Biobanks must be integral parts of university hospitals, says Prof. Dr Joachim L. Schultze, Professor of Genomics and Immunoregulation at the LIMES Institute of the University of Bonn and coordinator of the German Covid-19 Omics Initiative (DeCOI). DeCOI is a consortium of genome researchers founded in March 2020 who have pooled their expertise and sequencing infrastructure to make a scientific contribution to the management of the Covid-19 pandemic. The alliance is based on the DFG-funded network of NGS competence centres. An important partner in the field of bioinformatics is the German Human Genome-Phenome Archive (GHGA). In an interview with the German Biobank Node (GBN), Schultze talks about DeCOI's successes so far and why new structures are needed in science to fight pandemics.
What are your experiences with the network?
Joachim Schultze: DeCOI is team spirit in science. We started with partners from 22 German institutions in the spring. In the meantime, we have more than 65 groups from 45 institutes and are still receiving new enquiries from interested parties every week. Yet DeCOI is only a loose association - we don't even have a consortium agreement! We are simply scientists with the motivation to overcome this crisis faster together.
One of DeCOI's research areas is virus sequencing. What results have you been able to achieve here?
Schultze: Virus sequencing allows us to gain insights in many ways. For example, it plays a role in monitoring diagnostics. The PCR tests are based on the assumption that the gene sequence of the virus remains the same. We can use virus sequencing to check whether this is the case. If the vaccine is coming soon, we are also able to keep an eye on its effectiveness. Because so-called escape mutants - mutations in the genetic material of the virus to escape the immune system - would not escape us.
What role does virus sequencing play in monitoring the incidence of infection?
Schultze: Australia and New Zealand, which are now virus-free, both use virus sequencing in particular for surveillance. With this method, our colleagues in Düsseldorf were also able to show very early on that the Heinsberg outbreak occurred in isolation. With such findings, we can raise virus surveillance to a completely different level. Germany is still far away from an approach like in Australia or New Zealand, but we are trying to build the structures for it. Our colleagues in Düsseldorf have already succeeded in significantly reducing the time needed to evaluate the results. We are on the way to carrying out monitoring virtually in real time. At the moment, we are in discussions with clinically oriented associations such as the Network of University Medicine in order to anchor our expertise there.
What is the situation in the field of sequencing human genomes?
Schultze: Right at the beginning, our colleagues networked worldwide because much larger data sets are needed in this field. Through the international consortia, we learned that there are certain hotspots in the genome that increase the risk for a severe course of the Covid disease. Our colleagues in Kiel have successfully contributed to these findings. In addition, we have found out that certain immune system parameters also show genetic changes in severe courses.
The third research area of DeCOI is called "functional genomics". What has come out of this so far?
Schultze: "Functional genomics" includes all the methods we use to read out the transcriptome in various ways or to investigate epigenetic changes. This is done in the context of studies, longitudinal studies or at the single-cell level. In this way, we want to find out how the immune system works in Covid-19. In this field, we were the first to show that the innate immune system is quite severely disturbed in severe courses. In addition, we were able to read out from our transcriptome data as early as April that corticosteroids should have a good influence in severe courses. Since the summer, we know from clinical studies that this is indeed the case.
What types of biospecimens are necessary for the different research areas?
Schultze: For a viral disease like Covid-19, we need swabs for virus sequencing. For sequencing human genomes, we use blood samples. In the context of functional genomics, we also started with blood. What is added are biopsy samples and bronchoalveolar lavage. At many locations, cooperation for this is ongoing with the biobanks located there. For samples that come from autopsies, the pathologies are our contacts.
What conclusions do you draw from the cooperation with the biobanks?
Schultze: From my own experience and from what colleagues have told me, I can say that whenever there are already close links between clinicians, biobanks and genomicists, the cooperation has worked very well. If, on the other hand, processes have to be established first, it doesn't work at all in times of crisis. Many clinical colleagues also immediately saw the need to support the teamwork we are striving for in DeCOI. Unfortunately, this is not yet the case everywhere. We definitely need to work on that. In my opinion, biobanks should be understood much more as integral parts of university hospitals in the future.
What requirements must biobanking fulfil for single-cell omics methods?
Schultze: With single-cell omics, we are still in the technology development phase. In general, the requirements for biobanks here are no longer as high as they used to be. Every sample no longer has to be "fresh". Especially in this transitional phase, it would make sense for biobanks to join forces with single-cell experts to find answers to certain questions: When are cryopreserved cells suitable and how do they differ from native ones? How long can they be stored and under what conditions? We should arrive at a "gold standard" here together. Linking this to real research questions at the same time would of course make the projects more attractive and cause the publications to find more readers. With Single Cell Omics Germany we have a large network with many contacts and the approach of bringing knowledge into the community and exchanging ideas with others in order to really get single cell omics into the clinic.
Covid research has produced a lot nationally and internationally in a very short time. What do you think could be done better?
Schultze: Imagine: There is a forest fire and the inhabitants of a small village first sit down and think about buying a fire engine. That's not how crisis management works. As academic scientists, we have to work competitively, that's how innovation and creativity are encouraged. But at the beginning of the Corona pandemic, we should change all at once and work as a big team. There are now more than 80,000 publications on Covid-19 in PubMed - that is a great success. But this has only been possible because an incredible number of great scientists have taken things into their own hands. What we need in the future is a volunteer service for pandemic control - a volunteer fire brigade of science. This would ensure that the roles of those involved are immediately clear in the event of a crisis and that they also have appropriate resources at their disposal. We must be able to drop everything and extinguish the fire immediately - and not wait to discuss the fire engine.
The interview was conducted by Verena Huth.
