Effective high-throughput RT-qPCR screening for SARS-CoV-2 infections in children

Nat Commun. 2022 Jun 25;13(1):3640. doi: 10.1038/s41467-022-30664-2.


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 children, 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 >106 copies/ml and >103 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 developed 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 Testing
  • COVID-19* / diagnosis
  • COVID-19* / epidemiology
  • Child
  • Clinical Laboratory Techniques / methods
  • Humans
  • SARS-CoV-2 / genetics
  • Sensitivity and Specificity

Supplementary concepts

  • SARS-CoV-2 variants