The “COVID-SpiNGS” project will not save humanity from the dynamics of the Corona pandemic. Prof. Dr.-Ing. Piotr Dabrowski  harbours no illusions in that regard. But viruses such as COVID-19 could be targeted far more systematically in the not too distant future. The bioinformatician at HTW Berlin is working to make this a reality together with colleagues at the University of Freiburg and the research and development service provider Hahn-Schickard. The goal: to examine nasal swabs or saliva samples directly at doctor’s surgeries and to clarify which virus or virus variant is involved within two to three hours. The project is funded by the Federal Ministry for Economic Affairs and Climate Action  as part of the “Cooperative Industrial Research” programme.

If mutations could be detected quickly, it would, for instance, be easier to determine who infected whom, thus reconstructing the route of transmission. It would also be possible to identify which new virus variants are currently on the rise. “This would facilitate evidence-based health policy,” says Prof. Dr.-Ing. Dabrowski – and it would enable countries to implement measures that achieve the greatest possible effect with the fewest possible restrictions, doubtless a highly popular option in the current climate.

Currently, only a PCR test can provide certainty as to whether a person has been infected with the Corona virus and which variant is involved. However, this PCR test must be performed in a laboratory, because an acute risk of infection is present when the virus RNA, i.e. the genome, is handled. Even the genome by itself, without the enveloping virus particle, can be infectious. Laboratories and research facilities that handle viral RNA must therefore comply with high safety standards. The detection of new variants also requires sequencing with other relatively expensive, sensitive and high-maintenance devices. 

It goes without saying that technical innovations are now offering new options. The “MinION” device is used within the context of the “COVID-SpiNGS” project. About the size of a narrow matchbox, it proved its worth in mobile diagnostic centres in Africa during the Ebola pandemic. It is currently the only portable device that enables the sequencing of DNA and RNA in real time. “In terms of price, robustness and size, the device is ideal for use in medical practices,” says Prof. Dr.-Ing. Dabrowksi.

The partners’ sample preparation technology also permits mobile RNA extraction without a security lab. This is because the so-called SpinDisk, on which complete laboratory processes can be performed in small channels on a CD-like disc, is completely closed system. This means that the potentially infectious viral RNA remains contained within the disc, thus posing no threat of infection.

Prof. Dr.-Ing. Dabrowski’s scientific role is to develop and test the analysis algorithms that go hand in hand with these innovative technologies. He is confident that this will be possible during the project, which is set to run until 2023. In the meantime, he has put together his team: not an easy task, since bioinformaticians are in short supply. Conventional computer science expertise is not enough; in-depth biological knowledge is also essential.

All those involved in the research project share the same vision, namely the development of a device the size of a suitcase including laboratory equipment and computing technology that costs no more than 20,000 to 30,000 EUR. This would enable the expensive and complex process of decoding the viral genome, which has only been possible in the laboratory to date, to be performed directly in the doctor’s office. A functional prototype will be created as part of the project, with companies invited to get involved in the actual product development later.

The planned devices would not only make it easier to deal with a pandemic because much more diagnostic capacity would be available. This alone would be worth a lot. Rather, sequencing would work for the RNA of any virus. “So when the next virus is just around the corner, the technical infrastructure would already be in place and a software update would be enough to launch a counter-attack,” says Prof. Dr.-Ing. Dabrowski.

The bioinformatician deems this option particularly important. Because he firmly believes that “after the pandemic is before the pandemic”. Dangerous viruses that are transmitted from wildlife to humans are likely to become more common as humans increasingly invade and destroy wildlife habitats. Increasing globalization also ensures that they can spread at breakneck speed. The results of the research project “COVID-SpiNGS” will help counter this danger more effectively.