One of the most important tools in the fight against the corona pandemic is testing for the virus. Scientists around the world are working on developing other methods, in addition to conventional PCR tests, that are more suitable for certain applications. Recently, Julius Brennecke from the IMBA – Institute of Molecular Biotechnology of the Austrian Academy of Sciences (OeAW) – and colleagues from the Research Institute of Molecular Pathology (IMP) published the RT-LAMP rapid test, with which individuals can be tested easily and inexpensively, as a preprint.
Ulrich Elling from the OeAW's IMBA has now developed a further method, also in collaboration with the IMP, that could enable large groups to be tested quickly for SARS-CoV-2, as well as other infections such as the flu, at high throughput. "In Austria 15,000 to 20,000 tests are currently carried out every day, and we could easily double that with our test procedure," explains Elling in an interview. He and the research team have now presented the new method to the scientific community on the preprint server medRxiv.
How does the new SARSeq method work?
Ulrich Elling: The method is in principle similar to that of PCR tests. Both tests take the viral genome, i.e., an RNA genome, convert it into DNA and then amplify it. This gives you extremely high sensitivity, so that you can see individual molecules, including individual viruses. The special thing about our method is that we analyze the sequence of the virus directly.
How is this different to conventional PCR tests?
Elling: Conventional methods require expensive light probes and so-called qPCR machines (quantitative PCR machines), which are currently not available on the market in large quantities. The method we developed also turns the viral genome into DNA and amplifies it. But to detect it, we don't use a light probe; instead we sequence pieces of the viral genome. To do this, we use genome sequencers that can also sequence the human genome overnight, i.e., they generate an extremely high density of information in a very short time.
What do you mean by a high density of information?
Elling: Such a sequencing machine gives us 400 million sequences within ten hours, i.e., 400 million analysis points. If you were to print a book and write a sequence on each page, that would correspond to a book 40 kilometers thick. This book is evaluated by a computer program which, based on whether or not we have found virus sequences in the respective sample, makes an individual diagnosis for each patient.
What kind of sample do you need for this?
Elling: We can work with any type of sample: saliva, gargle, or nasal swabs. It was important to us to generate a pipeline that works for all samples. What's more, we designed our test so that it can diagnose rhinoviruses, i.e., common colds, as well as influenza A and influenza B in parallel to coronavirus. It is all read out at the same time.
How did the new test procedure come about?
Elling: It was a result of a close collaboration with colleagues at the IMP. Luisa Cochella and I jointly managed the development. And we had one of the best bioinformaticians on hand, Alex Stark, who wrote the computer program that reads and evaluates the 40-kilometer book within a few minutes.
When did you start working on the method?
Elling: We started very early. In March at the beginning of the lockdown, we received special permission from our institutes to conduct research on site. It was very eerie at first – we were completely on our own.
You set several conditions for your approach. What were they?
Elling: One of the conditions was that we wanted to be independent of the bottlenecks in the supply chains. We did not want to rely on reagents or equipment necessary for conventional diagnostics, which is so important at the moment, so as not to create competition. Instead, we set up our test procedure completely in parallel, based on what we have available in the laboratory. We also make the enzymes ourselves.
Was the suitability for mass testing also a condition?
Elling: Yes, we wanted to generate extremely high throughput. After optimizing the protocol, we can now simultaneously analyze up to a maximum of 36,000 samples on one machine overnight. And we have several machines here. In Austria, 15,000 to 20,000 tests are currently carried out every day, and we could easily double that.
How much does such a test cost?
Elling: If we run the tests here at high throughput, with enzymes produced in-house, the estimate is in the range of one to two euros per test.
How can the samples be assigned to individual people?
Elling: We developed a special system for this: we attach an eight-digit DNA barcode to each sample that is amplified to achieve the sensitivity with which we can see individual molecules, comparable to a zip code. This means that each DNA molecule can be clearly assigned. We had to develop a system that on the one hand is sensitive enough to see the molecule, and on the other hand prevents a "superspreader" from outshining and drowning out all other samples. Because the difference between patients who are weakly positive and patients who are strongly positive is a factor of ten to a hundred million.
How could these tests be used in the future?
Elling: Realistically, our test takes at least 24 hours. If someone wants to visit their grandmother in a nursing home and wants to quickly do a test first, the RT-LAMP test developed by Julius Brennecke and Andrea Pauli would be suitable. Our test, on the other hand, can be used for monitoring larger groups of people where tests are carried out once or twice a week. For example, if a large company tests its employees and collects the samples via the company doctor and sends them to us. In addition, we know that we can extend this method to future viruses as well.
Your study has just been published as a preprint. What's next?
Elling: There are two-way checks: on the one hand, the peer review process to check the scientific results for publication, and on the other hand, the approval for use in healthcare. The test will only be used if the regulatory authorities approve it.