Yelagandula R, Bykov A, Vogt A, Heinen R, Özkan E, Strobl MM, Baar JC, Uzunova K, Hajdusits B, Kordic D, Suljic E, Kurtovic-Kozaric A, Izetbegovic S, Schaeffer J, Hufnagl P, Zoufaly A, Seitz T, VCDI , Födinger M, Allerberger F, Stark A, Cochella L, Elling U
Nat Commun 12 (1) 3132 [2021-05-25; online 2021-05-25]
The COVID-19 pandemic has demonstrated the need for massively-parallel, cost-effective tests monitoring viral spread. Here we present SARSeq, saliva analysis by RNA sequencing, a method to detect SARS-CoV-2 and other respiratory viruses on tens of thousands of samples in parallel. SARSeq relies on next generation sequencing of multiple amplicons generated in a multiplexed RT-PCR reaction. Two-dimensional, unique dual indexing, using four indices per sample, enables unambiguous and scalable assignment of reads to individual samples. We calibrate SARSeq on SARS-CoV-2 synthetic RNA, virions, and hundreds of human samples of various types. Robustness and sensitivity were virtually identical to quantitative RT-PCR. Double-blinded benchmarking to gold standard quantitative-RT-PCR performed by human diagnostics laboratories confirms this high sensitivity. SARSeq can be used to detect Influenza A and B viruses and human rhinovirus in parallel, and can be expanded for detection of other pathogens. Thus, SARSeq is ideally suited for differential diagnostic of infections during a pandemic.
GEO: GSE163688 Sequencing data for all experiments