ARTICLE Effective high-throughput RT-qPCR screening for SARS-CoV-2 infections in children Felix Dewald 1,2,33 , Isabelle Suárez 2,3,4,33 , Ronja Johnen 5 , Jan Grossbach 5,6 , Roberto Moran-Tovar 7 , Gertrud Steger 1 , Alexander Joachim 8 , Gibran Horemheb Rubio 1,9 , Mira Fries 3,10 , Florian Behr 3,10 , Joao Kley 3 , Andreas Lingnau 11 , Alina Kretschmer 3 , Carina Gude 5 , Guadelupe Baeza-Flores 12 , David Laveaga del Valle 12 , Alberto Roblero-Hernandez 12 , Jesus Magana-Cerino 12 , Adriana Torres Hernandez 13 , Jesus Ruiz-Quinones 12 , Konstantin Schega 10 , Viktoria Linne 3 , Lena Junker 3 , Marie Wunsch 1 , Eva Heger 1 , Elena Knops 1 , Veronica Di Cristanziano 1 , Meike Meyer 8 , Christoph Hünseler 8 , Lutz T. Weber 8 , Jan-Christoffer Lüers 14 , Gustav Quade 15 , Hilmar Wisplinghoff 16 , Carsten Tiemann 17 , Rainer Zotz 18,19 , Hassan Jomaa 20 , Arthur Pranada 21 , Ileana Herzum 22 , Paul Cullen 23 , Franz-Josef Schmitz 24 , Paul Philipsen 25 , Georg Kirchner 26 , Cornelius Knabbe 27 , Martin Hellmich 28 , Michael Buess 10 , Anna Wolff 10 , Annelene Kossow 10,29 , Johannes Niessen 10 , Sebastian Jeworutzki 30 , Jörg-Peter Schräpler 30,31 , Michael Lässig 7 , Jörg Dötsch 8 , Gerd Fätkenheuer 2,3 , Rolf Kaiser 1,4 , Andreas Beyer 5,6,32,33 , Jan Rybniker 2,3,4,33 & Florian Klein 1,2,4,33 ✉ Systematic SARS-CoV-2 testing is a valuable tool for infection control and surveillance. However, broad application of high sensitive RT-qPCR testing in children is often hampered due to unpleasant sample collection, limited RT-qPCR capacities and high costs. Here, we developed a high-throughput approach (‘Lolli-Method’) for SARS-CoV-2 detection in chil- dren, combining non-invasive sample collection with an RT-qPCR-pool testing strategy. SARS-CoV-2 infections were diagnosed with sensitivities of 100% and 93.9% when viral loads were >10 6 copies/ml and >10 3 copies/ml in corresponding Naso-/Oropharyngeal- swabs, respectively. For effective application of the Lolli-Method in schools and daycare facilities, SEIR-modeling indicated a preferred frequency of two tests per week. The devel- oped test strategy was implemented in 3,700 schools and 698 daycare facilities in Germany, screening over 800,000 individuals twice per week. In a period of 3 months, 6,364 pool-RT- qPCRs tested positive (0.64%), ranging from 0.05% to 2.61% per week. Notably, infections correlated with local SARS-CoV-2 incidences and with a school social deprivation index. Moreover, in comparison with the alpha variant, statistical modeling revealed a 36.8% increase for multiple (≥2 children) infections per class following infections with the delta variant. We conclude that the Lolli-Method is a powerful tool for SARS-CoV-2 surveillance and can support infection control in schools and daycare facilities. https://doi.org/10.1038/s41467-022-30664-2 OPEN A full list of author affiliations appears at the end of the paper. NATURE COMMUNICATIONS | (2022)13:3640 | https://doi.org/10.1038/s41467-022-30664-2 | www.nature.com/naturecommunications 1 1234567890():,;