How does the novel coronavirus SARS-CoV-2 change its genetic information? What other infections occur in patients with the COVID-19 disease? Are there genetic risk factors that favor an infection? Numerous genome researchers around the world and in Germany are working intensively to pool their expertise and sequencing infrastructure to make a scientific contribution to combating the COVID-19 pandemic. Research teams have now officially combined their activities under the German COVID-19 OMICS Initiative (DeCOI) to accelerate research. Scientists at more than 22 institutions are actively involved in DeCOI – and the number is continuously growing.
The more sequencing that is done, the better scientists can understand the variations of the virus and draw conclusions about their origin and about different forms of the virus in the population. DeCOI research teams also want to sequence the metagenomes of up to 2,000 COVID-19 patients in Germany to find out what coinfections may accompany COVID-19.
Expertise from diverse institutions
A DeCOI team at the University Hospital of Bonn suspects that there are genetic risk factors that increase the likelihood of infection or influence the severity of the disease. In order to identify these factors, the genomes of thousands of patients need to be sequenced. Professor Markus Nöthen says: “So with DeCOI we reached out early on to our European and international colleagues to create a worldwide network.”
The aim of functional genomics is to functionally characterize entire organ systems. This often involves mapping and integrating multiple molecular levels of regulation (multi-omics analyses). Researchers across Germany are using these techniques in clinical trials to test the effectiveness of new medications to treat SARS-CoV-2. “With the help of multi-omics analyses, we can quickly and comprehensively determine which biological processes are triggered by the disease and how these can be positively influenced by medication,” says Professor Philip Rosenstiel from Kiel University. Such extensive data also provides an opportunity to better understand why some people get severely ill while others only show mild symptoms.
Single-cell sequencing offers promising insights
The still young field of single-cell sequencing enables researchers to see what SARS-CoV-2 does in individual cells, what signaling pathways it turns on, and what host proteins are suddenly produced in greater amounts – and all of this in thousands of cells at the same time. “This allows us to identify, for example, those signaling pathways that we could block to slow down the reproduction of the virus in cells,” says Professor Markus Landthaler from the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC). Professor Uwe Ohler adds: “To make progress as quickly as possible, we must be able to access and share patient and virus data from all of Germany in a controlled manner. Only so can we achieve the sample sizes needed to use statistical and machine-learning computing methods to understand the interrelated factors that lead, for example, to severe disease.”
DeCOI researchers are working in large international consortia to determine the distribution of the receptors on the body’s cells that are responsible for the entry of SARS-CoV-2. The goal is to pinpoint the immune cells involved in processes that particularly occur in patients with severe disease in order to identify new therapeutic strategies. “Many experts in single-cell genomics are also members of LifeTime, a large European-wide consortium of more than 90 leading European research institutions,” reports Professor Nikolaus Rajewsky from the MDC.
Genome research creates immense amounts of data that are analyzed using computational tools as part of the result evaluation process. “Only by linking clinical data to genome data in a meaningful way will be able to make a big contribution to understanding COVID-19,” says Professor Oliver Kohlbacher from the University of Tübingen.
“By joining forces under DeCOI, we should be able to answer many more questions in a shorter amount of time,” says Professor Joachim Schultze from the Life & Medical Sciences Institute (LIMES) at the University of Bonn, who is currently coordinating the initiative. “Now it is important that we at DeCOI forge close ties with other initiatives in order to ensure that sound knowledge for addressing the crisis reaches every corner of the globe.”
Professor Joachim L. Schultze
Life & Medical Sciences Institute (LIMES)
West German Genome Center (WGGC)
Central Coordination Unit of the NGS Competence Network
University of Bonn
+49 (0)228 7362 787
Editor, Communications Department
Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)
+49 (0)30 9406 2118
Members of the German COVID-19 OMICS Initiative (DeCOI)
Robert Bals (Saarland University), Ezio Bonifacio (TU Dresden), Maria Colome-Tatche (Helmholtz Zentrum München – German Research Center for Environmental Health/HMGU), Andreas Diefenbach (Charité – Universitätsmedizin Berlin), Alex Dilthey (Düsseldorf University Hospital), Nicole Fischer (University Medical Center Hamburg-Eppendorf), Konrad Förstner (ZB MED – Information Center for Life Sciences), Julien Gagneur (TU Munich), Michael Hummel (Charité), Birte Kehr (Charité), Andreas Keller (Saarland University), Sarah Kim-Hellmuth (TU Munich), Oliver Kohlbacher (University Hospital of Tübingen), Ingo Kurth (RWTH Aachen), Markus Landthaler (Max Delbrück Center for Molecular Medicine in the Helmholtz Association/MDC), Kerstin Ludwig (University Hospital of Bonn /UKB), Alice McHardy (Helmholtz Centre for Infection Research, Braunschweig), Christian Mertes (TU Munich), Markus Nöthen (UKB), Peter Nürnberg (University of Cologne), Uwe Ohler (MDC), Klaus Pfeffer (Düsseldorf University Hospital), Nikolaus Rajewsky (MDC), Markus Ralser (Charité), Olaf Rieß (University Hospital of Tübingen), Stephan Ripke (Charité), Philip Rosenstiel (Kiel University), Joachim L. Schultze (University of Bonn/DZNE), Oliver Stegle (German Cancer Research Center), Fabian Theis (HMGU), Janne Vehreschild (University of Cologne), Max von Kleist (Robert Koch Institute), Jörn Walter (Saarland University) und Dagmar Wieczorek (Düsseldorf University Hospital).