How is the genetic information of the novel coronavirus (SARS-CoV-2) evolving? What other infections arise in patients? Do genetic risk factors exist that mean people are predisposed to an infection? A great many genome researchers are currently pooling their expertise and sequencing infrastructure to make a scientific contribution to management of the Covid-19 pandemic. These activities have now officially been brought together within the German Covid-19 OMICS Initiative (DeCOI) in which the German Biobank Node (GBN) and German Biobank Alliance (GBA) are also involved. “To provide optimal support for high-throughput sequencing, DeCOI and GBN/GBA have agreed to cooperate closely to identify suitable biosamples at different biobanks as quickly as possible and to make them available for sequencing,” explains the head of GBN, Prof. Dr. Michael Hummel. Scientists from more than 22 institutions have already joined DeCOI – and this number continues to grow.
Sequencing: virus genome and metagenome
The SARS-CoV-2 genome is currently being sequenced in many parts of the world in order to characterise changes in the virus’ genetic information. The more such viral genomes are sequenced, the better scientists can understand variations in the virus and how it spreads. Analysing the lineage of individual viruses allows conclusions to be drawn about their origin and about different forms of the virus contracted by the population. In addition to sequencing the viral genomes, so-called metagenomes are also identified. These grant insights into other infections that may arise in patients with Covid-19. DeCOI scientists intend to sequence up to 2,000 metagenomes in Covid-19 patients in Germany to answer this question.
Genetic risk factors
One DeCOI group suspects that there are also genetic risk factors that can influence the likelihood of infection or the disease’s severity. In order to identify genetic risk factors, the genomes of many thousands of patients must be sequenced. Prof. Dr. Markus Nöthen from Bonn University Hospital explains: “It is for this reason that we also began networking with our European and international colleagues worldwide at an early stage within DeCOI.”
The aim of functional genomics is to characterise entire organ systems. Data is often collected on several molecular levels of regulation and combined (multi-omics analyses). Clinical trials underway at several locations in Germany use this approach – to test the effectiveness of new drugs for SARS-CoV-2, for example. “Multi-omics analyses allow us to quickly and comprehensively determine which biological processes are triggered by the disease itself and how medication can have a positive impact on these,” explains Prof. Dr. Philip Rosenstiel from the University of Kiel. This comprehensive data also helps scientists to understand why some people become seriously ill and others develop only mild symptoms.
Single cell sequencing
While still in its very early days, single cell sequencing provides extremely promising insights into the complex processes taking place in patients’ bodies. DeCOI researchers are involved in major international consortia, among others to determine the distribution of receptors on the cells believed to be responsible for the onset of SARS-CoV-2. The aim is to ascertain which immune cells are involved in processes that occur specifically in patients who suffer severe symptoms in order to develop new treatment possibilities.
Linked data, networked knowledge
Genome research generates huge quantities of data on which computer analyses are performed to evaluate the research findings. “We will only be able to contribute as much as possible to the understanding of Covid-19 if we combine clinical and genome data meaningfully,” explains Prof. Dr. Oliver Kohlbacher from the University of Tübingen. “By joining together to form DeCOI, we should be able to answer many more questions in parallel and more rapidly together,” says Prof. Dr. Joachim Schultze from the LIMES Institute at the University of Bonn and the German Center for Neurodegenerative Diseases (DZNE), who is currently coordinating the initiative. “It is now important to link DeCOI closely with other initiatives in order to contribute sound knowledge worldwide to overcome the crisis.”