TY - JOUR
T1 - Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq
AU - VCDI
AU - Yelagandula, Ramesh
AU - Bykov, Aleksandr
AU - Vogt, Alexander
AU - Heinen, Robert
AU - Özkan, Ezgi
AU - Strobl, Marcus Martin
AU - Baar, Juliane Christina
AU - Uzunova, Kristina
AU - Hajdusits, Bence
AU - Kordic, Darja
AU - Suljic, Erna
AU - Kurtovic-Kozaric, Amina
AU - Izetbegovic, Sebija
AU - Schaeffer, Justine
AU - Hufnagl, Peter
AU - Zoufaly, Alexander
AU - Seitz, Tamara
AU - Al-Rawi, Mariam
AU - Ameres, Stefan
AU - Baar, Juliane
AU - Bauer, Benedikt
AU - Beer, Nikolaus
AU - Bergauer, Katharina
AU - Binder, Wolfgang
AU - Blaukopf, Claudia
AU - Bochev, Boril
AU - Brennecke, Julius
AU - Brinnich, Selina
AU - Bundalo, Aleksandra
AU - Busslinger, Meinrad
AU - Clausen, Tim
AU - de Vries, Geert
AU - Dekens, Marcus
AU - Drechsel, David
AU - Dzupinkova, Zuzana
AU - Eckmann-Mader, Michaela
AU - Fellner, Michaela
AU - Fellner, Thomas
AU - Fin, Laura
AU - Gapp, Bianca Valeria
AU - Grabmann, Gerlinde
AU - Grishkovskaya, Irina
AU - Hagelkruys, Astrid
AU - Handler, Dominik
AU - Haselbach, David
AU - Hempel, Louisa
AU - Hill, Louisa
AU - Hoffmann, David
AU - Horer, Stefanie
AU - Cochella, Luisa
N1 - Funding Information:
In immediate response to the start of the pandemic, many people in our campus united to contribute with their skills in molecular biology toward the developing of various testing strategies. These acknowledgements inevitably fall short in thanking everyone involved, but we wish to highlight those who made the biggest contributions. In particular we thank Stefan Ameres, Julius Brennecke, Harald Isemann, Andrea Pauli, and Johannes Zuber for close interaction and support throughout. Harald Isemann coordinated the strong administrative and financial support from our institutes to these endeavors, for which we are extremely grateful. We thank the entire RT-LAMP team especially Max Kellner and Martin Matl for their close interaction and support in various aspects, Andrea Pauli and Julius Brennecke also for their tremendous help in obtaining patient samples. Various people invested their time and effort to implement the in-house testing pipeline that enabled us to safely come back to work (Johannes Zuber, Harald Scheuch, Peter Steinlein, Stefan Ameres, and Sabina Kula), and also provided samples for this work (Katharina Bergauer, Martina Weissenböck, and Barbara Werner). We are extremely grateful to Irma Salimović-Bešić and Sandra Vegar-Zubovic for providing patient samples in difficult days. We are indebted to Tim Clausen and Anton Meinhart for supporting enzyme purification efforts, to Andreas Sommer, Ido Tamir, and the entire NGS team at the VBCF. We also thank Raphael Manzenreither for technical help, Gijs Versteeg for virus preparations and other help, and Edith Soucek for support. We thank Katrina Woolcock from Life Science Editors for editing, as well as the community of COVID fighters worldwide. We thank all employees for consent to sample use and ethics boards for rapid processing of the requests. Last but not least we would also like to thank our labs and all coworkers for understanding and supporting us in so many ways. R. Y. was partially supported by Oliver Bell’s laboratory at USC. Curiosity-driven biomedical research at the IMP is largely sponsored by Boehringer Ingelheim. IMBA is generously funded by the OEAW.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12/1
Y1 - 2021/12/1
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=85106898457&partnerID=8YFLogxK
U2 - 10.1038/s41467-021-22664-5
DO - 10.1038/s41467-021-22664-5
M3 - Article
C2 - 34035246
AN - SCOPUS:85106898457
SN - 2041-1723
VL - 12
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 3132
ER -