SARSeq Enables Massive Parallel Testing for SARS-CoV-2

Researchers at the Vienna BioCenter have developed a method capable of massive parallel testing, enabling large groups to be tested for SARS-CoV-2 with the same sensitivity as regular PCR tests. SARSeq, or 'Saliva Analysis by RNA sequencing', has the power to process up to 36,000 samples in less than 48 hours. Their method was published in Nature Communications.

For SARSeq, individual patient samples are collected into the wells of a testing plate—one well for each sample. Then, a fragment of viral RNA unique to SARS-CoV-2—the nucleocapsid gene—is selectively converted to DNA and PCR-amplified in any well that contains it. "Amplifying the viral material from individual samples to a maximum homogenizes its quantity across positive samples, making SARSeq highly sensitive," explains lead researcher Luisa Cochella. "Within the thousands of samples that we could test simultaneously, some may contain up to 10 million times more coronavirus particles than others—if we pooled such samples before amplification, those with high amounts of viral material could mask other positive cases."

What distinguishes this first step to the usual PCR test is that each sample receives a unique set of short DNA sequences that attach to the amplifying viral DNA. In a second amplification step, all the samples from one plate are pooled into one well, which receives a second set of unique DNA barcodes. The contents of multiple plates can be pooled once more, as the DNA molecules from each sample carry a unique combination of two sets of barcodes. This pooling and barcoding strategy makes SARSeq highly specific and scalable.

"We combine the sensitivity of PCR with the high throughput of Next Generation Sequencing technology, or NGS, the same used to sequence the human genome. The NGS machine processes the pooled samples and tells us which samples contained any SARS-CoV-2 material. The barcodes allow us to distinguish each positive sample from the others, and trace it back to a patient," says Ramesh Yelagandula, first author of the study. Moreover, the NGS-based method allows to test several RNAs in parallel, including RNAs that control the sample quality or RNAs from other pathogens for differential diagnostics. The testing procedure can run in parallel to existing diagnostics, while being independent of the bottlenecks in supply chains. Therefore, it does not compete with other testing methods for reagents or equipment.