Konsiliarlabor für Coronaviren

German SARS-CoV-2 sequences

Last update: Sun Sep 13 20:07:32 2020 (UTC)

Charité sequences: 447

Below are links to early information regarding SARS-CoV-2 virus sequences that are the result of work done at the Institute for Virology at Charité Universitätsmedizin in Berlin, Germany. The team responsible for this site and these sequences is: Terry C. Jones, Barbara Mühlemann, Julia Schneider, Jörn Beheim-Schwarzbach, Talitha Veith, Victor M. Corman, and Christian Drosten.

Visualization of the German SARS-CoV-2 dataset , powered by auspice, including 447 unpublished sequences from Charité, plus (from GISAID) 412 other sequences from Germany and 17 additional sequences included to represent each major lineage assigned by GISAID, NextStrain, and Pangolin. All sequences are at least 95% complete (i.e., at most 5% of sites have an ambiguous 'N' nucleotide).

, powered by auspice, including 447 unpublished sequences from Charité, plus (from GISAID) 412 other sequences from Germany and 17 additional sequences included to represent each major lineage assigned by GISAID, NextStrain, and Pangolin. All sequences are at least 95% complete (i.e., at most 5% of sites have an ambiguous 'N' nucleotide). FASTA full-genome sequences and the TAB-separated metadata for the Charité-produced sequences used in the production of the above visualization. The additional German sequences included in the visualization above must be obtained independently via GISAID.

Please note

This page exists solely to provide you with early access to unpublished SARS-CoV-2 sequences assembled by Charité virology. It is not intended as a substitute for the much larger set of published sequences available to subscribers of GISAID.

Sequence assembly can be time-intensive and may require several rounds of careful laboratory and computational work. The sequences released here should be regarded as current best-effort drafts, subject to change, and minor changes should be expected. These can occur for a variety of reasons. For example, re-sequencing samples to resolve ambiguous nucleotides or to clarify the impact of minority variants on consensus sequences, or re-analysis to identify likely sequencing or computational errors. This is all standard practice.

If you plan to use these sequence as part of a publication, please contact us to check for additional detail regarding planned sequence updates, specific nucleotide uncertainties, or for additional sample metadata that we may have available.

Worldwide, the production of full-genome sequences of SARS-CoV-2 viruses represents only a tiny fraction of the number of actual infections. It is not safe to draw conclusions regarding geographic transmission routes based on such a small and under-sampled data set. For example, it was argued by some that the Munich cases seeded the northern Italian outbreak in late February. This was based on the sample collection dates of a handful of sequences that included three identical mutations. But this explanation overlooked other possibilities, including that this genetic variant was already circulating in China and that both European regions had been seeded from there. On March 20th 2020, the misinterpretation was definitively confirmed: a sequence with the identical pattern of mutations was uploaded to GISAID (id EPI_ISL_416327). The upload was done almost two months after sample collection on Jan 28, 2020. Such a delay should be considered normal given the extreme conditions of a pandemic crisis. This example shows the danger of prematurely drawing conclusions based on highly incomplete data. Virology institutes currently have much more pressing priorities than curating and annotating sequences for upload, and the priority for doing so will certainly only decrease if unjustified and illogical nationalistic conclusions are being jumped to based on such incomplete data. The number of available SARS-CoV-2 sequences is dwarfed by the number of cases worldwide. The available data is certainly not representative of the unknown early genetic diversity or of the initial global spread of the virus. Many early samples will likely have been discarded and many may never be sequenced. We may never have conclusive answers to questions regarding early geographic spread.

Acknowledgments

Many thanks to Prof. Ron Fouchier, Deputy Head of the Erasmus MC Department of Viroscience and Co-Chair of the GISAID Scientific Advisory Council and to Dr. Peter Bogner, President of the GISAID Initiative and its many dedicated curation teams across the globe that ensure a round-the-clock data quality processing, enabling real-time sharing of the rapidly-growing collection of SARS-CoV-2 genome sequences and associated metadata, thereby providing time-sensitive information during the COVID-19 pandemic. Among them, the teams from the Bioinformatics Institute Singapore A*Star, CNRS and Institut Pasteur, The Francis Crick Institute, Genome Institute of Singapore A*STAR, Hospital de Niños Dr. Ricardo Gutiérrez, Fundação Oswaldo Cruz (Fiocruz), Luxembourg Centre for Systems Biomedicine, Beijing Genomics Institute, National Scientific and Technical Research Council, University of Adelaide, Public Health Agency of Sweden, Universidad Nacional de La Plata, University of Edinburgh - MRC Human Genetics Unit. We are grateful for their efforts and contributions.

Thanks to the Max Delbrück Center for Molecular Medicine for their help in the sequencing work that produced some of the Charité sequences.

For their work collecting and sequencing other German and Chinese samples in the visualization, many thanks to: ; Institut für Mikrobiologie der Bundeswehr, Munich; 40225 Düsseldorf; A. Krumbholz, Labor Dr. Krause und Kollegen MVZ GmbH, Kiel; AG Thiel; Bergthaler laboratory, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Bioscientia/ Ingelheim/Küsters; Bundeswehr Institute of Microbiology; Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene; Center of Medical Microbiology, Virology, and Hospital Hygiene, Heinrich Heine University Düsseldorf; Center of Medical Microbiology, Virology, and Hospital Hygiene, University of Duesseldorf; Centogene AG; Charité Universitätsmedizin Berlin, Institut für Virologie; Charité Universitätsmedizin Berlin, Institut für Virologie/Labor Berlin; Cicin-Sain Lab; Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital; Department of Health Technology and Informatics, Faculty of Health and Social Science, The Hong Kong Polytechnic University; Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg; Department of Virology; Friedrich-Loeffler-Institut, Laboratory for NGS and Microarray Diagnostics; Goethe University Hospital Frankfurt; Goethe University Hospital Frankfurt, Institute for Medical Virology; Heinrich Pette Institute, Leibniz Institute for Experimental Virology; IL Department of Public Health Chicago Laboratory; INMI Lazzaro Spallanzani IRCCS; Institut für Virologie am Department für Hygiene, Mikrobiologie und Public Health; Institut für Virologie und Epidemiologie der Viruskrankheiten, Universitätsklinikum Tübingen; Institut für Medizinische Virologie, Universitätsklinikum Frankfurt, Paul-Ehrlich-Straße 40, 60596 Frankfurt a.M.; Institute for Medical Virology, Goethe University Hospital Frankfurt; Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg; Institute of Human Genetics, University Medical Center Goettingen; Institute of Medical Microbiology, University Medical Center Goettingen; Institute of Molecular Virology, University Münster; Instituto de Diagnostico y Referencia Epidemiologicos (INDRE); Japanese Quarantine Stations; LADR; LGA Baden Wuerttemberg; Labor Dr. Schumacher, Bremerhaven; Labor Kneißler GmbH & Co. KG; Laboratory for Functional Genome Analysis, Dept. Genomics, Gene Center of the LMU Munich; Laboratory of Biology, Department of Medicine, Democritus University of Thrace; Laboratory of Microbiology, Medical School, National and Kapodistrian University of Athens; Laboratory of Virology, INMI Lazzaro Spallanzani IRCCS; Laboratory of molecular-genetic research, National Center for Expertise, Kazakhstan; Laboratory of virology, National Center of Expertise; MDV Karlsruhe.; MGZ Medical Genetics Center; Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU Munich; Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU München; Microbiology, The University of Hong Kong; Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo , Pavia; München Klinik Schwabing; NCDC/CSIR-IGIB; NGS Competence Center Tübingen, Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen; National Centre for Disease control (NCDC), CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB); National Institute for Communicable Disease Control and Prevention (ICDC) Chinese Center for Disease Control and Prevention (China CDC); National Institute of Health. Department of medical Sciences, Ministry of Public Health, Thailand; Pathogen Discovery, Respiratory Viruses Branch, Division of Viral Diseases, Centers for Dieases Control and Prevention; Pathogen Genomics Center, National Institute of Infectious Diseases; Respiratory Virus Unit, Microbiology Services Colindale, Public Health England; Robert Koch Institute, Bioinformatics MF1, Berlin, Germany; Robert Koch Institute, National Reference center for Influenza, Berlin, Germany; Robert Koch Institute, ZBS1 Highly Pathogenic Viruses, Berlin, Germany; Seattle Flu Study; State Health Office Baden-Württemberg; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University; The First Affiliated Hospital of Guangzhou Medical University & BGI-Shenzhen; Thüringer Landesamt für Verbraucherschutz; Uni Rostock; Universitaet Duesseldorf; Universitätstr.1; University Hospital Regensburg; University Medical Center Hamburg-Eppendorf; Victorian Infectious Diseases Reference Laboratory (VIDRL); Victorian Infectious Diseases Reference Laboratory and Microbiological Diagnostic Unit Public Health Laboratory, Doherty Institute; Washington State Department of Health; n/a.

Many thanks to Professors Trevor Bedford and Richard Neher and the team at Nextstrain for their excellent open-source tools auspice and augur, and the effort involved in documenting them and rapidly responding to technical questions. See also James Hadfield et al., Nextstrain: real-time tracking of pathogen evolution. Nextstrain also provide a full visualization of all published SARS-CoV-2 sequences from GISAID.