Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq

Author:

Yelagandula RameshORCID, ,Bykov AleksandrORCID,Vogt Alexander,Heinen Robert,Özkan Ezgi,Strobl Marcus Martin,Baar Juliane ChristinaORCID,Uzunova Kristina,Hajdusits Bence,Kordic Darja,Suljic Erna,Kurtovic-Kozaric Amina,Izetbegovic Sebija,Schaeffer Justine,Hufnagl Peter,Zoufaly AlexanderORCID,Seitz Tamara,Födinger Manuela,Allerberger FranzORCID,Stark AlexanderORCID,Cochella LuisaORCID,Elling UlrichORCID

Abstract

AbstractThe 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.

Publisher

Springer Science and Business Media LLC

Subject

General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry

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