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

Ramesh Yelagandula, Aleksandr Bykov, Alexander Vogt, Robert Heinen, Ezgi Özkan, Marcus Martin Strobl, Juliane Christina Baar, Kristina Uzunova, Bence Hajdusits, Darja Kordic, Erna Suljic, Amina Kurtovic-Kozaric, Sebija Izetbegovic, Justine Schaeffer, Peter Hufnagl, Alexander Zoufaly, Tamara Seitz, Manuela Födinger, Franz Allerberger, Alexander Stark, Luisa Cochella () and Ulrich Elling ()
Additional contact information
Ramesh Yelagandula: Vienna BioCenter (VBC)
Aleksandr Bykov: Vienna BioCenter (VBC)
Alexander Vogt: Vienna Biocenter Core Facilities GmbH (VBCF)
Robert Heinen: Vienna BioCenter (VBC)
Ezgi Özkan: Vienna BioCenter (VBC)
Marcus Martin Strobl: Vienna BioCenter (VBC)
Juliane Christina Baar: Vienna BioCenter (VBC)
Kristina Uzunova: Vienna BioCenter (VBC)
Bence Hajdusits: Vienna BioCenter (VBC)
Darja Kordic: Vienna BioCenter (VBC)
Erna Suljic: Clinical Center of the University of Sarajevo
Amina Kurtovic-Kozaric: Clinical Center of the University of Sarajevo
Sebija Izetbegovic: Clinical Center of the University of Sarajevo
Justine Schaeffer: Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES)
Peter Hufnagl: Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES)
Alexander Zoufaly: Clinic Favoriten
Tamara Seitz: Clinic Favoriten
Manuela Födinger: Sigmund Freud Private University
Franz Allerberger: Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES)
Alexander Stark: Vienna BioCenter (VBC)
Luisa Cochella: Vienna BioCenter (VBC)
Ulrich Elling: Vienna BioCenter (VBC)

Nature Communications, 2021, vol. 12, issue 1, 1-17

Abstract: Abstract 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.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-22664-5

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DOI: 10.1038/s41467-021-22664-5

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