Publications

Some publications from our partners

Genetic structure of SARS-CoV-2 in Western Germany reflects clonal superspreading and multiple independent introduction events

Andreas Walker1,#, Torsten Houwaart2,#, Tobias Wienemann2 , Malte Kohns Vasconcelos2 , Daniel Strelow2 , Tina Senff1 , Lisanna Hülse2 , Ortwin Adams1 , Marcel Andree1 , Sandra Hauka1 , Torsten Feldt3 , Björn-Erik Jensen3 , Verena Keitel3 , Detlef KindgenMilles4 , Jörg Timm1 , Klaus Pfeffer2 , Alexander T Dilthey2,*

# contributed equally * alexander.dilthey@med.uni-duesseldorf.de

1 Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany 2 Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany 3 Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany 4 Department of Anaesthesiology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

The whole-genome sequenced 55 SARS-CoV-2 isolates from Western Germany and investigated the genetic structure of SARS-CoV-2 outbreaks in the Heinsberg district and Düsseldorf. While the genetic structure of the Heinsberg outbreak indicates a clonal origin, reflective of superspreading dynamics during the carnival season, distinct viral strains are circulating in Düsseldorf, 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. 

Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics

Christoph B. Messner1,#, Vadim Demichev1,2,#, Daniel Wendisch3, Laura Michalick4, Matthew White1, Anja Freiwald5, Kathrin Textoris-Taube5, Spyros I. Vernardis1, Anna-Sophia Egger1, Marco Kreidl1, Daniela Ludwig6, Christiane Kilian6, Federica Agostini6, Aleksej Zelezniak1,7, Charlotte Thibeault3, Moritz Pfeiffer3, Stefan Hippenstiel3 Andreas Hocke3, Christof von Kalle8, Archie Campbell9,10, Caroline Hayward11, David J. Porteous9, Riccardo E. Marioni9, Claudia Langenberg1,12, Kathryn S. Lilley2, Wolfgang M. Kuebler4, Michael Mülleder5, Christian Drosten13, Martin Witzenrath3, Florian Kurth3,14, Leif Erik Sander3and Markus Ralser1,6,15*

1The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom, 2Department of Biochemistry, The University of Cambridge, Cambridge, CB21GA, United Kingdom, 3Charité Universitätsmedizin Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany, 4Charité Universitätsmedizin Berlin, Institute of Physiology, 10117 Berlin, Germany, 5Charité Universitätsmedizin Berlin, Core Facility – High Throughput Mass Spectrometry, 10117 Berlin, Germany, 6Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany, 7 Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96,Sweden, 8Berlin Institute of Health (BIH), and Charité Universitätsmedizin, Clinical Study Center (CSC), 10117 Berlin, Germany, 9 Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU, United Kingdom, 10 Usher Institute, University of Edinburgh, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4UX, United Kingdom, 11 MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom, 12 MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, United Kingdom, 13Charité Universitätsmedizin Berlin, Department of Virology, 10117 Berlin, Germany, 14Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, 15Lead Contact* Correspondence: markus.ralser@charite.de #These authors contributed equally 

The COVID-19 pandemic is an unprecedented global challenge. Highly variable in its presentation, spread and clinical outcome, novel point-of-care diagnostic classifiers are urgently required. Here, we describe a set of COVID-19 clinical classifiers discovered using a newly designed low-cost high throughput mass spectrometry-based platform. Introducing a new sample preparation pipeline coupled with short-gradient high-flow liquid chromatography and mass spectrometry, our methodology facilitates clinical implementation and increases sample throughput and quantification precision. Providing a rapid assessment of serum or plasma samples at scale, we report 27 biomarkers that distinguish mild and severe forms of COVID-19, of which some may have potential as therapeutic targets. These proteins highlight the role of complement factors, the coagulation system, inflammation modulators as well as pro-inflammatory signalling upstream and downstream of Interleukin 6. Application of novel methodologies hence transforms proteomics from a research tool into a rapid-response, clinically actionable technology adaptable to infectious outbreaks.

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

Waradon Sungnak  1 , Ni Huang1, Christophe Bécavin  2, Marijn Berg3,4, Rachel Queen5,Monika Litvinukova1,6, Carlos Talavera-López1, Henrike Maatz6, Daniel Reichart7,Fotios Sampaziotis  8,9,10, Kaylee B. Worlock11, Masahiro Yoshida  11, Josephine L. Barnes11 and HCA Lung Biological Network

1Wellcome Sanger Institute, Cambridge, UK. 2Université Côte d’Azur, CNRS, IPMC, Sophia-Antipolis, France. 3Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands. 4Groningen Research Institute for Asthma and COPD, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands. 5Bioinformatics Core Facility, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK. 6Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. 7Department of Genetics, Harvard Medical School, Boston, MA, USA. 8Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK. 9Department of Medicine, Addenbrookes Hospital, Cambridge, UK. 10Cambridge Liver Unit, Cambridge University Hospitals, Cambridge, UK. 11UCL Respiratory, Division of Medicine, University College London, London, UK. *A list of authors and their affiliations appears at the end of the paper. e-mail: ws4@sanger.ac.uk; lung@humancellatlas.org

We investigated SARS-CoV-2 potential tropism by surveying expression of viral entry-associated genes in single-cell RNA-sequencing data from multiple tissues from healthy human donors. We co-detected these transcripts in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission. These genes are co-expressed in nasal epithelial cells with genes involved in innate immunity, highlighting the cells’ potential role in initial viral infection, spread and clearance. The study offers a useful resource for further lines of inquiry with valuable clinical samples from COVID-19 patients and we provide our data in a comprehensive, open and user-friendly fashion at www.covid19cellatlas.org.

Studying the pathophysiology of coronavirus disease 2019 – a protocol for the Berlin prospective COVID-19 patient cohort (Pa- COVID-19)

Florian Kurth1,2*#, Maria Roennefarth3*, Charlotte Thibeault1, Victor M. Corman4, Holger Müller-Redetzky1,Mirja Mittermaier1, Christoph Ruwwe-Glösenkamp1, Alexander Krannich3, Sein Schmidt3, Lucie Kretzler3, Chantip Dang-Heine3, Matthias Rose5, Michael Hummel6, Andreas Hocke1, Ralf H. Hübner1, Marcus A. Mall7, Jobst Röhmel7, Ulf Landmesser8, Burkert Pieske9, Samuel Knauss10, Matthias Endres10, Joachim Spranger11, Frank P. Mockenhaupt12, Frank Tacke13, Sascha Treskatsch14, Stefan Angermair14, Britta Siegmund 15, Claudia Spies16, Steffen Weber-Carstens16, Kai-Uwe Eckardt17, Alexander Uhrig1, Thomas Zoller1, Christian Drosten4, Norbert Suttorp1, Martin Witzenrath1, Stefan Hippenstiel1, Christof von Kalle3#, Leif Erik Sander1

1 Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 2Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University, Medical Center Hamburg-Eppendorf, Hamburg, Germany, 3 Clinical Study Center (CSC), Berlin Institute of Health, and Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany, 4 Institute of Virology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, HumboldtUniversität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 5Department of Psychosomatic Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 6 Central Biobank Charité (ZeBanC), Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 7 Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 8 Department of Cardiology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, HumboldtUniversität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 9 Medical Department, Division of Cardiology, Campus Virchow-Klinikum, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 10 Department of Neurology with Experimental Neurology and Center for Stroke Research Berlin, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin,Germany, 11 Department of Endocrinology and Metabolism, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 12 Institute of Tropical Medicine and International Health Berlin, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 13 Department of Hepatology and Gastroenterology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 14Department of Anaesthesiology and Intensive Care Medicine, Charite Campus Benjamin Franklin, Charité -Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 15 Medical Department, Division of Gastroenterology, Infectious Diseases, Rheumatology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 16Department of Anesthesiology and Operative Intensive Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, 17 Department of Nephrology and Internal Intensive Care Medicine, Charité – , Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.

Purpose Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide causing a global health emergency. Pa-COVID-19 aims to provide comprehensive data on clinical course, pathophysiology, immunology and outcome of COVID-19, in order to identify prognostic biomarkers, clinical scores, and therapeutic targets for improved clinical management and preventive interventions. Methods Pa-COVID-19 is a prospective observational cohort study of patients with confirmed SARS-CoV-2 infection treated at Charite – Universitaetsmedizin Berlin. We collect data on epidemiology, demography, medical history, symptoms, clinical course, pathogen testing and treatment. Systematic, serial blood sampling will allow deep molecular and immunological phenotyping, transcriptomic profiling, and comprehensive biobanking. Longitudinal data and sample collection during hospitalization will be supplemented by long-term follow-up. Results Outcome measures include the WHO clinical ordinal scale on day 15 and clinical, functional and health-related quality of life assessments at discharge and during follow-up. We developed a scalable dataset to (i) suit national standards of care (ii) facilitate comprehensive data collection in medical care facilities with varying resources and (iii) allow for rapid implementation of interventional trials based on the standardized study design and data collection. We propose this scalable protocol as blueprint for harmonized data collection and deep phenotyping in COVID-19 in Germany. Conclusion We established a basic platform for harmonized, scalable data collection, pathophysiological analysis, and deep phenotyping of COVID-19, which enables rapid generation of evidence for improved medical care and identification of candidate therapeutic and preventive strategies. The electronic database accredited for interventional trials allows fast trial implementation for candidate therapeutic agents.

SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues

Carly G. K. Ziegler1,2,3,4,5,6*, Samuel J. Allon2,4,5,7,*, Sarah K. Nyquist2,4,5,8,9,*, Ian M. Mbano10,11,*, Vincent N. Miao1,2,4,5, Constantine N. Tzouanas1,2,4,5, Yuming Cao12, Ashraf S. Yousif4, Julia Bals4, Blake M. Hauser4,13, Jared Feldman4,13,14, Christoph Muus5,15, Marc H. Wadsworth II2,3,4,5,7, Samuel W. Kazer2,4,5,7, Travis K. Hughes1,4,5,16, Benjamin Doran2,4,5,7,17,18, G. James Gatter2,4,5, Marko Vukovic2,3,4,5,7, Faith Taliaferro5,18, Benjamin E. Mead2,3,4,5,7, Zhiru Guo12, Jennifer P. Wang12, Delphine Gras19, Magali Plaisant20, Meshal Ansari21,22,23, Ilias Angelidis21,22, Heiko Adler22,24, Jennifer M.S. Sucre25, Chase J. Taylor26, Brian Lin27, Avinash Waghray27, Vanessa Mitsialis18,28, Daniel F. Dwyer29, Kathleen M. Buchheit29, Joshua A. Boyce29, Nora A. Barrett29, Tanya M. Laidlaw29, Shaina L. Carroll30, Lucrezia Colonna31, Victor Tkachev17,32,33, Christopher W. Peterson34,35, Alison Yu17,36, Hengqi Betty Zheng36, Hannah P. Gideon37,38, Caylin G. Winchell37,38,39, Philana Ling Lin38,40,41, Colin D. Bingle42, Scott B. Snapper18,28, Jonathan A. Kropski43,44,45, Fabian J. Theis23, Herbert B. Schiller21,22, Laure-Emmanuelle Zaragosi20, Pascal Barbry20 Alasdair Leslie10,46, Hans-Peter Kiem34,35, JoAnne L. Flynn37,38, Sarah M. Fortune4,5,47, Bonnie Berger9,48, Robert W. Finberg12, Leslie S. Kean17,32,33,  Manuel Garber12, Aaron G. Schmidt4,13, Daniel Lingwood4,  Alex K. Shalek1-8,16,33,49,#, Jose Ordovas-Montanes5,16,18,49,#, HCA Lung Biological Network
 
HCA Lung Biological Network Author List: Nicholas Banovich, Pascal Barbry, Alvis Brazma, Tushar Desai, Thu Elizabeth Duong, Oliver Eickelberg, Christine Falk, Michael Farzan, Ian Glass, Muzlifah Haniffa, Peter Horvath, Deborah Hung, Naftali Kaminski, Mark Krasnow, Jonathan A. Kropski, Malte Kuhnemund, Robert Lafyatis, Haeock Lee, Sylvie Leroy, Sten Linnarson, Joakim Lundeberg, Kerstin Meyer, Alexander Misharin, Martijn Nawijn, Marko Z. Nikolic, Jose Ordovas-Montanes, Dana Pe’er, Joseph Powell, Stephen Quake, Jay Rajagopal, Purushothama Rao Tata, Emma L. Rawlins, Aviv Regev, Paul A. Reyfman, Mauricio Rojas, Orit Rosen, Kourosh Saeb-Parsy, Christos Samakovlis, Herbert Schiller, Joachim L. Schultze, Max A. Seibold, Alex K. Shalek, Douglas Shepherd, Jason Spence, Avrum Spira, Xin Sun, Sarah Teichmann, Fabian Theis, Alexander Tsankov, Maarten van den Berge, Michael von Papen, Jeffrey Whitsett, Ramnik Xavier, Yan Xu, Laure-Emmanuelle Zaragosi and Kun Zhang. Pascal Barbry, Alexander Misharin, Martijn Nawijn and Jay Rajagopal serve as the coordinators for the HCA Lung Biological Network

1Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA, 2 Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA, 3 Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, 4 Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA, 5 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, 6 Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA, 7 Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, 8 Program in Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, 9 Computer Science & Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, 10 African Health Research Institute, Durban, South Africa, 11 School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa, 12 University of Massachusetts Medical School, Worcester, MA 01655, USA, 13 Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA, 14 Program in Virology, Harvard Medical School, Boston, MA 02115, USA, 15 John A. Paulson School of Engineering & Applied Sciences, Harvard University, Cambridge, MA 02138, USA, 16 Program in Immunology, Harvard Medical School, Boston, MA 02115, USA, 17 Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA, 18 Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA 02115, USA 19Aix-Marseille University, INSERM, INRA, C2VN, Marseille, France 20Université Côte d’Azur, CNRS, IPMC, Sophia-Antipolis, France 21Comprehensive Pneumology Center & Institute of Lung Biology and Disease, Helmholtz Zentrum München, Munich, Germany 22German Center for Lung Research, Munich, Germany 23Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany 24Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Munich, Germany 25Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA 26Divison of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA 27Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA 28Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA 02115, USA 29Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA 30University of California, Berkeley, CA 94720, USA 31University of Washington, Seattle, WA 98195, USA 32Dana Farber Cancer Institute, Boston, MA 02115, USA 33Harvard Medical School, Boston, MA 02115, USA 34Stem Cell & Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA 35Department of Medicine, University of Washington, Seattle, WA 98195, USA 36Seattle Children’s Hospital, Seattle, WA 98145, USA 37Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA 38Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA 39Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA 40UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA

There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) which causes the disease COVID-19. SARS-CoV2 spike (S)-protein binds ACE2, and in concert with host proteases, principally TMPRSS2, promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues, and the factors that regulate ACE2 expression, remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 amongst tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells. Strikingly, we discover that ACE2 is a human interferonstimulated gene (ISG) in vitro using airway epithelial cells, and extend our findings to in vivo viral infections. Our data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection.