Researchers have designed a testing protocol for SARS-CoV-2 that can process tens of thousands of samples in less than 48 hours. The method, called SARSeq, could be adapted to many more pathogens.

The COVID-19 pandemic has lasted more than a year and continues to impact our lives tremendously. Although some countries have launched speedy vaccination campaigns, many still await large-scale immunization schemes and effective antiviral therapies — before that happens, the world urgently needs to regain a semblance of normalcy.

One way to bring us closer to that point is massive parallel testing. Molecular tests that detect the presence of SARS-CoV-2 have become the best way to isolate positive cases and contain the spread of the virus. Several methods have come forward, some that detect viral proteins from nasopharyngeal swabs (such as antigen tests), and some that detect the presence of viral RNA from swabs, gargle samples, or saliva samples (such as reverse transcription and polymerase chain reaction tests, or RT-PCR).

Although antigen tests facilitate some logistical aspects of mass testing, their detection power is relatively weak — infected individuals carrying low amounts of virus remain undetected and can continue to infect other people. PCR tests, on the other hand, are more sensitive because they multiply fragments of the viral genome before scanning samples for the virus. However, they rely on the detection of fluorescent labels that tag viral sequences, which means that pooling samples coming from different people makes the process rather inefficient: if a pool tests positive, all the samples within the pool must be tested again individually to identify the source of the fluorescent signal. Too many machines needed, too expensive, too slow.

During the very first lockdown, scientists at the Vienna BioCenter were mulling over the situation: there had to be a way to scale up testing. Ulrich Elling, group leader at the Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), and Luisa Cochella, group leader at the Research Institute of Molecular Pathology (IMP), decided to channel their frustration into an innovative solution. IMP group leader Alexander Stark and IMBA postdoc Ramesh Yelangandula joined their efforts, and the project took off.

Combining their expertise in genomics, RNA biochemistry and data analysis, they developed a method that could enable large groups to be tested for SARS-CoV-2 with the same sensitivity as regular PCR tests. SARSeq, or ‘Saliva Analysis by RNA sequencing’, achieves high sensitivity, specificity, and the power to process up to 36,000 samples in less than 48 hours. The method is now published in the journal Nature Communications.

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Materials provided by IMBA- Institute of Molecular Biotechnology of the Austrian Academy of Sciences. Note: Content may be edited for style and length.