1
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Price JL, Ziv O, Pinckert ML, Lim A, Miska EA. rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments. Bioinformatics 2024; 40:btae193. [PMID: 38597883 PMCID: PMC11060868 DOI: 10.1093/bioinformatics/btae193] [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: 11/30/2023] [Revised: 03/06/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024] Open
Abstract
SUMMARY RNA (ribonucleic acid) molecules have secondary and tertiary structures in vivo which play a crucial role in cellular processes such as the regulation of gene expression, RNA processing and localization. The ability to investigate these structures will enhance our understanding of their function and contribute to the diagnosis and treatment of diseases caused by RNA dysregulation. However, there are no mature pipelines or packages for processing and analyzing complex in vivo RNA structural data. Here, we present rnaCrosslinkOO (RNA Crosslink Object-Oriented), a novel software package for the comprehensive analysis of data derived from the COMRADES (Crosslinking of Matched RNA and Deep Sequencing) method. rnaCrosslinkOO offers a comprehensive pipeline from raw sequencing reads to the identification and comparison of RNA structural features. It includes read processing and alignment, clustering of duplexes, data exploration, folding and comparisons of RNA structures. rnaCrosslinkOO also enables comparisons between conditions, the identification of inter-RNA interactions, and the incorporation of reactivity data to improve structure prediction. AVAILABILITY AND IMPLEMENTATION rnaCrosslinkOO is freely available to noncommercial users and implemented in R, with the source code and documentation accessible at https://CRAN.R-project.org/package=rnaCrosslinkOO. The software is supported on Linux, macOS, and Windows platforms.
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Affiliation(s)
- Jonathan L Price
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Omer Ziv
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
- Eleven Therapeutics, Cambridge, CB2 0RE, United Kingdom
| | - Malte L Pinckert
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom
| | - Andrew Lim
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Eric A Miska
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
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2
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Osman MM, Shanahan JK, Chu F, Takaki KK, Pinckert ML, Pagán AJ, Brosch R, Conrad WH, Ramakrishnan L. The C terminus of the mycobacterium ESX-1 secretion system substrate ESAT-6 is required for phagosomal membrane damage and virulence. Proc Natl Acad Sci U S A 2022; 119:e2122161119. [PMID: 35271388 PMCID: PMC8931374 DOI: 10.1073/pnas.2122161119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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] [Received: 12/08/2021] [Accepted: 01/15/2022] [Indexed: 12/21/2022] Open
Abstract
SignificanceTuberculosis (TB), an ancient disease of humanity, continues to be a major cause of worldwide death. The causative agent of TB, Mycobacterium tuberculosis, and its close pathogenic relative Mycobacterium marinum, initially infect, evade, and exploit macrophages, a major host defense against invading pathogens. Within macrophages, mycobacteria reside within host membrane-bound compartments called phagosomes. Mycobacterium-induced damage of the phagosomal membranes is integral to pathogenesis, and this activity has been attributed to the specialized mycobacterial secretion system ESX-1, and particularly to ESAT-6, its major secreted protein. Here, we show that the integrity of the unstructured ESAT-6 C terminus is required for macrophage phagosomal damage, granuloma formation, and virulence.
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Affiliation(s)
- Morwan M. Osman
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Jonathan K. Shanahan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Frances Chu
- Department of Microbiology, University of Washington, Seattle, WA 98105
| | - Kevin K. Takaki
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Malte L. Pinckert
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Antonio J. Pagán
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Roland Brosch
- Institut Pasteur, Université de Paris, CNRS UMR 3525, Unit for Integrated Mycobacterial Pathogenomics, 75724 Paris Cedex 15, France
| | - William H. Conrad
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Lalita Ramakrishnan
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, CB2 OQH Cambridge, United Kingdom
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
- Department of Microbiology, University of Washington, Seattle, WA 98105
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3
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Illingworth CJR, Hamilton WL, Jackson C, Warne B, Popay A, Meredith L, Hosmillo M, Jahun A, Fieldman T, Routledge M, Houldcroft CJ, Caller L, Caddy S, Yakovleva A, Hall G, Khokhar FA, Feltwell T, Pinckert ML, Georgana I, Chaudhry Y, Curran M, Parmar S, Sparkes D, Rivett L, Jones NK, Sridhar S, Forrest S, Dymond T, Grainger K, Workman C, Gkrania-Klotsas E, Brown NM, Weekes MP, Baker S, Peacock SJ, Gouliouris T, Goodfellow I, Angelis DD, Török ME. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events. Mol Biol Evol 2022; 39:6519868. [PMID: 35106603 PMCID: PMC8892943 DOI: 10.1093/molbev/msac025] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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] [Indexed: 01/19/2023] Open
Abstract
Identifying linked cases of infection is a critical component of the public health response to viral infectious diseases. In a clinical context, there is a need to make rapid assessments of whether cases of infection have arrived independently onto a ward, or are potentially linked via direct transmission. Viral genome sequence data are of great value in making these assessments, but are often not the only form of data available. Here, we describe A2B-COVID, a method for the rapid identification of potentially linked cases of COVID-19 infection designed for clinical settings. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and evolutionary analysis of genome sequences to assess whether data collected from cases of infection are consistent or inconsistent with linkage via direct transmission. A retrospective analysis of data from two wards at Cambridge University Hospitals NHS Foundation Trust during the first wave of the pandemic showed qualitatively different patterns of linkage between cases on designated COVID-19 and non-COVID-19 wards. The subsequent real-time application of our method to data from the second epidemic wave highlights its value for monitoring cases of infection in a clinical context.
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Affiliation(s)
- Christopher J R Illingworth
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom,MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom,Institut für Biologische Physik, Universität zu Köln, Köln, Germany,Corresponding author: E-mail:
| | - William L Hamilton
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | - Ben Warne
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ashley Popay
- Public Health England Field Epidemiology Unit, Cambridge Institute of Public Health, Cambridge, United Kingdom
| | - Luke Meredith
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Myra Hosmillo
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Aminu Jahun
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Tom Fieldman
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Matthew Routledge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | | | - Sarah Caddy
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Anna Yakovleva
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Grant Hall
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Fahad A Khokhar
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Theresa Feltwell
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Malte L Pinckert
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Iliana Georgana
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Yasmin Chaudhry
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Martin Curran
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Surendra Parmar
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Dominic Sparkes
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Lucy Rivett
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Nick K Jones
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Sushmita Sridhar
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom,Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Tom Dymond
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Kayleigh Grainger
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Chris Workman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Effrossyni Gkrania-Klotsas
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,MRC Epidemiology Unit, University of Cambridge, Level 3 Institute of Metabolic Science, Cambridge, United Kingdom,School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Michael P Weekes
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ian Goodfellow
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Daniela De Angelis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom,Public Health England, National Infection Service, London, United Kingdom
| | - M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
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4
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Illingworth CJR, Hamilton WL, Warne B, Routledge M, Popay A, Jackson C, Fieldman T, Meredith LW, Houldcroft CJ, Hosmillo M, Jahun AS, Caller LG, Caddy SL, Yakovleva A, Hall G, Khokhar FA, Feltwell T, Pinckert ML, Georgana I, Chaudhry Y, Curran MD, Parmar S, Sparkes D, Rivett L, Jones NK, Sridhar S, Forrest S, Dymond T, Grainger K, Workman C, Ferris M, Gkrania-Klotsas E, Brown NM, Weekes MP, Baker S, Peacock SJ, Goodfellow IG, Gouliouris T, de Angelis D, Török ME. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections. eLife 2021; 10:e67308. [PMID: 34425938 PMCID: PMC8384420 DOI: 10.7554/elife.67308] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 02/07/2021] [Accepted: 07/15/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2 is notable both for its rapid spread, and for the heterogeneity of its patterns of transmission, with multiple published incidences of superspreading behaviour. Here, we applied a novel network reconstruction algorithm to infer patterns of viral transmission occurring between patients and health care workers (HCWs) in the largest clusters of COVID-19 infection identified during the first wave of the epidemic at Cambridge University Hospitals NHS Foundation Trust, UK. Based upon dates of individuals reporting symptoms, recorded individual locations, and viral genome sequence data, we show an uneven pattern of transmission between individuals, with patients being much more likely to be infected by other patients than by HCWs. Further, the data were consistent with a pattern of superspreading, whereby 21% of individuals caused 80% of transmission events. Our study provides a detailed retrospective analysis of nosocomial SARS-CoV-2 transmission, and sheds light on the need for intensive and pervasive infection control procedures.
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Affiliation(s)
- Christopher JR Illingworth
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson WayCambridgeUnited Kingdom
- Institut für Biologische Physik, Universität zu KölnKölnGermany
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical SciencesCambridgeUnited States
| | - William L Hamilton
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Ben Warne
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Matthew Routledge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Ashley Popay
- Public Health England Field Epidemiology Unit, Cambridge Institute of Public Health, Forvie Site, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Chris Jackson
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson WayCambridgeUnited Kingdom
| | - Tom Fieldman
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Luke W Meredith
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Charlotte J Houldcroft
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Myra Hosmillo
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Aminu S Jahun
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Laura G Caller
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Sarah L Caddy
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Anna Yakovleva
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Grant Hall
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Fahad A Khokhar
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Theresa Feltwell
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Malte L Pinckert
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Iliana Georgana
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Martin D Curran
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Surendra Parmar
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Dominic Sparkes
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Lucy Rivett
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Nick K Jones
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Sushmita Sridhar
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome CampusHinxtonUnited Kingdom
| | - Sally Forrest
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Tom Dymond
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Kayleigh Grainger
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Chris Workman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Mark Ferris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Effrossyni Gkrania-Klotsas
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- MRC Epidemiology Unit, University of Cambridge, Level 3 Institute of Metabolic ScienceCambridgeUnited Kingdom
- University of Cambridge, School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Michael P Weekes
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Stephen Baker
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Sharon J Peacock
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome CampusHinxtonUnited Kingdom
- Public Health England, National Infection ServiceLondonUnited Kingdom
| | - Ian G Goodfellow
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Theodore Gouliouris
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Daniela de Angelis
- Institut für Biologische Physik, Universität zu KölnKölnGermany
- Public Health England, National Infection ServiceLondonUnited Kingdom
| | - M Estée Török
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
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5
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Tonkin-Hill G, Martincorena I, Amato R, Lawson ARJ, Gerstung M, Johnston I, Jackson DK, Park N, Lensing SV, Quail MA, Gonçalves S, Ariani C, Spencer Chapman M, Hamilton WL, Meredith LW, Hall G, Jahun AS, Chaudhry Y, Hosmillo M, Pinckert ML, Georgana I, Yakovleva A, Caller LG, Caddy SL, Feltwell T, Khokhar FA, Houldcroft CJ, Curran MD, Parmar S, Alderton A, Nelson R, Harrison EM, Sillitoe J, Bentley SD, Barrett JC, Torok ME, Goodfellow IG, Langford C, Kwiatkowski D. Patterns of within-host genetic diversity in SARS-CoV-2. eLife 2021; 10:e66857. [PMID: 34387545 PMCID: PMC8363274 DOI: 10.7554/elife.66857] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [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: 01/24/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.
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Affiliation(s)
| | | | | | | | | | | | | | - Naomi Park
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | | | | | | | | | | | - Luke W Meredith
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Grant Hall
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Aminu S Jahun
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Myra Hosmillo
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Malte L Pinckert
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Iliana Georgana
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Anna Yakovleva
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Laura G Caller
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Sarah L Caddy
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Theresa Feltwell
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Fahad A Khokhar
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of CambridgeCambridgeUnited Kingdom
| | | | | | | | | | | | | | - Ewan M Harrison
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- European Bioinformatics InstituteHinxtonUnited Kingdom
| | | | | | | | - M Estee Torok
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Ian G Goodfellow
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | | | - Dominic Kwiatkowski
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
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6
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Hamilton WL, Tonkin-Hill G, Smith ER, Aggarwal D, Houldcroft CJ, Warne B, Meredith LW, Hosmillo M, Jahun AS, Curran MD, Parmar S, Caller LG, Caddy SL, Khokhar FA, Yakovleva A, Hall G, Feltwell T, Pinckert ML, Georgana I, Chaudhry Y, Brown CS, Gonçalves S, Amato R, Harrison EM, Brown NM, Beale MA, Spencer Chapman M, Jackson DK, Johnston I, Alderton A, Sillitoe J, Langford C, Dougan G, Peacock SJ, Kwiatowski DP, Goodfellow IG, Torok ME. Genomic epidemiology of COVID-19 in care homes in the east of England. eLife 2021; 10:e64618. [PMID: 33650490 PMCID: PMC7997667 DOI: 10.7554/elife.64618] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 11/04/2020] [Accepted: 02/25/2021] [Indexed: 01/12/2023] Open
Abstract
COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1167 residents from 337 care homes were identified from a dataset of 6600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns - outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population.
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Affiliation(s)
- William L Hamilton
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | | | - Emily R Smith
- Cambridgeshire County CouncilCambridgeUnited Kingdom
| | - Dinesh Aggarwal
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
- Public Health EnglandColindaleUnited Kingdom
| | - Charlotte J Houldcroft
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Ben Warne
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | - Luke W Meredith
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Myra Hosmillo
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Aminu S Jahun
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Martin D Curran
- Public Health England Clinical Microbiology and Public Health LaboratoryCambridgeUnited Kingdom
| | - Surendra Parmar
- Public Health England Clinical Microbiology and Public Health LaboratoryCambridgeUnited Kingdom
| | - Laura G Caller
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
- The Francis Crick InstituteLondonUnited Kingdom
| | - Sarah L Caddy
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Fahad A Khokhar
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | - Anna Yakovleva
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Grant Hall
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Theresa Feltwell
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Malte L Pinckert
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Iliana Georgana
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | | | | | | | | | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health LaboratoryCambridgeUnited Kingdom
| | | | - Michael Spencer Chapman
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS TrustLondonUnited Kingdom
| | | | | | | | | | | | - Gordon Dougan
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | - Sharon J Peacock
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | | | - Ian G Goodfellow
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - M Estee Torok
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
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