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Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Bashton M, Batty EM, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Molina Mora JA, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C, de Oliveira T, Peto TE, Crook D, Corbett-Detig R, Iqbal Z. Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny. bioRxiv 2024:2024.04.29.591666. [PMID: 38746185 PMCID: PMC11092452 DOI: 10.1101/2024.04.29.591666] [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: 05/16/2024]
Abstract
The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 3,960,704 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of March 2023, viewable at https://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. Phase 2 of our project will address the fact that the data in the public archives is heavily geographically biased towards the Global North. We therefore have contributed new raw data to ENA/SRA from many countries including Ghana, Thailand, Laos, Sri Lanka, India, Argentina and Singapore. We will incorporate these, along with all public raw data submitted between March 2023 and the current day, into an updated set of assemblies, and phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.
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Affiliation(s)
- Martin Hunt
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Angie S Hinrichs
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
| | - Daniel Anderson
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Lily Karim
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA
| | - Bethany L Dearlove
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria
| | - Jeff Knaggs
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Bede Constantinides
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Philip W Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Gillian Rodger
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Teresa Street
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
| | - Sheila Lumley
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, John Radcliffe Hospital, Oxford, UK
| | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Christopher Ruis
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nicola de Maio
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Lucas N Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Dominic S Y Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Martin Avaro
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Reuben Ayivor-Djanie
- Laboratory for Medical Biotechnology and Biomanufacturing, International Centre for Genetic Engineering and Biotechnology, Tristie, Italy
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Elizabeth M Batty
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Denise De Belder
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Estefania Benedetti
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Andreas Bergthaler
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria
| | - Stefan A Boers
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Josefina Campos
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Rosina Afua Ampomah Carr
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, Ann Arbor, MI, USA
| | - Facundo Cuba
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Maria Elena Dattero
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Wanwisa Dejnirattisai
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok 10700, Thailand
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kwabena Obeng Duedu
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
- College of Life Sciences, Birmingham City University, Birmingham, UK
| | - Lukas Endler
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria
| | - Ilka Engelmann
- Pathogenesis and Control of Chronic and Emerging Infections, Univ Montpellier, INSERM, Etablissement Français du Sang, Virology Laboratory, CHU Montpellier, Montpellier, France
| | - Ngiambudulu M Francisco
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Jonas Fuchs
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Etienne Z Gnimpieba
- Biomedical Engineering Department, University of South Dakota, Sioux Falls, SD 57107
| | - Soraya Groc
- Virology Laboratory, CHU Montpellier, Montpellier, France
| | - Jones Gyamfi
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK
| | - Dennis Heemskerk
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nei-Yuan Hsiao
- Divison of Medical Virology, University of Cape Town and National Health Laboratory Service
| | - Matthew Huska
- Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | | | - Hanna Jarva
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Chandima Jeewandara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Bani Jolly
- Karkinos Healthcare Private Limited (KHPL), Aurbis Business Parks, Bellandur, Bengaluru, Karnataka, 560103, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | | | - Ravi Kant
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, 81-519 Gdynia, Poland
| | | | - Satu Kurkela
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maija Lappalainen
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marie Lataretu
- Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gathsaurie Neelika Malavige
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Tapfumanei Mashe
- Health System Strengthening Unit, World Health Organisation, Harare, Zimbabwe
| | - Juthathip Mongkolsapaya
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Jose Arturo Molina Mora
- Centro de investigación en Enfermedades Tropicales & Facultad de Microbiología, Universidad de Costa Rica, Costa Rica
| | - Collins M Morang'a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Bernard Mvula
- Public Health Institute of Malawi, Ministry of Health, Malawi
| | - Niranjan Nagarajan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Andrew Nelson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Joyce M Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Joana Paula da Paixão
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Marcus Panning
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tomas Poklepovich
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Peter K Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Diyanath Ranasinghe
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Mara Russo
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - James Emmanuel San
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710
- University of KwaZulu Natal, Durban, South Africa, 4001
| | - Nicholas D Sanderson
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
| | - Vinod Scaria
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
- Vishwanath Cancer Care Foundation (VCCF), Neelkanth Business Park Kirol Village, West Mumbai, Maharashtra, 400086, India
| | - Gavin Screaton
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tarja Sironen
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Darren Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Teemu Smura
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chayaporn Suphavilai
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Bryan Tegomoh
- Centre de Coordination des Opérations d'Urgences de Santé Publique, Ministere de Sante Publique, Cameroun
- University of California, Berkeley, Berkeley, California, USA
- Nebraska Department of Health and Human Services, Lincoln, Nebraska, USA
| | - Olli Vapalahti
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Robert J Wilkinson
- Francis Crick Institute, London, UK
- Centre for Infectious Diseases Research in Africa, University of Cape Town
- Imperial College London, UK
| | | | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, South Africa
| | - Timothy Ea Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Russell Corbett-Detig
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA
| | - Zamin Iqbal
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
- Milner Centre for Evolution, University of Bath, UK
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2
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Houwaart T, Scholz S, Pollock NR, Palmer WH, Kichula KM, Strelow D, Le DB, Belick D, Hülse L, Lautwein T, Wachtmeister T, Wollenweber TE, Henrich B, Köhrer K, Parham P, Guethlein LA, Norman PJ, Dilthey AT. Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures. HLA 2023; 102:28-43. [PMID: 36932816 PMCID: PMC10986641 DOI: 10.1111/tan.15020] [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: 05/30/2022] [Revised: 02/10/2023] [Accepted: 02/24/2023] [Indexed: 03/19/2023]
Abstract
Accurate and comprehensive immunogenetic reference panels are key to the successful implementation of population-scale immunogenomics. The 5Mbp Major Histocompatibility Complex (MHC) is the most polymorphic region of the human genome and associated with multiple immune-mediated diseases, transplant matching and therapy responses. Analysis of MHC genetic variation is severely complicated by complex patterns of sequence variation, linkage disequilibrium and a lack of fully resolved MHC reference haplotypes, increasing the risk of spurious findings on analyzing this medically important region. Integrating Illumina, ultra-long Nanopore, and PacBio HiFi sequencing as well as bespoke bioinformatics, we completed five of the alternative MHC reference haplotypes of the current (GRCh38/hg38) build of the human reference genome and added one other. The six assembled MHC haplotypes encompass the DR1 and DR4 haplotype structures in addition to the previously completed DR2 and DR3, as well as six distinct classes of the structurally variable C4 region. Analysis of the assembled haplotypes showed that MHC class II sequence structures, including repeat element positions, are generally conserved within the DR haplotype supergroups, and that sequence diversity peaks in three regions around HLA-A, HLA-B+C, and the HLA class II genes. Demonstrating the potential for improved short-read analysis, the number of proper read pairs recruited to the MHC was found to be increased by 0.06%-0.49% in a 1000 Genomes Project read remapping experiment with seven diverse samples. Furthermore, the assembled haplotypes can serve as references for the community and provide the basis of a structurally accurate genotyping graph of the complete MHC region.
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Affiliation(s)
- Torsten Houwaart
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Stephan Scholz
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Nicholas R. Pollock
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - William H. Palmer
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - Katherine M. Kichula
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - Daniel Strelow
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Duyen B. Le
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Dana Belick
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Lisanna Hülse
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Tobias Lautwein
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Thorsten Wachtmeister
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Tassilo E. Wollenweber
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Karl Köhrer
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Peter Parham
- Department of Structural Biology, and Department of Microbiology and ImmunologyStanford UniversityStanfordCaliforniaUSA
| | - Lisbeth A. Guethlein
- Department of Structural Biology, and Department of Microbiology and ImmunologyStanford UniversityStanfordCaliforniaUSA
| | - Paul J. Norman
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - Alexander T. Dilthey
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
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3
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Houwaart T, Belhaj S, Tawalbeh E, Nagels D, Fröhlich Y, Finzer P, Ciruela P, Sabrià A, Herrero M, Andrés C, Antón A, Benmoumene A, Asskali D, Haidar H, von Dahlen J, Nicolai J, Stiller M, Blum J, Lange C, Adelmann C, Schroer B, Osmers U, Grice C, Kirfel PP, Jomaa H, Strelow D, Hülse L, Pigulla M, Kreuzer P, Tyshaieva A, Weber J, Wienemann T, Kohns Vasconcelos M, Hoffmann K, Lübke N, Hauka S, Andree M, Scholz CJ, Jazmati N, Göbels K, Zotz R, Pfeffer K, Timm J, Ehlkes L, Walker A, Dilthey AT. Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021. Euro Surveill 2022; 27. [PMID: 36305336 PMCID: PMC9615415 DOI: 10.2807/1560-7917.es.2022.27.43.2101089] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Background Tracking person-to-person SARS-CoV-2 transmission in the population is important to understand the epidemiology of community transmission and may contribute to the containment of SARS-CoV-2. Neither contact tracing nor genomic surveillance alone, however, are typically sufficient to achieve this objective. Aim We demonstrate the successful application of the integrated genomic surveillance (IGS) system of the German city of Düsseldorf for tracing SARS-CoV-2 transmission chains in the population as well as detecting and investigating travel-associated SARS-CoV-2 infection clusters. Methods Genomic surveillance, phylogenetic analysis, and structured case interviews were integrated to elucidate two genetically defined clusters of SARS-CoV-2 isolates detected by IGS in Düsseldorf in July 2021. Results Cluster 1 (n = 67 Düsseldorf cases) and Cluster 2 (n = 36) were detected in a surveillance dataset of 518 high-quality SARS-CoV-2 genomes from Düsseldorf (53% of total cases, sampled mid-June to July 2021). Cluster 1 could be traced back to a complex pattern of transmission in nightlife venues following a putative importation by a SARS-CoV-2-infected return traveller (IP) in late June; 28 SARS-CoV-2 cases could be epidemiologically directly linked to IP. Supported by viral genome data from Spain, Cluster 2 was shown to represent multiple independent introduction events of a viral strain circulating in Catalonia and other European countries, followed by diffuse community transmission in Düsseldorf. Conclusion IGS enabled high-resolution tracing of SARS-CoV-2 transmission in an internationally connected city during community transmission and provided infection chain-level evidence of the downstream propagation of travel-imported SARS-CoV-2 cases.
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Affiliation(s)
- Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Samir Belhaj
- Düsseldorf Health Authority (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | - Emran Tawalbeh
- Düsseldorf Health Authority (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | - Dirk Nagels
- Düsseldorf Health Authority (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | - Yara Fröhlich
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Patrick Finzer
- Zotz
- Klimas, Düsseldorf, Germany
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Pilar Ciruela
- CIBER Epidemiologia y Salud Pública (CIBERESP), Instituto Salud Carlos III, Madrid, Spain
- Sub-Directorate General of Surveillance and Response to Public Health Emergencies, Public Health Agency of Catalonia, Barcelona, Spain
| | - Aurora Sabrià
- Sub-Directorate General of Surveillance and Response to Public Health Emergencies, Public Health Agency of Catalonia, Barcelona, Spain
| | - Mercè Herrero
- Sub-Directorate General of Surveillance and Response to Public Health Emergencies, Public Health Agency of Catalonia, Barcelona, Spain
| | - Cristina Andrés
- Microbiology Unit, Vall d’Hebron University Hospital, Barcelona, Spain
| | - Andrés Antón
- Microbiology Unit, Vall d’Hebron University Hospital, Barcelona, Spain
| | - Assia Benmoumene
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dounia Asskali
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Hussein Haidar
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Janina von Dahlen
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jessica Nicolai
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mygg Stiller
- Medizinische Laboratorien Düsseldorf, Düsseldorf, Germany
| | | | | | - Carla Adelmann
- Solingen Health Authority (Gesundheitsamt Solingen), Solingen, Germany
| | - Britta Schroer
- Solingen Health Authority (Gesundheitsamt Solingen), Solingen, Germany
| | - Ute Osmers
- MVZ SYNLAB Leverkusen GmbH, Leverkusen, Germany
| | | | | | | | - Daniel Strelow
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lisanna Hülse
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Moritz Pigulla
- Düsseldorf Health Authority (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | - Pascal Kreuzer
- Düsseldorf Health Authority (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | - Alona Tyshaieva
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jonas Weber
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias Wienemann
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Malte Kohns Vasconcelos
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Nadine Lübke
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sandra Hauka
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marcel Andree
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Klaus Göbels
- Düsseldorf Health Authority (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | - Rainer Zotz
- Department of Hemostasis and Transfusion Medicine, Heinrich Heine University Medical Center, Düsseldorf, Germany
- Zotz
- Klimas, Düsseldorf, Germany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jörg Timm
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Ehlkes
- Düsseldorf Health Authority (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | - Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexander T. Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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4
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Ebler J, Ebert P, Clarke WE, Rausch T, Audano PA, Houwaart T, Mao Y, Korbel JO, Eichler EE, Zody MC, Dilthey AT, Marschall T. Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes. Nat Genet 2022; 54:518-525. [PMID: 35410384 PMCID: PMC9005351 DOI: 10.1038/s41588-022-01043-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [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: 02/15/2021] [Accepted: 03/03/2022] [Indexed: 12/30/2022]
Abstract
Typical genotyping workflows map reads to a reference genome before identifying genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. Furthermore, short-read lengths limit the ability to characterize repetitive genomic regions, which are particularly challenging for fast k-mer-based genotypers. In the present study, we propose a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference together with k-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation-a process we refer to as genome inference. Compared with mapping-based approaches, PanGenie is more than 4 times faster at 30-fold coverage and achieves better genotype concordances for almost all variant types and coverages tested. Improvements are especially pronounced for large insertions (≥50 bp) and variants in repetitive regions, enabling the inclusion of these classes of variants in genome-wide association studies. PanGenie efficiently leverages the increasing amount of haplotype-resolved assemblies to unravel the functional impact of previously inaccessible variants while being faster compared with alignment-based workflows.
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Affiliation(s)
- Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter Ebert
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Tobias Rausch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, GeneCore, Heidelberg, Germany
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | | | - Alexander T Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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5
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Walker A, Houwaart T, Finzer P, Ehlkes L, Tyshaieva A, Damagnez M, Strelow D, Duplessis A, Nicolai J, Wienemann T, Tamayo T, Kohns Vasconcelos M, Hülse L, Hoffmann K, Lübke N, Hauka S, Andree M, Däumer MP, Thielen A, Kolbe-Busch S, Göbels K, Zotz R, Pfeffer K, Timm J, Dilthey AT. Characterization of SARS-CoV-2 infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting. Clin Infect Dis 2021; 74:1039-1046. [PMID: 34181711 PMCID: PMC8406867 DOI: 10.1093/cid/ciab588] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 04/19/2021] [Indexed: 01/02/2023] Open
Abstract
Background Tracing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission chains is still a major challenge for public health authorities, when incidental contacts are not recalled or are not perceived as potential risk contacts. Viral sequencing can address key questions about SARS-CoV-2 evolution and may support reconstruction of viral transmission networks by integration of molecular epidemiology into classical contact tracing. Methods In collaboration with local public health authorities, we set up an integrated system of genomic surveillance in an urban setting, combining a) viral surveillance sequencing, b) genetically based identification of infection clusters in the population, c) integration of public health authority contact tracing data, and d) a user-friendly dashboard application as a central data analysis platform. Results Application of the integrated system from August to December 2020 enabled a characterization of viral population structure, analysis of 4 outbreaks at a maximum care hospital, and genetically based identification of 5 putative population infection clusters, all of which were confirmed by contact tracing. The system contributed to the development of improved hospital infection control and prevention measures and enabled the identification of previously unrecognized transmission chains, involving a martial arts gym and establishing a link between the hospital to the local population. Conclusions Integrated systems of genomic surveillance could contribute to the monitoring and, potentially, improved management of SARS-CoV-2 transmission in the population.
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Affiliation(s)
- Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Patrick Finzer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Zotz
- Klimas, Düsseldorf, Germany
| | - Lutz Ehlkes
- Düsseldorf Health Department (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | - Alona Tyshaieva
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Maximilian Damagnez
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Strelow
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ashley Duplessis
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jessica Nicolai
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias Wienemann
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Teresa Tamayo
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Malte Kohns Vasconcelos
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lisanna Hülse
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Nadine Lübke
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sandra Hauka
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marcel Andree
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Susanne Kolbe-Busch
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Klaus Göbels
- Düsseldorf Health Department (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | | | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jörg Timm
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexander T Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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6
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Ramani A, Müller L, Ostermann PN, Gabriel E, Abida-Islam P, Müller-Schiffmann A, Mariappan A, Goureau O, Gruell H, Walker A, Andrée M, Hauka S, Houwaart T, Dilthey A, Wohlgemuth K, Omran H, Klein F, Wieczorek D, Adams O, Timm J, Korth C, Schaal H, Gopalakrishnan J. SARS-CoV-2 targets neurons of 3D human brain organoids. EMBO J 2020; 39:e106230. [PMID: 32876341 PMCID: PMC7560208 DOI: 10.15252/embj.2020106230] [Citation(s) in RCA: 317] [Impact Index Per Article: 79.3] [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: 07/13/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
COVID‐19 pandemic caused by SARS‐CoV‐2 infection is a public health emergency. COVID‐19 typically exhibits respiratory illness. Unexpectedly, emerging clinical reports indicate that neurological symptoms continue to rise, suggesting detrimental effects of SARS‐CoV‐2 on the central nervous system (CNS). Here, we show that a Düsseldorf isolate of SARS‐CoV‐2 enters 3D human brain organoids within 2 days of exposure. We identified that SARS‐CoV‐2 preferably targets neurons of brain organoids. Imaging neurons of organoids reveal that SARS‐CoV‐2 exposure is associated with altered distribution of Tau from axons to soma, hyperphosphorylation, and apparent neuronal death. Our studies, therefore, provide initial insights into the potential neurotoxic effect of SARS‐CoV‐2 and emphasize that brain organoids could model CNS pathologies of COVID‐19.
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Affiliation(s)
- Anand Ramani
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Philipp N Ostermann
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Elke Gabriel
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Pranty Abida-Islam
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Andreas Müller-Schiffmann
- Institute of Neuropathology, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Aruljothi Mariappan
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Olivier Goureau
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Henning Gruell
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Andreas Walker
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Marcel Andrée
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Sandra Hauka
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hygiene, University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hygiene, University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Kai Wohlgemuth
- Department of General Pediatrics, University Children's Hospital Muenster, Muenster, Germany
| | - Heymut Omran
- Department of General Pediatrics, University Children's Hospital Muenster, Muenster, Germany
| | - Florian Klein
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Ortwin Adams
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jörg Timm
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Carsten Korth
- Institute of Neuropathology, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
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7
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Walker A, Houwaart T, Wienemann T, Vasconcelos MK, Strelow D, Senff T, Hülse L, Adams O, Andree M, Hauka S, Feldt T, Jensen BE, Keitel V, Kindgen-Milles D, Timm J, Pfeffer K, Dilthey AT. Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020. ACTA ACUST UNITED AC 2020; 25. [PMID: 32524946 PMCID: PMC7336109 DOI: 10.2807/1560-7917.es.2020.25.22.2000746] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 01/12/2023]
Abstract
We whole-genome sequenced 55 SARS-CoV-2 isolates from Germany to investigate SARS-CoV-2 outbreaks in 2020 in the Heinsberg district and Düsseldorf. While the genetic structure of the Heinsberg outbreak indicates a clonal origin, reflecting superspreading dynamics from mid-February during the carnival season, distinct viral strains were circulating in Düsseldorf in March, reflecting the city’s international links. Limited detection of Heinsberg strains in the Düsseldorf area despite geographical proximity may reflect efficient containment and contact-tracing efforts.
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Affiliation(s)
- Andreas Walker
- These authors contributed equally.,Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,These authors contributed equally
| | - Tobias Wienemann
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Malte Kohns Vasconcelos
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Strelow
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tina Senff
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lisanna Hülse
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ortwin Adams
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marcel Andree
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sandra Hauka
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Torsten Feldt
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Björn-Erik Jensen
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Detlef Kindgen-Milles
- Department of Anaesthesiology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jörg Timm
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexander T Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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8
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Miladi M, Sokhoyan E, Houwaart T, Heyne S, Costa F, Grüning B, Backofen R. GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. Gigascience 2019; 8:giz150. [PMID: 31808801 PMCID: PMC6897289 DOI: 10.1093/gigascience/giz150] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/23/2019] [Accepted: 11/20/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND RNA plays essential roles in all known forms of life. Clustering RNA sequences with common sequence and structure is an essential step towards studying RNA function. With the advent of high-throughput sequencing techniques, experimental and genomic data are expanding to complement the predictive methods. However, the existing methods do not effectively utilize and cope with the immense amount of data becoming available. RESULTS Hundreds of thousands of non-coding RNAs have been detected; however, their annotation is lagging behind. Here we present GraphClust2, a comprehensive approach for scalable clustering of RNAs based on sequence and structural similarities. GraphClust2 bridges the gap between high-throughput sequencing and structural RNA analysis and provides an integrative solution by incorporating diverse experimental and genomic data in an accessible manner via the Galaxy framework. GraphClust2 can efficiently cluster and annotate large datasets of RNAs and supports structure-probing data. We demonstrate that the annotation performance of clustering functional RNAs can be considerably improved. Furthermore, an off-the-shelf procedure is introduced for identifying locally conserved structure candidates in long RNAs. We suggest the presence and the sparseness of phylogenetically conserved local structures for a collection of long non-coding RNAs. CONCLUSIONS By clustering data from 2 cross-linking immunoprecipitation experiments, we demonstrate the benefits of GraphClust2 for motif discovery under the presence of biological and methodological biases. Finally, we uncover prominent targets of double-stranded RNA binding protein Roquin-1, such as BCOR's 3' untranslated region that contains multiple binding stem-loops that are evolutionary conserved.
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Affiliation(s)
- Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Eteri Sokhoyan
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, University of Dusseldorf, Universitaetsstr. 1, 40225 Dusseldorf, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Stuebeweg 51, 79108 Freiburg, Germany
| | - Fabrizio Costa
- Department of Computer Science, University of Exeter, North Park Road, EX4 4QF Exeter, UK
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- ZBSA Centre for Biological Systems Analysis, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- ZBSA Centre for Biological Systems Analysis, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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9
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Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D, Taylor J, Backofen R, Nekrutenko A, Grüning B. Community-Driven Data Analysis Training for Biology. Cell Syst 2019; 6:752-758.e1. [PMID: 29953864 DOI: 10.1016/j.cels.2018.05.012] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [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: 11/28/2017] [Revised: 03/10/2018] [Accepted: 05/18/2018] [Indexed: 01/12/2023]
Abstract
The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.
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Affiliation(s)
- Bérénice Batut
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany
| | - Saskia Hiltemann
- Erasmus Medical Centre, Wytemaweg 80, Rotterdam 3015 CN, the Netherlands
| | - Andrea Bagnacani
- Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstraße 69, Rostock 18051, Germany
| | - Dannon Baker
- Johns Hopkins University, 3400 N Charles Street, Mudd Hall 144, Baltimore 21218, MD, USA
| | - Vivek Bhardwaj
- Department of Biology, Albert-Ludwigs-University, Schänzlestraße 1, Freiburg 79104, Germany
| | - Clemens Blank
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany
| | - Anthony Bretaudeau
- INRA, UMR IGEPP, BIPAA/GenOuest, INRIA/Irisa - Campus de Beaulieu, 35042 RENNES Cedex, France
| | | | - Martin Čech
- The Pennsylvania State University, 505 Wartik Lab, University Park, PA 16802, USA
| | - John Chilton
- The Pennsylvania State University, 505 Wartik Lab, University Park, PA 16802, USA
| | - Dave Clements
- Johns Hopkins University, 3400 N Charles Street, Mudd Hall 144, Baltimore 21218, MD, USA
| | - Olivia Doppelt-Azeroual
- Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 Institut Pasteur et CNRS), Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Anika Erxleben
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany
| | | | - Simon Gladman
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Youri Hoogstrate
- Erasmus Medical Centre, Wytemaweg 80, Rotterdam 3015 CN, the Netherlands
| | - Hans-Rudolf Hotz
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
| | - Torsten Houwaart
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany
| | - Pratik Jagtap
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Delphine Larivière
- The Pennsylvania State University, 505 Wartik Lab, University Park, PA 16802, USA
| | - Gildas Le Corguillé
- PMC, CNRS, FR2424, ABiMS, Station Biologique, Place Georges Teissier, Roscoff 29680, France
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg 79108, Germany
| | - Fabien Mareuil
- Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 Institut Pasteur et CNRS), Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Fidel Ramírez
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg 79108, Germany
| | - Devon Ryan
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg 79108, Germany
| | - Florian Christoph Sigloch
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany
| | - Nicola Soranzo
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Joachim Wolff
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany
| | - Pavankumar Videm
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany
| | - Markus Wolfien
- Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstraße 69, Rostock 18051, Germany
| | - Aisanjiang Wubuli
- Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, Dummerstorf 18196, Germany
| | - Dilmurat Yusuf
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany
| | | | - James Taylor
- Johns Hopkins University, 3400 N Charles Street, Mudd Hall 144, Baltimore 21218, MD, USA
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany.
| | - Anton Nekrutenko
- The Pennsylvania State University, 505 Wartik Lab, University Park, PA 16802, USA.
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany.
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10
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Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R. The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Res 2019; 45:W560-W566. [PMID: 28582575 PMCID: PMC5570170 DOI: 10.1093/nar/gkx409] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 03/02/2017] [Accepted: 05/31/2017] [Indexed: 01/23/2023] Open
Abstract
RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis. AVAILABILITY The RNA workbench is available at https://github.com/bgruening/galaxy-rna-workbench.
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Affiliation(s)
- Björn A Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, D-79110 Freiburg, Germany.,Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstr. 49, D-79104 Freiburg, Germany
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Dilmurat Yusuf
- Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, D-13125, Berlin, Germany
| | - Sebastian Will
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
| | - Anika Erxleben
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, D-79110 Freiburg, Germany
| | - Florian Eggenhofer
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, D-79110 Freiburg, Germany
| | - Torsten Houwaart
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, D-79110 Freiburg, Germany
| | - Bérénice Batut
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, D-79110 Freiburg, Germany
| | - Pavankumar Videm
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, D-79110 Freiburg, Germany
| | - Andrea Bagnacani
- Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstr. 69, D-18051 Rostock, Germany
| | - Markus Wolfien
- Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstr. 69, D-18051 Rostock, Germany
| | - Steffen C Lott
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Youri Hoogstrate
- Department of Urology, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstr. 69, D-18051 Rostock, Germany
| | - Steve Hoffmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, D-13125, Berlin, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, D-13125, Berlin, Germany.,Departments of Biology and Computer Science, Humboldt University, Unter den Linden 6, D-10099 Berlin
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.,Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, Germany.,Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, D-79110 Freiburg, Germany.,Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstr. 49, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Schänzlestr. 18, D-79104 Freiburg, Germany
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11
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Johnston CM, Rog-Zielinska EA, Wülfers EM, Houwaart T, Siedlecka U, Naumann A, Nitschke R, Knöpfel T, Kohl P, Schneider-Warme F. Optogenetic targeting of cardiac myocytes and non-myocytes: Tools, challenges and utility. Prog Biophys Mol Biol 2017; 130:140-149. [PMID: 28919131 DOI: 10.1016/j.pbiomolbio.2017.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/08/2017] [Accepted: 09/09/2017] [Indexed: 10/18/2022]
Abstract
In optogenetics, light-activated proteins are used to monitor and modulate cellular behaviour with light. Combining genetic targeting of distinct cellular populations with defined patterns of optical stimulation enables one to study specific cell classes in complex biological tissues. In the current study we attempted to investigate the functional relevance of heterocellular electrotonic coupling in cardiac tissue in situ. In order to do that, we used a Cre-Lox approach to express the light-gated cation channel Channelrhodopsin-2 (ChR2) specifically in either cardiac myocytes or non-myocytes. Despite high specificity when using the same Cre driver lines in a previous study in combination with a different optogenetic probe, we found patchy off-target ChR2 expression in cryo-sections and extended z-stack imaging through the ventricular wall of hearts cleared using CLARITY. Based on immunohistochemical analysis, single-cell electrophysiological recordings and whole-genome sequencing, we reason that non-specificity is caused on the Cre recombination level. Our study highlights the importance of careful design and validation of the Cre recombination targets for reliable cell class specific expression of optogenetic tools.
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Affiliation(s)
- Callum M Johnston
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg - Bad Krozingen, Medical Faculty of the University of Freiburg, Freiburg, Germany; National Heart and Lung Institute, Imperial College London, Harefield, United Kingdom
| | - Eva A Rog-Zielinska
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg - Bad Krozingen, Medical Faculty of the University of Freiburg, Freiburg, Germany; National Heart and Lung Institute, Imperial College London, Harefield, United Kingdom
| | - Eike M Wülfers
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg - Bad Krozingen, Medical Faculty of the University of Freiburg, Freiburg, Germany
| | - Torsten Houwaart
- Bioinformatics, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Urszula Siedlecka
- National Heart and Lung Institute, Imperial College London, Harefield, United Kingdom
| | - Angela Naumann
- Life Imaging Center, Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Roland Nitschke
- Life Imaging Center, Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Thomas Knöpfel
- Faculty of Medicine, Department of Medicine, Imperial College London, London, United Kingdom
| | - Peter Kohl
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg - Bad Krozingen, Medical Faculty of the University of Freiburg, Freiburg, Germany; National Heart and Lung Institute, Imperial College London, Harefield, United Kingdom
| | - Franziska Schneider-Warme
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg - Bad Krozingen, Medical Faculty of the University of Freiburg, Freiburg, Germany; National Heart and Lung Institute, Imperial College London, Harefield, United Kingdom.
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12
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Uhl M, Houwaart T, Corrado G, Wright PR, Backofen R. Computational analysis of CLIP-seq data. Methods 2017; 118-119:60-72. [PMID: 28254606 DOI: 10.1016/j.ymeth.2017.02.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 10/04/2016] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
CLIP-seq experiments are currently the most important means for determining the binding sites of RNA binding proteins on a genome-wide level. The computational analysis can be divided into three steps. In the first pre-processing stage, raw reads have to be trimmed and mapped to the genome. This step has to be specifically adapted for each CLIP-seq protocol. The next step is peak calling, which is required to remove unspecific signals and to determine bona fide protein binding sites on target RNAs. Here, both protocol-specific approaches as well as generic peak callers are available. Despite some peak callers being more widely used, each peak caller has its specific assets and drawbacks, and it might be advantageous to compare the results of several methods. Although peak calling is often the final step in many CLIP-seq publications, an important follow-up task is the determination of binding models from CLIP-seq data. This is central because CLIP-seq experiments are highly dependent on the transcriptional state of the cell in which the experiment was performed. Thus, relying solely on binding sites determined by CLIP-seq from different cells or conditions can lead to a high false negative rate. This shortcoming can, however, be circumvented by applying models that predict additional putative binding sites.
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Affiliation(s)
- Michael Uhl
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany
| | - Torsten Houwaart
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany
| | - Gianluca Corrado
- Department of Information Engineering and Computer Science, University of Trento, Italy
| | - Patrick R Wright
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
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13
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Kleinkauf R, Houwaart T, Backofen R, Mann M. antaRNA--Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization. BMC Bioinformatics 2015; 16:389. [PMID: 26581440 PMCID: PMC4652366 DOI: 10.1186/s12859-015-0815-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 07/20/2015] [Accepted: 10/20/2015] [Indexed: 01/14/2023] Open
Abstract
Background Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA’s 3D structure. Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within biotechnological applications, is lacking the feature of incorporating pseudoknot structures into the design. Hairpin-(H)- and kissing hairpin-(K)-type pseudoknots cover a wide range of biologically functional pseudoknots and can be represented on a secondary structure level. Results The RNA inverse folding program antaRNA, which takes secondary structure, target GC-content and sequence constraints as input, is extended to provide solutions for such H- and K-type pseudoknotted secondary structure constraint. We demonstrate the easy and flexible interchangeability of modules within the antaRNA framework by incorporating pKiss as structure prediction tool capable of predicting the mentioned pseudoknot types. The performance of the approach is demonstrated on a subset of the Pseudobase ++ dataset. Conclusions This new service is available via a standalone version and is also part of the Freiburg RNA Tools webservice. Furthermore, antaRNA is available in Galaxy and is part of the RNA-workbench Docker image.
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Affiliation(s)
- Robert Kleinkauf
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany.
| | - Torsten Houwaart
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany.
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany. .,Center for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany. .,Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany. .,Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, 1870, Denmark.
| | - Martin Mann
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany.
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14
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Vijayaraghavan S, Auwärter W, Ecija D, Seufert K, Rusponi S, Houwaart T, Sautet P, Bocquet ML, Thakur P, Stepanow S, Schlickum U, Etzkorn M, Brune H, Barth JV. Restoring the Co magnetic moments at interfacial Co-porphyrin arrays by site-selective uptake of iron. ACS Nano 2015; 9:3605-3616. [PMID: 25856066 DOI: 10.1021/nn507346x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Magnetochemistry recently emerged as a promising approach to control addressable spin arrays on surfaces. Here we report on the binding, spatial ordering, and magnetic properties of Fe on a highly regular Co-tetraphenylporphyrin (Co-TPP) template and highlight how the Fe controls the magnetism of the Co centers. As evidenced by scanning tunneling microscopy (STM) single Fe atoms attach to the saddle-shape conformers site-selectively in a unique coordination environment offered through a heptamer defined by the Co-N-C-C-C-N cyclic subunit. While the magnetic moment of Co is quenched for bare Co-TPP/Ag(111), the Fe presence revives it. Our X-ray magnetic circular dichroism (XMCD) experiments, complemented by density functional theory (DFT) calculations, evidence a ferromagnetic coupling between the Fe and the Co center concomitant with a complex charge redistribution involving the porphyrin ligand. Thus, we demonstrate an unusual metalloporphyrin coordination geometry that opens pathways to spatially order and engineer magnetic moments in surface-based nanostructures.
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Affiliation(s)
| | - Willi Auwärter
- †Physik-Department E20, Technische Universität München, D-85748 Garching, Germany
| | - David Ecija
- †Physik-Department E20, Technische Universität München, D-85748 Garching, Germany
| | - Knud Seufert
- †Physik-Department E20, Technische Universität München, D-85748 Garching, Germany
| | - Stefano Rusponi
- ‡Institute of Condensed Matter Physics (ICMP), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Torsten Houwaart
- §Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon, Laboratoire de Chimie, F-69364 Cedex 07 Lyon, France
| | - Philippe Sautet
- §Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon, Laboratoire de Chimie, F-69364 Cedex 07 Lyon, France
| | - Marie-Laure Bocquet
- §Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon, Laboratoire de Chimie, F-69364 Cedex 07 Lyon, France
| | - Pardeep Thakur
- ⊥European Synchrotron Radiation Facility (ESRF), B.P. 220, Grenoble Cedex F-38043, France
| | - Sebastian Stepanow
- ∥Department of Materials, ETH Zürich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Uta Schlickum
- ‡Institute of Condensed Matter Physics (ICMP), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- #Max Planck Institut für Festkörperforschung, D-70569 Stuttgart, Germany
| | - Markus Etzkorn
- ‡Institute of Condensed Matter Physics (ICMP), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- #Max Planck Institut für Festkörperforschung, D-70569 Stuttgart, Germany
| | - Harald Brune
- ‡Institute of Condensed Matter Physics (ICMP), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Johannes V Barth
- †Physik-Department E20, Technische Universität München, D-85748 Garching, Germany
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15
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Ebenhöh O, Houwaart T, Lokstein H, Schlede S, Tirok K. A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence. Biosystems 2011; 103:196-204. [DOI: 10.1016/j.biosystems.2010.10.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 10/13/2010] [Accepted: 10/15/2010] [Indexed: 10/18/2022]
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