The testing technology of the future: 36,000 samples in one night

A new method developed by researchers of the Vienna BioCenter, SARSeq, will allow testing of thousands of samples for SARS-CoV-2 and other pathogens in just 15 to 24 hours. One area of application could be the monitoring of large groups of people, for example in companies, tested at regular intervals.

One of the most important tools in the fight against the corona pandemic is testing for the presence of the virus. Scientists around the world are working on developing novel methods, in addition to conventional PCR tests, that are more suitable for specific applications.

Ulrich Elling from IMBA – Institute of Molecular Biotechnology of the Austrian Academy of Sciences – together with Luisa Cochella and Alexander Stark from the neighboring Research Institute of Molecular Pathology (IMP) have now developed an additional method that could enable large groups to be tested for SARS-CoV-2, as well as other infections such as influenza, with high throughput and a turnaround time of one day.

"In Austria about 20,000 tests are currently carried out every day, and we could easily double that with our test procedure," explains Elling. The research team has now presented the new method on the preprint server medRxiv.

The method takes advantage of Next Generation Sequencing (NGS) technology, the same used to sequence the human genome. NGS machines can sequence millions of base pairs of DNA in a single run. In the current protocol, individual patient samples are collected, viral RNA is converted to DNA, and then PCR amplified, similar to the principle of current PCR tests. During this amplification, DNA barcodes, which are specific to a single sample, are added to any viral DNA that is amplified. Tens of thousands of samples are then mixed together and sequenced on an NGS machine. The presence of viral genetic material indicates a positive result, and the barcodes added in the PCR step conclusively identify the positive sample that contained the viral material.

“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 influenza A and influenza B viruses, as well as rhinoviruses, which cause common colds, at the same time as coronavirus,” explains IMP group leader Luisa Cochella.

The test procedure can run completely in parallel to already existing diagnostics, while being independent of the bottlenecks in supply chains – it therefore does not represent a competition for reagents or equipment needed for the diagnostics already in place.

“We were able to generate an extremely high throughput. After optimizing the protocol, we can now simultaneously analyse up to 36,000 samples on one machine overnight,” says Alexander Stark of the IMP. When using machines already available at the Vienna BioCenter together with in-house produced enzymes, the cost is expected to be below 5 Euros per test.

Preprint available on medRxiv, DOI 10.1101/2020.10.28.20217778