Konsiliarlabor für Coronaviren

German SARS-CoV-2 sequences

Last update: Wed Jun 3 18:18:46 2020 (UTC)
Charité sequences: 235

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Visualization of the German SARS-CoV-2 dataset, powered by auspice, including 235 unpublished sequences from Charité, plus (from GISAID) 221 other sequences from Germany and 3 sequences from China included to help shape the phylogenetic tree. 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This page exists solely to provide you with early access to unpublished SARS-CoV-2 sequences assembled by Charité virology.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; A. Krumbholz, Labor Dr. Krause und Kollegen MVZ GmbH, Kiel; Andreas Walker, Tobias Wienemann"; Bundeswehr Institute of Microbiology; Center for Diagnostics; 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; D12-20 lung; Department of Virology; Institute for Medical Virology; Jensen, Detlef Kindgen-Milles, Malte Kohns Vasconcelos, Klaus Pfeffer, Tina Senff, Daniel Strelow, Jörg Timm,; LGA Baden Wuerttemberg; Labor Dr. Schumacher, Bremerhaven; Laboratory for Functional Genome Analysis, Dept. Genomics, Gene Center of the LMU Munich; MDV Karlsruhe.; Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU Munich; Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU München; National Institute for Communicable Disease Control and Prevention (ICDC) Chinese Center for Disease Control and Prevention (China CDC); National Research Center for Translational Medicine (Shanghai), Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine & Shanghai Public Health Clinical Center; Shanghai Public Health Clinical Center, Shanghai Medical College, Fudan University; State Health Office Baden-Wuerttemberg; Thüringer Landesamt für Verbraucherschutz; Universitaet Duesseldorf; University Hospital Frankfurt; Widera/Toptan.

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.