Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq
Authors: Yelagandula Ramesh , Bykov Aleksandr , Vogt Alexander , Heinen Robert , Özkan Ezgi , Strobl Marcus Martin , Baar Juliane Christina , Uzunova Kristina , Hajdusits Bence , Kordic Darja , Suljic Erna , Kurtovic-Kozaric Amina , Izetbegovic Sebija , Schaeffer Justine , Hufnagl Peter , Zoufaly Alexander , Seitz Tamara ,   VCDI, Al-Rawi Mariam , Ameres Stefan , Baar Juliane , Bauer Benedikt , Beer Nikolaus , Bergauer Katharina , Binder Wolfgang , Blaukopf Claudia , Bochev Boril , Brennecke Julius , Brinnich Selina , Bundalo Aleksandra , Busslinger Meinrad , Clausen Tim , de Vries Geert , Dekens Marcus , Drechsel David , Dzupinkova Zuzana , Eckmann-Mader Michaela , Fellner Michaela , Fellner Thomas , Fin Laura , Gapp Bianca Valeria , Grabmann Gerlinde , Grishkovskaya Irina , Hagelkruys Astrid , Handler Dominik , Haselbach David , Hempel Louisa , Hill Louisa , Hoffmann David , Horer Stefanie , Isemann Harald , Kalis Robert , Kellner Max , Kley Juliane , Köcher Thomas , Köhler Alwin , Krauditsch Christian , Kula Sabina , Lang Sonja , Latham Richard , Leitner Marie-Christin , Leonard Thomas , Lindenhofer Dominik , Manzenreither Raphael Arthur , Matl Martin , Mechtler Karl , Meinhart Anton , Mereiter Stefan , Micheler Thomas , Moeseneder Paul , Neumann Tobias , Nimpf Simon , Nordborg Magnus , Ogris Egon , Pagani Michaela , Pauli Andrea , Peters Jan-Michael , Pjevac Petra , Plaschka Clemens , Rath Martina , Reumann Daniel , Rieser Sarah , Rocha-Hasler Marianne , Rodriguez Alan , Ropek Nathalie , Ross James Julian , Scheuch Harald , Schindler Karina , Schmidt Clara , Schmidt Hannes , Schnabl Jakob , Schüchner Stefan , Schwickert Tanja , Sommer Andreas , Soldoroni Daniele , Stadlmann Johannes , Steinlein Peter , Strobl Marcus , Strobl Simon , Sun Qiong , Tang Wen , Trübestein Linda , Trupke Johanna , Umkehrer Christian , Urmosi-Incze Sandor , Versteeg Gijs , Vogt Vivien , Wagner Michael , Weissenboeck Martina , Werner Barbara , Zuber Johannes , Födinger Manuela , Allerberger Franz , Stark Alexander , Cochella Luisa , Elling Ulrich 
Published: May 2021

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.