i) determining the number of viral strains present in the sample analysed; (ii) monitoring the extent to which the data represent these strains and assessing the quality of these data; (iii) dealing with the effects of cross-contamination; and (iv) ensuring that the results are reproducible. We investigated these factors by generating sequence datasets, including biological and technical replicates, directly from clinical samples obtained from a small cohort of patients who had been infected congenitally with the herpesvirus human cytomegalovirus, with the aim of developing a strategy for identifying high-confidence intrahost variants. We found that such variants were few in number and typically present in low proportions, and concluded that human cytomegalovirus exhibits a very low level of intrahost variability. In addition to clarifying the situation regarding human cytomegalovirus, our strategy has wider applicability to understanding the intrahost variability of other viruses.
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Affiliation(s)
- Salvatore Camiolo
- MRC-University of Glasgow Centre for Virus Research , Glasgow G61 1QH, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research , Glasgow G61 1QH, United Kingdom
| | - Fausto Baldanti
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia; Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo , Pavia 27100, Italy
| | - Milena Furione
- Microbiology and Virology Department Fondazione IRCCS Policlinico San Matteo ,Pavia 27100, Italy
| | - Daniele Lilleri
- Microbiology and Virology Department Fondazione IRCCS Policlinico San Matteo ,Pavia 27100, Italy
| | - Giuseppina Lombardi
- Neonatal and Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo , Pavia 27100, Italy
| | - Micol Angelini
- Neonatal and Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo , Pavia 27100, Italy
| | - Giuseppe Gerna
- Transplant Research Area and Centre for Inherited Cardiovascular Diseases Fondazione IRCCS Policlinico San Matteo , Pavia 27100, Italy
| | - Maurizio Zavattoni
- Microbiology and Virology Department Fondazione IRCCS Policlinico San Matteo ,Pavia 27100, Italy
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research , Glasgow G61 1QH, United Kingdom
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research , Glasgow G61 1QH, United Kingdom
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Chai H, Gu Q, Robertson DL, Hughes J. Defining the characteristics of interferon-alpha-stimulated human genes: insight from expression data and machine learning. Gigascience 2022; 11:6833046. [PMID: 36399061 PMCID: PMC9673497 DOI: 10.1093/gigascience/giac103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/07/2022] [Accepted: 10/02/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND A virus-infected cell triggers a signalling cascade, resulting in the secretion of interferons (IFNs), which in turn induces the upregulation of the IFN-stimulated genes (ISGs) that play a role in antipathogen host defence. Here, we conducted analyses on large-scale data relating to evolutionary gene expression, sequence composition, and network properties to elucidate factors associated with the stimulation of human genes in response to IFN-α. RESULTS We find that ISGs are less evolutionary conserved than genes that are not significantly stimulated in IFN experiments (non-ISGs). ISGs show obvious depletion of GC content in the coding region. This influences the representation of some compositions following the translation process. IFN-repressed human genes (IRGs), downregulated genes in IFN experiments, can have similar properties to the ISGs. Additionally, we design a machine learning framework integrating the support vector machine and novel feature selection algorithm that achieves an area under the receiver operating characteristic curve (AUC) of 0.7455 for ISG prediction. Its application in other IFN systems suggests the similarity between the ISGs triggered by type I and III IFNs. CONCLUSIONS ISGs have some unique properties that make them different from the non-ISGs. The representation of some properties has a strong correlation with gene expression following IFN-α stimulation, which can be used as a predictive feature in machine learning. Our model predicts several genes as putative ISGs that so far have shown no significant differential expression when stimulated with IFN-α in the cell/tissue types in the available databases. A web server implementing our method is accessible at http://isgpre.cvr.gla.ac.uk/. The docker image at https://hub.docker.com/r/hchai01/isgpre can be downloaded to reproduce the prediction.
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Affiliation(s)
- Haiting Chai
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Campus, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Campus, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK
| | - David L Robertson
- Correspondence address. David L. Robertson, MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK, E-mail:
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Sugrue E, Wickenhagen A, Mollentze N, Aziz MA, Sreenu VB, Truxa S, Tong L, da Silva Filipe A, Robertson DL, Hughes J, Rihn SJ, Wilson SJ. The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness. PLoS Pathog 2022; 18:e1010973. [PMID: 36399512 PMCID: PMC9718408 DOI: 10.1371/journal.ppat.1010973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 12/02/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
HIV-1 transmission via sexual exposure is an inefficient process. When transmission does occur, newly infected individuals are colonized by the descendants of either a single virion or a very small number of establishing virions. These transmitted founder (TF) viruses are more interferon (IFN)-resistant than chronic control (CC) viruses present 6 months after transmission. To identify the specific molecular defences that make CC viruses more susceptible to the IFN-induced 'antiviral state', we established a single pair of fluorescent TF and CC viruses and used arrayed interferon-stimulated gene (ISG) expression screening to identify candidate antiviral effectors. However, we observed a relatively uniform ISG resistance of transmitted HIV-1, and this directed us to investigate possible underlying mechanisms. Simple simulations, where we varied a single parameter, illustrated that reduced growth rate could possibly underly apparent interferon sensitivity. To examine this possibility, we closely monitored in vitro propagation of a model TF/CC pair (closely matched in replicative fitness) over a targeted range of IFN concentrations. Fitting standard four-parameter logistic growth models, in which experimental variables were regressed against growth rate and carrying capacity, to our in vitro growth curves, further highlighted that small differences in replicative growth rates could recapitulate our in vitro observations. We reasoned that if growth rate underlies apparent interferon resistance, transmitted HIV-1 would be similarly resistant to any growth rate inhibitor. Accordingly, we show that two transmitted founder HIV-1 viruses are relatively resistant to antiretroviral drugs, while their matched chronic control viruses were more sensitive. We propose that, when present, the apparent IFN resistance of transmitted HIV-1 could possibly be explained by enhanced replicative fitness, as opposed to specific resistance to individual IFN-induced defences. However, further work is required to establish how generalisable this mechanism of relative IFN resistance might be.
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Affiliation(s)
- Elena Sugrue
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Nardus Mollentze
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Muhamad Afiq Aziz
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Vattipally B. Sreenu
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Sven Truxa
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- Division of Systems Immunology and Single Cell Biology, German Cancer Research Center, Heidelberg, Germany
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Suzannah J. Rihn
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
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31
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Mann B, Rose A, Hughes J, Skandarajah A, Murugasu A, Spillane A, Chua B, Zdenkowski N, Badger H, Braggett H, Gebski V, Eggins R, Park A, Collins J. Primary results of ANZ 1002 : Post-operative Radiotherapy Omission in Selected Patients with Early breast Cancer Trial (PROSPECT) following pre-operative breast MRI. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)01476-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC. Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat Microbiol 2022; 7:1709. [PMID: 36114232 PMCID: PMC9483304 DOI: 10.1038/s41564-022-01241-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Joe Grove
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Craig Wilkie
- School of Mathematics & Statistics, University of Glasgow, Glasgow, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Diego Cantoni
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sam Scott
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Nicola Logan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Maria Manali
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Agnieszka Szemiel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Elen Vink
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Patawee Asamaphan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | | | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - Matthew T G Holden
- Public Health Scotland, Glasgow, UK
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | | | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Surajit Ray
- School of Mathematics & Statistics, University of Glasgow, Glasgow, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
- NHS Greater Glasgow & Clyde, Glasgow, UK.
- London School of Hygiene and Tropical Medicine, London, UK.
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Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K, Saluja T, Taha Y, Mahida N, Pope C, Chawla A, Cutino-Moguel MT, Tamuri A, Williams R, Darby A, Robertson DL, Flaviani F, Nastouli E, Robson S, Smith D, Laing K, Monahan I, Kele B, Haldenby S, George R, Bashton M, Witney AA, Byott M, Coll F, Chapman M, Peacock SJ, Hughes J, Nebbia G, Partridge DG, Parker M, Price JR, Peters C, Roy S, Snell LB, de Silva TI, Thomson E, Flowers P, Copas A, Breuer J. Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study. eLife 2022; 11:78427. [PMID: 36098502 PMCID: PMC9596156 DOI: 10.7554/elife.78427] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48h) and 4 weeks of 'longer-turnaround' (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected ≥48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated. Results: A total of 2170 HOCI cases were recorded from October 2020-April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources. Conclusion: While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days. Funding: COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) [grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute. Clinical trial number: ClinicalTrials.gov Identifier: NCT04405934.
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Affiliation(s)
- Oliver Stirrup
- Institute for Global Health, University College London, London, United Kingdom
| | - James Blackstone
- The Comprehensive Clinical Trials Unit, University College London, London, United Kingdom
| | - Fiona Mapp
- Institute for Global Health, University College London, London, United Kingdom
| | - Alyson MacNeil
- Comprehensive Clinical Trials Unit, University College London, London, United Kingdom
| | - Monica Panca
- Comprehensive Clinical Trials Unit, University College London, London, United Kingdom
| | - Alison Holmes
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Nicholas Machin
- Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Gee Yen Shin
- University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Tabitha Mahungu
- Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Kordo Saeed
- University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Tranprit Saluja
- Sandwell & West Birmingham Hospitals NHS Trust, Birmingham, United Kingdom
| | - Yusri Taha
- Department of Virology and Infectious Diseases, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, United Kingdom
| | - Nikunj Mahida
- Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Cassie Pope
- St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Anu Chawla
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | | | - Asif Tamuri
- Research Computing, University College London, London, United Kingdom
| | - Rachel Williams
- Department of Genetics and Genomic Medicine, University College London, London, United Kingdom
| | - Alistair Darby
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - David L Robertson
- MRC-University of Glasgow Centre For Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Flavia Flaviani
- Guy's and St Thomas' Hospital NHS Foundation Trust, London, United Kingdom
| | - Eleni Nastouli
- University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Samuel Robson
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, United Kingdom
| | - Darren Smith
- Department of Applied Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
| | - Kenneth Laing
- Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | - Irene Monahan
- Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | | | - Sam Haldenby
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - Ryan George
- Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Matthew Bashton
- Department of Applied Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | - Matthew Byott
- Advanced Pathogen Diagnostics, University College London, London, United Kingdom
| | - Francesc Coll
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Gaia Nebbia
- Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - David G Partridge
- Directorate of Laboratory Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - Matthew Parker
- Sheffield Bioinformatics Core, University of Sheffield, Sheffield, United Kingdom
| | | | | | - Sunando Roy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Luke B Snell
- Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Paul Flowers
- School of Psychological Sciences and Health, University of Strathclyde, Glasgow, United Kingdom
| | - Andrew Copas
- Institute for Global Health, University College London, London, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, United Kingdom
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Li YT, Polotan FGM, Sotelo GIS, Alpino APA, Dolor AYM, Tujan MAA, Gomez MRR, Onza OJT, Chang AKT, Bautista CT, Carandang JC, Yangzon MSL, Pangilinan EAR, Mantaring RJ, Telles AJE, Egana JMC, Endozo JJS, Cruz RPS, Tablizo FA, Yap JMC, Maralit BA, Ayes MEC, de la Paz EMC, Saloma CP, Lim DR, Dancel LLM, Uy-Lumandas M, Medado IAP, Dizon TJR, Hampson K, Daldry S, Hughes J, Brunker K. Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines. Virus Evol 2022; 8:veac078. [PMID: 36090771 PMCID: PMC9452094 DOI: 10.1093/ve/veac078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/11/2022] [Accepted: 08/18/2022] [Indexed: 11/14/2022] Open
Abstract
The Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant led to a dramatic global epidemic wave following detection in South Africa in November 2021. The BA.1 Omicron lineage was dominant and responsible for most SARS-CoV-2 outbreaks in countries around the world during December 2021-January 2022, while other Omicron lineages, including BA.2, accounted for the minority of global isolates. Here, we describe the Omicron wave in the Philippines by analysing genomic data. Our results identify the presence of both BA.1 and BA.2 lineages in the Philippines in December 2021, before cases surged in January 2022. We infer that only the BA.2 lineage underwent sustained transmission in the country, with an estimated emergence around 18 November 2021 (95 per cent highest posterior density: 6-28 November), while despite multiple introductions, BA.1 transmission remained limited. These results suggest that the Philippines was one of the earliest areas affected by BA.2 and reiterate the importance of whole genome sequencing for monitoring outbreaks.
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Affiliation(s)
- Yao-Tsun Li
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Francisco Gerardo M Polotan
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Gerald Ivan S Sotelo
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Anne Pauline A Alpino
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Ardiane Ysabelle M Dolor
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Ma. Angelica A Tujan
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Ma. Ricci R Gomez
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Othoniel Jan T Onza
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Angela Kae T Chang
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Criselda T Bautista
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - June C Carandang
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Maria Sofia L Yangzon
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Elcid Aaron R Pangilinan
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Renato Jacinto Mantaring
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Alyssa Joyce E Telles
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - John Michael C Egana
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Joshua Jose S Endozo
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Rianna Patricia S Cruz
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Francis A Tablizo
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Jan Michael C Yap
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Benedict A Maralit
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Marc Edsel C Ayes
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Eva Marie C de la Paz
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
- National Institutes of Health, University of the Philippines Manila, 623 Pedro Gil Street, Ermita, Manila 1000, Philippine
| | - Cynthia P Saloma
- Philippine Genome Center, National Science Complex, U.P. Campus, University of the Philippines, A. Ma. Regidor Street, Quezon City, Metro Manila 1101, Philippines
| | - Dodge R Lim
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Lei Lanna M Dancel
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Mayan Uy-Lumandas
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Inez Andrea P Medado
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Timothy John R Dizon
- Research Institute for Tropical Medicine, 9002 Research Drive, Filinvest Corporate City, Alabang, Muntinlupa, Metro Manila 1781, Philippines
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Simon Daldry
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
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Evans RA, Leavy OC, Richardson M, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Saunders RM, Harris VC, Houchen-Wolloff L, Aul R, Beirne P, Bolton CE, Brown JS, Choudhury G, Diar-Bakerly N, Easom N, Echevarria C, Fuld J, Hart N, Hurst J, Jones MG, Parekh D, Pfeffer P, Rahman NM, Rowland-Jones SL, Shah AM, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Greening NJ, Heaney LG, Heller S, Howard LS, Jacob J, Jenkins RG, Lord JM, Man WDC, McCann GP, Neubauer S, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Semple MG, Singh SJ, Thomas DC, Toshner M, Lewis KE, Thwaites RS, Briggs A, Docherty AB, Kerr S, Lone NI, Quint J, Sheikh A, Thorpe M, Zheng B, Chalmers JD, Ho LP, Horsley A, Marks M, Poinasamy K, Raman B, Harrison EM, Wain LV, Brightling CE, Abel K, Adamali H, Adeloye D, Adeyemi O, Adrego R, Aguilar Jimenez LA, Ahmad S, Ahmad Haider N, Ahmed R, Ahwireng N, Ainsworth M, Al-Sheklly B, Alamoudi A, Ali M, Aljaroof M, All AM, Allan L, Allen RJ, Allerton L, Allsop L, Almeida P, Altmann D, Alvarez Corral M, Amoils S, Anderson D, Antoniades C, Arbane G, Arias A, Armour C, Armstrong L, Armstrong N, Arnold D, Arnold H, Ashish A, Ashworth A, Ashworth M, Aslani S, Assefa-Kebede H, Atkin C, Atkin P, Aung H, Austin L, Avram C, Ayoub A, Babores M, Baggott R, Bagshaw J, Baguley D, Bailey L, Baillie JK, Bain S, Bakali M, Bakau M, Baldry E, Baldwin D, Ballard C, Banerjee A, Bang B, Barker RE, Barman L, Barratt S, Barrett F, Basire D, Basu N, Bates M, Bates A, Batterham R, Baxendale H, Bayes H, Beadsworth M, Beckett P, Beggs M, Begum M, Bell D, Bell R, Bennett K, Beranova E, Bermperi A, Berridge A, Berry C, Betts S, Bevan E, Bhui K, Bingham M, Birchall K, Bishop L, Bisnauthsing K, Blaikely J, Bloss A, Bolger A, Bonnington J, Botkai A, Bourne C, Bourne M, Bramham K, Brear L, Breen G, Breeze J, Bright E, Brill S, Brindle K, Broad L, Broadley A, Brookes C, Broome M, Brown A, Brown A, Brown J, Brown J, Brown M, Brown M, Brown V, Brugha T, Brunskill N, Buch M, Buckley P, Bularga A, Bullmore E, Burden L, Burdett T, Burn D, Burns G, Burns A, Busby J, Butcher R, Butt A, Byrne S, Cairns P, Calder PC, Calvelo E, Carborn H, Card B, Carr C, Carr L, Carson G, Carter P, Casey A, Cassar M, Cavanagh J, Chablani M, Chambers RC, Chan F, Channon KM, Chapman K, Charalambou A, Chaudhuri N, Checkley A, Chen J, Cheng Y, Chetham L, Childs C, Chilvers ER, Chinoy H, Chiribiri A, Chong-James K, Choudhury N, Chowienczyk P, Christie C, Chrystal M, Clark D, Clark C, Clarke J, Clohisey S, Coakley G, Coburn Z, Coetzee S, Cole J, Coleman C, Conneh F, Connell D, Connolly B, Connor L, Cook A, Cooper B, Cooper J, Cooper S, Copeland D, Cosier T, Coulding M, Coupland C, Cox E, Craig T, Crisp P, Cristiano D, Crooks MG, Cross A, Cruz I, Cullinan P, Cuthbertson D, Daines L, Dalton M, Daly P, Daniels A, Dark P, Dasgin J, David A, David C, Davies E, Davies F, Davies G, Davies GA, Davies K, Dawson J, Daynes E, Deakin B, Deans A, Deas C, Deery J, Defres S, Dell A, Dempsey K, Denneny E, Dennis J, Dewar A, Dharmagunawardena R, Dickens C, Dipper A, Diver S, Diwanji SN, Dixon M, Djukanovic R, Dobson H, Dobson SL, Donaldson A, Dong T, Dormand N, Dougherty A, Dowling R, Drain S, Draxlbauer K, Drury K, Dulawan P, Dunleavy A, Dunn S, Earley J, Edwards S, Edwardson C, El-Taweel H, Elliott A, Elliott K, Ellis Y, Elmer A, Evans D, Evans H, Evans J, Evans R, Evans RI, Evans T, Evenden C, Evison L, Fabbri L, Fairbairn S, Fairman A, Fallon K, Faluyi D, Favager C, Fayzan T, Featherstone J, Felton T, Finch J, Finney S, Finnigan J, Finnigan L, Fisher H, Fletcher S, Flockton R, Flynn M, Foot H, Foote D, Ford A, Forton D, Fraile E, Francis C, Francis R, Francis S, Frankel A, Fraser E, Free R, French N, Fu X, Furniss J, Garner L, Gautam N, George J, George P, Gibbons M, Gill M, Gilmour L, Gleeson F, Glossop J, Glover S, Goodman N, Goodwin C, Gooptu B, Gordon H, Gorsuch T, Greatorex M, Greenhaff PL, Greenhalgh A, Greenwood J, Gregory H, Gregory R, Grieve D, Griffin D, Griffiths L, Guerdette AM, Guillen Guio B, Gummadi M, Gupta A, Gurram S, Guthrie E, Guy Z, H Henson H, Hadley K, Haggar A, Hainey K, Hairsine B, Haldar P, Hall I, Hall L, Halling-Brown M, Hamil R, Hancock A, Hancock K, Hanley NA, Haq S, Hardwick HE, Hardy E, Hardy T, Hargadon B, Harrington K, Harris E, Harrison P, Harvey A, Harvey M, Harvie M, Haslam L, Havinden-Williams M, Hawkes J, Hawkings N, Haworth J, Hayday A, Haynes M, Hazeldine J, Hazelton T, Heeley C, Heeney JL, Heightman M, Henderson M, Hesselden L, Hewitt M, Highett V, Hillman T, Hiwot T, Hoare A, Hoare M, Hockridge J, Hogarth P, Holbourn A, Holden S, Holdsworth L, Holgate D, Holland M, Holloway L, Holmes K, Holmes M, Holroyd-Hind B, Holt L, Hormis A, Hosseini A, Hotopf M, Howard K, Howell A, Hufton E, Hughes AD, Hughes J, Hughes R, Humphries A, Huneke N, Hurditch E, Husain M, Hussell T, Hutchinson J, Ibrahim W, Ilyas F, Ingham J, Ingram L, Ionita D, Isaacs K, Ismail K, Jackson T, James WY, Jarman C, Jarrold I, Jarvis H, Jastrub R, Jayaraman B, Jezzard P, Jiwa K, Johnson C, Johnson S, Johnston D, Jolley CJ, Jones D, Jones G, Jones H, Jones H, Jones I, Jones L, Jones S, Jose S, Kabir T, Kaltsakas G, Kamwa V, Kanellakis N, Kaprowska S, Kausar Z, Keenan N, Kelly S, Kemp G, Kerslake H, Key AL, Khan F, Khunti K, Kilroy S, King B, King C, Kingham L, Kirk J, Kitterick P, Klenerman P, Knibbs L, Knight S, Knighton A, Kon O, Kon S, Kon SS, Koprowska S, Korszun A, Koychev I, Kurasz C, Kurupati P, Laing C, Lamlum H, Landers G, Langenberg C, Lasserson D, Lavelle-Langham L, Lawrie A, Lawson C, Lawson C, Layton A, Lea A, Lee D, Lee JH, Lee E, Leitch K, Lenagh R, Lewis D, Lewis J, Lewis V, Lewis-Burke N, Li X, Light T, Lightstone L, Lilaonitkul W, Lim L, Linford S, Lingford-Hughes A, Lipman M, Liyanage K, Lloyd A, Logan S, Lomas D, Loosley R, Lota H, Lovegrove W, Lucey A, Lukaschuk E, Lye A, Lynch C, MacDonald S, MacGowan G, Macharia I, Mackie J, Macliver L, Madathil S, Madzamba G, Magee N, Magtoto MM, Mairs N, Majeed N, Major E, Malein F, Malim M, Mallison G, Mandal S, Mangion K, Manisty C, Manley R, March K, Marciniak S, Marino P, Mariveles M, Marouzet E, Marsh S, Marshall B, Marshall M, Martin J, Martineau A, Martinez LM, Maskell N, Matila D, Matimba-Mupaya W, Matthews L, Mbuyisa A, McAdoo S, Weir McCall J, McAllister-Williams H, McArdle A, McArdle P, McAulay D, McCormick J, McCormick W, McCourt P, McGarvey L, McGee C, Mcgee K, McGinness J, McGlynn K, McGovern A, McGuinness H, McInnes IB, McIntosh J, McIvor E, McIvor K, McLeavey L, McMahon A, McMahon MJ, McMorrow L, Mcnally T, McNarry M, McNeill J, McQueen A, McShane H, Mears C, Megson C, Megson S, Mehta P, Meiring J, Melling L, Mencias M, Menzies D, Merida Morillas M, Michael A, Milligan L, Miller C, Mills C, Mills NL, Milner L, Misra S, Mitchell J, Mohamed A, Mohamed N, Mohammed S, Molyneaux PL, Monteiro W, Moriera S, Morley A, Morrison L, Morriss R, Morrow A, Moss AJ, Moss P, Motohashi K, Msimanga N, Mukaetova-Ladinska E, Munawar U, Murira J, Nanda U, Nassa H, Nasseri M, Neal A, Needham R, Neill P, Newell H, Newman T, Newton-Cox A, Nicholson T, Nicoll D, Nolan CM, Noonan MJ, Norman C, Novotny P, Nunag J, Nwafor L, Nwanguma U, Nyaboko J, O'Donnell K, O'Brien C, O'Brien L, O'Regan D, Odell N, Ogg G, Olaosebikan O, Oliver C, Omar Z, Orriss-Dib L, Osborne L, Osbourne R, Ostermann M, Overton C, Owen J, Oxton J, Pack J, Pacpaco E, Paddick S, Painter S, Pakzad A, Palmer S, Papineni P, Paques K, Paradowski K, Pareek M, Parfrey H, Pariante C, Parker S, Parkes M, Parmar J, Patale S, Patel B, Patel M, Patel S, Pattenadk D, Pavlides M, Payne S, Pearce L, Pearl JE, Peckham D, Pendlebury J, Peng Y, Pennington C, Peralta I, Perkins E, Peterkin Z, Peto T, Petousi N, Petrie J, Phipps J, Pimm J, Piper Hanley K, Pius R, Plant H, Plein S, Plekhanova T, Plowright M, Polgar O, Poll L, Porter J, Portukhay S, Powell N, Prabhu A, Pratt J, Price A, Price C, Price C, Price D, Price L, Price L, Prickett A, Propescu J, Pugmire S, Quaid S, Quigley J, Qureshi H, Qureshi IN, Radhakrishnan K, Ralser M, Ramos A, Ramos H, Rangeley J, Rangelov B, Ratcliffe L, Ravencroft P, Reddington A, Reddy R, Redfearn H, Redwood D, Reed A, Rees M, Rees T, Regan K, Reynolds W, Ribeiro C, Richards A, Richardson E, Rivera-Ortega P, Roberts K, Robertson E, Robinson E, Robinson L, Roche L, Roddis C, Rodger J, Ross A, Ross G, Rossdale J, Rostron A, Rowe A, Rowland A, Rowland J, Roy K, Roy M, Rudan I, Russell R, Russell E, Saalmink G, Sabit R, Sage EK, Samakomva T, Samani N, Sampson C, Samuel K, Samuel R, Sanderson A, Sapey E, Saralaya D, Sargant J, Sarginson C, Sass T, Sattar N, Saunders K, Saunders P, Saunders LC, Savill H, Saxon W, Sayer A, Schronce J, Schwaeble W, Scott K, Selby N, Sewell TA, Shah K, Shah P, Shankar-Hari M, Sharma M, Sharpe C, Sharpe M, Shashaa S, Shaw A, Shaw K, Shaw V, Shelton S, Shenton L, Shevket K, Short J, Siddique S, Siddiqui S, Sidebottom J, Sigfrid L, Simons G, Simpson J, Simpson N, Singh C, Singh S, Sissons D, Skeemer J, Slack K, Smith A, Smith D, Smith S, Smith J, Smith L, Soares M, Solano TS, Solly R, Solstice AR, Soulsby T, Southern D, Sowter D, Spears M, Spencer LG, Speranza F, Stadon L, Stanel S, Steele N, Steiner M, Stensel D, Stephens G, Stephenson L, Stern M, Stewart I, Stimpson R, Stockdale S, Stockley J, Stoker W, Stone R, Storrar W, Storrie A, Storton K, Stringer E, Strong-Sheldrake S, Stroud N, Subbe C, Sudlow CL, Suleiman Z, Summers C, Summersgill C, Sutherland D, Sykes DL, Sykes R, Talbot N, Tan AL, Tarusan L, Tavoukjian V, Taylor A, Taylor C, Taylor J, Te A, Tedd H, Tee CJ, Teixeira J, Tench H, Terry S, Thackray-Nocera S, Thaivalappil F, Thamu B, Thickett D, Thomas C, Thomas S, Thomas AK, Thomas-Woods T, Thompson T, Thompson AAR, Thornton T, Tilley J, Tinker N, Tiongson GF, Tobin M, Tomlinson J, Tong C, Touyz R, Tripp KA, Tunnicliffe E, Turnbull A, Turner E, Turner S, Turner V, Turner K, Turney S, Turtle L, Turton H, Ugoji J, Ugwuoke R, Upthegrove R, Valabhji J, Ventura M, Vere J, Vickers C, Vinson B, Wade E, Wade P, Wainwright T, Wajero LO, Walder S, Walker S, Walker S, Wall E, Wallis T, Walmsley S, Walsh JA, Walsh S, Warburton L, Ward TJC, Warwick K, Wassall H, Waterson S, Watson E, Watson L, Watson J, Welch C, Welch H, Welsh B, Wessely S, West S, Weston H, Wheeler H, White S, Whitehead V, Whitney J, Whittaker S, Whittam B, Whitworth V, Wight A, Wild J, Wilkins M, Wilkinson D, Williams N, Williams N, Williams J, Williams-Howard SA, Willicombe M, Willis G, Willoughby J, Wilson A, Wilson D, Wilson I, Window N, Witham M, Wolf-Roberts R, Wood C, Woodhead F, Woods J, Wormleighton J, Worsley J, Wraith D, Wrey Brown C, Wright C, Wright L, Wright S, Wyles J, Wynter I, Xu M, Yasmin N, Yasmin S, Yates T, Yip KP, Young B, Young S, Young A, Yousuf AJ, Zawia A, Zeidan L, Zhao B, Zongo O. Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study. Lancet Respir Med 2022; 10:761-775. [PMID: 35472304 PMCID: PMC9034855 DOI: 10.1016/s2213-2600(22)00127-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge. METHODS The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing. FINDINGS 2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters. INTERPRETATION The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials. FUNDING UK Research and Innovation and National Institute for Health Research.
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Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat Microbiol 2022; 7:1161-1179. [PMID: 35798890 PMCID: PMC9352574 DOI: 10.1038/s41564-022-01143-7] [Citation(s) in RCA: 266] [Impact Index Per Article: 133.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.
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Affiliation(s)
- Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Joe Grove
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Craig Wilkie
- School of Mathematics & Statistics, University of Glasgow, Glasgow, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Diego Cantoni
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sam Scott
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Nicola Logan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Maria Manali
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Agnieszka Szemiel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Elen Vink
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Patawee Asamaphan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | | | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - Matthew T G Holden
- Public Health Scotland, Glasgow, UK
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | | | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Surajit Ray
- School of Mathematics & Statistics, University of Glasgow, Glasgow, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
- NHS Greater Glasgow & Clyde, Glasgow, UK.
- London School of Hygiene and Tropical Medicine, London, UK.
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Nickbakhsh S, Hughes J, Christofidis N, Griffiths E, Shaaban S, Enright J, Smollett K, Nomikou K, Palmalux N, Tong L, Carmichael S, Sreenu VB, Orton R, Goldstein EJ, Tomb RM, Templeton K, Gunson RN, da Silva Filipe A, Milosevic C, Thomson E, Robertson DL, Holden MTG, Illingworth CJR, Smith-Palmer A. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Sci Rep 2022; 12:11735. [PMID: 35853960 PMCID: PMC9296497 DOI: 10.1038/s41598-022-15661-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/27/2022] [Indexed: 11/09/2022] Open
Abstract
Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These four outbreaks were curtailed within a week following implementation of control measures. The impact of student infections on the local community was short-term despite an underlying increase in community infections. Our study highlights the need for context-specific information in the formation of public health policy for higher educational settings.
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Affiliation(s)
- Sema Nickbakhsh
- Public Health Scotland, Meridian Court, 5 Cadogan Street, Glasgow, G2 6QE, UK.
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK.
| | - Joseph Hughes
- Public Health Scotland, Meridian Court, 5 Cadogan Street, Glasgow, G2 6QE, UK
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | | | - Emily Griffiths
- Public Health Scotland, Meridian Court, 5 Cadogan Street, Glasgow, G2 6QE, UK
| | - Sharif Shaaban
- Public Health Scotland, Meridian Court, 5 Cadogan Street, Glasgow, G2 6QE, UK
| | - Jessica Enright
- School of Computing Science, University of Glasgow, 18 Lilybank Gardens, Glasgow, G12 8RZ, UK
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Stephen Carmichael
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Vattipally B Sreenu
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Emily J Goldstein
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow Royal Infirmary, New Lister Building, Glasgow, G31 2ER, UK
| | - Rachael M Tomb
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow Royal Infirmary, New Lister Building, Glasgow, G31 2ER, UK
| | - Kate Templeton
- Royal Infirmary of Edinburgh, NHS Lothian, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Rory N Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow Royal Infirmary, New Lister Building, Glasgow, G31 2ER, UK
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Catriona Milosevic
- NHS Greater Glasgow and Clyde, Gartnavel General Hospital, 1055 Great Western Road, Glasgow, G12 0XH, UK
| | - Emma Thomson
- Public Health Scotland, Meridian Court, 5 Cadogan Street, Glasgow, G2 6QE, UK
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - David L Robertson
- Public Health Scotland, Meridian Court, 5 Cadogan Street, Glasgow, G2 6QE, UK
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Matthew T G Holden
- Public Health Scotland, Meridian Court, 5 Cadogan Street, Glasgow, G2 6QE, UK
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
| | - Christopher J R Illingworth
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK.
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK.
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK.
| | - Alison Smith-Palmer
- Public Health Scotland, Meridian Court, 5 Cadogan Street, Glasgow, G2 6QE, UK
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Gatfield E, Hughes J, Kumaran M, Doherty G, Daly M, Stancliffe M, Jephcott C, Wilson C, Smith S, Jadon R. P-226 Outcomes using induction chemotherapy followed by long-course chemoradiotherapy as total neoadjuvant therapy for locally advanced rectal cancer. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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39
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Tahir B, Reilly J, Tay J, Clinch H, Boindala N, Hughes J, Riley S, Roxby P, Tozer-Loft S, Aung T, Qureshi M, Das T, Hatton M. 146P Impact of heart, lung and oesophageal doses on overall survival (OS) of small cell lung cancer (SCLC) patients following radical chemo-radiotherapy (RT). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.02.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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40
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Wright DW, Harvey WT, Hughes J, Cox M, Peacock TP, Colquhoun R, Jackson B, Orton R, Nielsen M, Hsu NS, Harrison EM, de Silva TI, Rambaut A, Peacock SJ, Robertson DL, Carabelli AM. Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer. Virus Evol 2022; 8:veac023. [PMID: 35502202 PMCID: PMC9037374 DOI: 10.1093/ve/veac023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/03/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
COG-UK Mutation Explorer (COG-UK-ME, https://sars2.cvr.gla.ac.uk/cog-uk/-last accessed date 16 March 2022) is a web resource that displays knowledge and analyses on SARS-CoV-2 virus genome mutations and variants circulating in the UK, with a focus on the observed amino acid replacements that have an antigenic role in the context of the human humoral and cellular immune response. This analysis is based on more than 2 million genome sequences (as of March 2022) for UK SARS-CoV-2 data held in the CLIMB-COVID centralised data environment. COG-UK-ME curates these data and displays analyses that are cross-referenced to experimental data collated from the primary literature. The aim is to track mutations of immunological importance that are accumulating in current variants of concern and variants of interest that could alter the neutralising activity of monoclonal antibodies (mAbs), convalescent sera, and vaccines. Changes in epitopes recognised by T cells, including those where reduced T cell binding has been demonstrated, are reported. Mutations that have been shown to confer SARS-CoV-2 resistance to antiviral drugs are also included. Using visualisation tools, COG-UK-ME also allows users to identify the emergence of variants carrying mutations that could decrease the neutralising activity of both mAbs present in therapeutic cocktails, e.g. Ronapreve. COG-UK-ME tracks changes in the frequency of combinations of mutations and brings together the curated literature on the impact of those mutations on various functional aspects of the virus and therapeutics. Given the unpredictable nature of SARS-CoV-2 as exemplified by yet another variant of concern, Omicron, continued surveillance of SARS-CoV-2 remains imperative to monitor virus evolution linked to the efficacy of therapeutics.
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Affiliation(s)
- Derek W Wright
- MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Garscube Campus, 464 Bearsden Road,
Glasgow G61 1QH, UK
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Garscube Campus, 464 Bearsden Road,
Glasgow G61 1QH, UK
| | - MacGregor Cox
- Department of Medicine, University of
Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ,
UK
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary’s
Medical School, Imperial College London, Praed Street, London,
Westminster W2 1NY, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of
Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
- MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Garscube Campus, 464 Bearsden Road,
Glasgow G61 1QH, UK
| | - Ben Jackson
- Institute of Evolutionary Biology, University of
Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Garscube Campus, 464 Bearsden Road,
Glasgow G61 1QH, UK
| | - Morten Nielsen
- Department of Health Technology, Technical
University of Denmark, Lyngby DK-2800, Denmark
| | - Nienyun Sharon Hsu
- The Florey Institute for Host-Pathogen
Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical
School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX,
UK
| | | | - Ewan M Harrison
- Department of Medicine, University of
Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ,
UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton
CB10 1SA, UK
- Department of Public Health and Primary Care,
University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Thushan I de Silva
- The Florey Institute for Host-Pathogen
Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical
School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX,
UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of
Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Sharon J Peacock
- Department of Medicine, University of
Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ,
UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Garscube Campus, 464 Bearsden Road,
Glasgow G61 1QH, UK
| | - Alessandro M Carabelli
- Department of Medicine, University of
Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ,
UK
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41
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Hughes J, Harris M, Snaith B, Benn H. Comparison of scattered entrance skin dose burden in MSCT, CBCT, and X-ray for suspected scaphoid injury: Regional dose measurements in a phantom model. Radiography (Lond) 2022; 28:811-816. [PMID: 35183441 DOI: 10.1016/j.radi.2022.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Scaphoid radiography has poor sensitivity for acute fracture detection and often requires repeat delayed imaging. Although magnetic resonance (MR) imaging is considered the gold standard, computed tomography (CT) is often used as an alternative due to ease of access. Cone-Beam CT (CBCT) offers equivalent diagnostic efficacy to Multi Slice CT (MSCT) at reduced dose. We aimed to establish the difference in scattered dose between modalities for scaphoid imaging. METHODS Anatomical regional entrance surface dose measurements were taken at 3 regions on an anthropomorphic torso phantom positioned as a patient to a wrist phantom undergoing scaphoid imaging for three modalities (CBCT, MSCT, four-view projection radiography). Exposure factors were based on audit of clinical exposures. Each dose measurement was repeated three times per anatomical region, modality, exposure setting and projection. RESULTS Under unpaired T-test CBCT gave significantly lower mean dose at the neck (1.64 vs 18 mGy), chest (2.78 vs 8.01) and abdomen (1.288 vs 2.93) than MSCT (p < .0001). However CBCT had significantly higher mean dose than four-view radiography at the neck, chest and abdomen (0.031, 0.035, and 0.021 mGy) (p < .0001). CONCLUSION CBCT of the wrist carries a significantly higher scattered radiation dose to the neck, chest and abdomen than four view scaphoid radiography, but significantly lower scattered dose than MSCT of the wrist of equivalent diagnostic value. IMPLICATIONS FOR PRACTICE The use of CBCT for scaphoid injury carries significantly lower scattered dose to radio-sensitive structures investigated here than equivalent MSCT, and may be of greater use as an early cross-sectional investigation for suspected scaphoid fracture.
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Affiliation(s)
- J Hughes
- Mid Yorkshire Hospitals NHS Trust, Pinderfields Hospital, Aberford Road, Wakefield, WF1 4DG, United Kingdom.
| | - M Harris
- Mid Yorkshire Hospitals NHS Trust, Pinderfields Hospital, Aberford Road, Wakefield, WF1 4DG, United Kingdom
| | - B Snaith
- University of Bradford, Richmond Road, Bradford, BD7 1DP, United Kingdom
| | - H Benn
- Mid Yorkshire Hospitals NHS Trust, Pinderfields Hospital, Aberford Road, Wakefield, WF1 4DG, United Kingdom
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Xu R, Aranday-Cortes E, Leitch ECM, Hughes J, Singer JB, Sreenu V, Tong L, da Silva Filipe A, Bamford CGG, Rong X, Huang J, Wang M, Fu Y, McLauchlan J. The Evolutionary Dynamics and Epidemiological History of Hepatitis C Virus Genotype 6, Including Unique Strains from the Li Community of Hainan Island, China. Virus Evol 2022; 8:veac012. [PMID: 35600095 PMCID: PMC9115904 DOI: 10.1093/ve/veac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/17/2022] [Accepted: 02/15/2022] [Indexed: 12/09/2022] Open
Abstract
Abstract
Hepatitis C virus (HCV) is a highly diverse pathogen that frequently establishes a chronic long-term infection, but the origins and drivers of HCV diversity in the human population remain unclear. Previously unidentified strains of HCV genotype 6 (gt6) were recently discovered in chronically infected individuals of the Li ethnic group living in Baisha County, Hainan Island, China. The Li community, who were early settlers on Hainan Island, have a distinct host genetic background and cultural identity compared to other ethnic groups on the island and mainland China. In this report, we generated 33 whole virus genome sequences to conduct a comprehensive molecular epidemiological analysis of these novel gt6 strains in the context of gt6 isolates present in Southeast Asia. With the exception of one gt6a isolate, the Li gt6 sequences formed 3 novel clades from two lineages which constituted 3 newly assigned gt6 subtypes and 30 unassigned strains. Using Bayesian inference methods, we dated the most recent common ancestor for all available gt6 whole virus genome sequences to approximately 2767 BCE (95% HPD intervals, 3670 to 1397 BCE), which is far earlier than previous estimates. The substitution rate was 1.20 x 10-4 substitutions/site/year (s/s/y) and this rate varied across the genome regions, from 1.02 x 10-5 s/s/y in the 5ʹUTR region to 3.07 x 10-4 s/s/y in E2. Thus, our study on an isolated ethnic minority group within a small geographical area of Hainan Island has substantially increased the known diversity of HCV gt6, already acknowledged as the most diverse HCV genotype. The extant HCV gt6 sequences from this study were probably transmitted to the Li through at least three independent events dating perhaps from around 4000 years ago. This analysis describes deeper insight into basic aspects of HCV gt6 molecular evolution including the extensive diversity of gt6 sequences in the isolated Li ethnic group.
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Affiliation(s)
- Ru Xu
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong, China
| | | | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | - Xia Rong
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Jieting Huang
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Min Wang
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Yongshui Fu
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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43
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Chai H, Gu Q, Hughes J, Robertson DL. In silico prediction of HIV-1-host molecular interactions and their directionality. PLoS Comput Biol 2022; 18:e1009720. [PMID: 35134057 PMCID: PMC8856524 DOI: 10.1371/journal.pcbi.1009720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 02/18/2022] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) continues to be a major cause of disease and premature death. As with all viruses, HIV-1 exploits a host cell to replicate. Improving our understanding of the molecular interactions between virus and human host proteins is crucial for a mechanistic understanding of virus biology, infection and host antiviral activities. This knowledge will potentially permit the identification of host molecules for targeting by drugs with antiviral properties. Here, we propose a data-driven approach for the analysis and prediction of the HIV-1 interacting proteins (VIPs) with a focus on the directionality of the interaction: host-dependency versus antiviral factors. Using support vector machine learning models and features encompassing genetic, proteomic and network properties, our results reveal some significant differences between the VIPs and non-HIV-1 interacting human proteins (non-VIPs). As assessed by comparison with the HIV-1 infection pathway data in the Reactome database (sensitivity > 90%, threshold = 0.5), we demonstrate these models have good generalization properties. We find that the ‘direction’ of the HIV-1-host molecular interactions is also predictable due to different characteristics of ‘forward’/pro-viral versus ‘backward’/pro-host proteins. Additionally, we infer the previously unknown direction of the interactions between HIV-1 and 1351 human host proteins. A web server for performing predictions is available at http://hivpre.cvr.gla.ac.uk/.
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Affiliation(s)
- Haiting Chai
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- * E-mail:
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Lytras S, Hughes J, Martin D, Swanepoel P, de Klerk A, Lourens R, Kosakovsky Pond SL, Xia W, Jiang X, Robertson DL. Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination. Genome Biol Evol 2022; 14:evac018. [PMID: 35137080 PMCID: PMC8882382 DOI: 10.1093/gbe/evac018] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2022] [Indexed: 11/19/2022] Open
Abstract
The lack of an identifiable intermediate host species for the proximal animal ancestor of SARS-CoV-2, and the large geographical distance between Wuhan and where the closest evolutionary related coronaviruses circulating in horseshoe bats (members of the Sarbecovirus subgenus) have been identified, is fueling speculation on the natural origins of SARS-CoV-2. We performed a comprehensive phylogenetic study on SARS-CoV-2 and all the related bat and pangolin sarbecoviruses sampled so far. Determining the likely recombination events reveals a highly reticulate evolutionary history within this group of coronaviruses. Distribution of the inferred recombination events is nonrandom with evidence that Spike, the main target for humoral immunity, is beside a recombination hotspot likely driving antigenic shift events in the ancestry of bat sarbecoviruses. Coupled with the geographic ranges of their hosts and the sampling locations, across southern China, and into Southeast Asia, we confirm that horseshoe bats, Rhinolophus, are the likely reservoir species for the SARS-CoV-2 progenitor. By tracing the recombinant sequence patterns, we conclude that there has been relatively recent geographic movement and cocirculation of these viruses' ancestors, extending across their bat host ranges in China and Southeast Asia over the last 100 years. We confirm that a direct proximal ancestor to SARS-CoV-2 has not yet been sampled, since the closest known relatives collected in Yunnan shared a common ancestor with SARS-CoV-2 approximately 40 years ago. Our analysis highlights the need for dramatically more wildlife sampling to: 1) pinpoint the exact origins of SARS-CoV-2's animal progenitor, 2) the intermediate species that facilitated transmission from bats to humans (if there is one), and 3) survey the extent of the diversity in the related sarbecoviruses' phylogeny that present high risk for future spillovers.
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Affiliation(s)
- Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Darren Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Phillip Swanepoel
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Arné de Klerk
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Rentia Lourens
- Division of Neurosurgery, Department of Surgery, Neuroscience Institute, University of Cape Town, South Africa
| | | | - Wei Xia
- National School of Agricultural Institution and Development, South China Agricultural University, Guangzhou, China
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University (XJTLU), Suzhou, China
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Iannucci S, Harvey W, Hughes J, Robertson DL, Hutchinson E, Poyade M. Using Molecular Visualisation Techniques to Explain the Molecular Biology of SARS-CoV-2 Spike Protein Mutations to a General Audience. Adv Exp Med Biol 2022; 1388:129-152. [PMID: 36104619 DOI: 10.1007/978-3-031-10889-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Since the COVID-19 pandemic started in 2019, the virus responsible for the outbreak-SARS-CoV-2-has continued to evolve. Mutations of the virus' spike protein, the main protein driving infectivity and transmissibility, are especially concerning as they may allow the virus to improve its infectivity, transmissibility, and ability to evade the immune system. Understanding how specific molecular changes can alter the behaviour of a virus is challenging for non-experts, but this information helps us to understand the pandemic we are living through and the public health measures and interventions needed to bring it under control. In response to communication challenges arising from the COVID-19 pandemic, we recently developed an online educational application to explain the molecular biology of SARS-CoV-2 spike protein mutations to the general public. We used visualisation techniques such as 3D modelling and animation, which have been shown to be highly effective teaching tools in molecular biology, allowing the viewer to better understand protein structure, function, and dynamics. We also included interactive elements for users to learn actively by engaging with the digital content, and consequently improve information retention.This chapter presents the methodological and technological framework which we used to create this resource, the 'SARS-CoV-2 Spike Protein Mutation Explorer' (SSPME). It explains how molecular visualisation and 3D modelling software were used to develop accurate models of relevant proteins; how 3D animation software was used to accurately visualise the dynamic molecular processes of SARS-CoV-2 infection, transmission, and antibody evasion; and how game development software was used to compile the 3D models and animations into a comprehensive, informative interactive application on SARS-CoV-2 spike protein mutations. This chapter indicates how cutting-edge visualisation techniques and technologies can be used to improve science communication about complex topics in molecular biology and infection biology to the general public, something that is critical to gaining control of the continuing COVID-19 pandemic.
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Affiliation(s)
- Sarah Iannucci
- The School of Simulation and Visualisation, The Glasgow School of Art, Glasgow, UK.
- the Anatomy Facility, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| | - William Harvey
- MRC-University of Glasgow Centre for Virus Research, The University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, The University of Glasgow, Glasgow, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, The University of Glasgow, Glasgow, UK
| | - Edward Hutchinson
- MRC-University of Glasgow Centre for Virus Research, The University of Glasgow, Glasgow, UK
| | - Matthieu Poyade
- The School of Simulation and Visualisation, The Glasgow School of Art, Glasgow, UK
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46
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Boshier FAT, Venturini C, Stirrup O, Guerra-Assunção JA, Alcolea-Medina A, Becket AH, Byott M, Charalampous T, Filipe ADS, Frampton D, Glaysher S, Khan T, Kulasegara-Shylini R, Kele B, Monahan IM, Mollett G, Parker M, Pelosi E, Randell P, Roy S, Taylor JF, Weller SJ, Wilson-Davies E, Wade P, Williams R, Copas AJ, Cutino-Moguel T, Freemantle N, Hayward AC, Holmes A, Hughes J, Mahungu TW, Nebbia G, Nastouli E, Partridge DG, Pope CF, Price JR, Robson SC, Saeed K, Shin GY, de Silva TI, Snell LB, Thomson EC, Witney AA, Breuer J. The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. J Infect 2021; 83:693-700. [PMID: 34610391 PMCID: PMC8487101 DOI: 10.1016/j.jinf.2021.09.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Recently emerging SARS-CoV-2 variants have been associated with an increased rate of transmission within the community. We sought to determine whether this also resulted in increased transmission within hospitals. METHODS We collected viral sequences and epidemiological data of patients with community and healthcare associated SARS-CoV-2 infections, sampled from 16th November 2020 to 10th January 2021, from nine hospitals participating in the COG-UK HOCI study. Outbreaks were identified using ward information, lineage and pairwise genetic differences between viral sequences. RESULTS Mixed effects logistic regression analysis of 4184 sequences showed healthcare-acquired infections were no more likely to be identified as the Alpha variant than community acquired infections. Nosocomial outbreaks were investigated based on overlapping ward stay and SARS-CoV-2 genome sequence similarity. There was no significant difference in the number of patients involved in outbreaks caused by the Alpha variant compared to outbreaks caused by other lineages. CONCLUSIONS We find no evidence to support it causing more nosocomial transmission than previous lineages. This suggests that the stringent infection prevention measures already in place in UK hospitals contained the spread of the Alpha variant as effectively as other less transmissible lineages, providing reassurance of their efficacy against emerging variants of concern.
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Affiliation(s)
- Florencia A T Boshier
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Cristina Venturini
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Oliver Stirrup
- Institute for Global Health, University College London, London, United Kingdom
| | - José Afonso Guerra-Assunção
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Infection Sciences, Viapath, London, United Kingdom
| | - Angela H Becket
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom; School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Matthew Byott
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Dan Frampton
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; Division of Infection and Immunity, University College London, London, United Kingdom
| | - Sharon Glaysher
- Portsmouth Hospitals University NHS Trust, Queen Alexandra Hospital, Portsmouth PO6 3LY, United Kingdom
| | - Tabassum Khan
- Division of Infection, The Royal London Hospital, Barts Health, United Kingdom
| | | | - Beatrix Kele
- Division of Infection, The Royal London Hospital, Barts Health, United Kingdom
| | - Irene M Monahan
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom
| | - Guy Mollett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Matthew Parker
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, United Kingdom; Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom; Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield, United Kingdom
| | - Emanuela Pelosi
- Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Paul Randell
- Department of Infection and Immunity, North West London Pathology, London, United Kingdom
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Joshua F Taylor
- Department of Microbiology, South West London Pathology, Jenner Wing, St. George's Hospital, Blackshaw Road, London SW17 0QT, United Kingdom
| | - Sophie J Weller
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Eleri Wilson-Davies
- Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Phillip Wade
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Rachel Williams
- Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Andrew J Copas
- Institute for Global Health, University College London, London, United Kingdom
| | | | - Nick Freemantle
- Institute for Clinical Trials and Methodology, University College London, London, United Kingdom
| | - Andrew C Hayward
- Institute of Epidemiology and Health Care, University College London, London, United Kingdom
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, United Kingdom; Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Tabitha W Mahungu
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, United Kingdom
| | - Eleni Nastouli
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Cassie F Pope
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom; Infection Care Group, St George's University Hospitals NHS Foundation Trust, Blackshaw Road, London SW17 0QT, United Kingdom
| | - James R Price
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Samuel C Robson
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom; School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom; School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Kordo Saeed
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, United Kingdom; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Tremona Road, Southampton, United Kingdom
| | - Gee Yen Shin
- Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, United Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
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Hughes J. Recruiting a dental nurse. BDJ Team 2021. [PMCID: PMC8603895 DOI: 10.1038/s41407-021-0770-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Borzage M, Saunders A, Hughes J, McComb JG, Blüml S, King KS. The First Examination of Diagnostic Performance of Automated Measurement of the Callosal Angle in 1856 Elderly Patients and Volunteers Indicates That 12.4% of Exams Met the Criteria for Possible Normal Pressure Hydrocephalus. AJNR Am J Neuroradiol 2021; 42:1942-1948. [PMID: 34620589 PMCID: PMC8583275 DOI: 10.3174/ajnr.a7294] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/03/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Many patients with dementia may have comorbid or misdiagnosed normal pressure hydrocephalus, a treatable neurologic disorder. The callosal angle is a validated biomarker for normal pressure hydrocephalus with 93% diagnostic accuracy. Our purpose was to develop and evaluate an algorithm for automatically computing callosal angles from MR images of the brain. MATERIALS AND METHODS This article reports the results of analyzing callosal angles from 1856 subjects with 5264 MR images from the Open Access Series of Imaging Studies and the Alzheimer's Disease Neuroimaging Initiative databases. Measurement variability was examined between 2 neuroradiologists (n = 50) and between manual and automatic measurements (n = 281); from differences in simulated head orientation; and from real-world changes in patients with multiple examinations (n = 906). We evaluated the effectiveness of the automatic callosal angle to differentiate normal pressure hydrocephalus from Alzheimer disease in a simulated cohort. RESULTS The algorithm identified that 12.4% of subjects from these carefully screened cohorts had callosal angles of <90°, a published threshold for possible normal pressure hydrocephalus. The intraclass correlation coefficient was 0.97 for agreement between neuroradiologists and 0.90 for agreement between manual and automatic measurement. The method was robust to different head orientations. The median coefficient of variation for repeat examinations was 4.2% (Q1 = 3.1%, Q3 = 5.8%). The simulated classification of normal pressure hydrocephalus versus Alzheimer using the automatic callosal angle had an accuracy, sensitivity, and specificity of 0.87 each. CONCLUSIONS In even the most pristine research databases, analyses of the callosal angle indicate that some patients may have normal pressure hydrocephalus. The automatic callosal angle measurement can rapidly and objectively screen for normal pressure hydrocephalus in patients who would otherwise be misdiagnosed.
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Affiliation(s)
- M Borzage
- From the Fetal and Neonatal Institute, Division of Neonatology (M.B.)
- Department of Pediatrics (M.B.)
- Rudi Schulte Research Institute (M.B., A.S., S.B., K.S.K.), Santa Barbara, California
| | - A Saunders
- Department of Radiology (A.S., S.B.)
- Rudi Schulte Research Institute (M.B., A.S., S.B., K.S.K.), Santa Barbara, California
| | - J Hughes
- Department of Neuroradiology (J.H., K.S.K.), Barrow Neurological Institute, Phoenix, Arizona
| | - J G McComb
- Division of Neurosurgery (J.G.M.), Children's Hospital Los Angeles, Los Angeles, California
- Neurological Surgery (J.G.M.), Keck School of Medicine, University of Southern California, Los Angeles, California
| | - S Blüml
- Department of Radiology (A.S., S.B.)
- Rudi Schulte Research Institute (M.B., A.S., S.B., K.S.K.), Santa Barbara, California
| | - K S King
- Rudi Schulte Research Institute (M.B., A.S., S.B., K.S.K.), Santa Barbara, California
- Department of Neuroradiology (J.H., K.S.K.), Barrow Neurological Institute, Phoenix, Arizona
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Tonge M, Diaz-Delgado O, Hughes J, Maddox T, Alderson B. Effect of anaesthetic maintenance with propofol or isoflurane on ease of endoscopic duodenal intubation in dogs – preliminary results. Vet Anaesth Analg 2021. [DOI: 10.1016/j.vaa.2021.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, Wilson SJ. A prenylated dsRNA sensor protects against severe COVID-19. Science 2021; 374:eabj3624. [PMID: 34581622 PMCID: PMC7612834 DOI: 10.1126/science.abj3624] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022]
Abstract
Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that 2′-5′-oligoadenylate synthetase 1 (OAS1), through ribonuclease L, potently inhibits severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We show that a common splice-acceptor single-nucleotide polymorphism (Rs10774671) governs whether patients express prenylated OAS1 isoforms that are membrane-associated and sense-specific regions of SARS-CoV-2 RNAs or if they only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. In hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting that this antiviral defense is a major component of a protective antiviral response.
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Affiliation(s)
- Arthur Wickenhagen
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Elena Sugrue
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Spyros Lytras
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Srikeerthana Kuchi
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Marko Noerenberg
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Matthew L. Turnbull
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Colin Loney
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Vanessa Herder
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jay Allan
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Innes Jarmson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Natalia Cameron-Ruiz
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Margus Varjak
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Rute M. Pinto
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jeffrey Y. Lee
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Louisa Iselin
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natasha Palmalux
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Douglas G. Stewart
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Simon Swingler
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Edward J. D. Greenwood
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Thomas W. M. Crozier
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Quan Gu
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Emma L. Davies
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
| | - Monique Freire Santana
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
| | - Luiz Carlos de Lima Ferreira
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Alison Meynert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Graeme Grimes
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - ISARIC4C Investigators
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Joao Luiz Da Silva Filho
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Matthias Marti
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Eddie C. Y. Wang
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
| | - Antonia Ho
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ruth F. Jarrett
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Alfredo Castello
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - David L. Robertson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
| | - Massimo Palmarini
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Paul J. Lehner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Suzannah J. Rihn
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sam J. Wilson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
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