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

Abstract

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 sensitive 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 >10E6 copies/ml and >10E3 copies/ml in corresponding Naso-/Oropharyngeal-swabs, respectively. For effective application of the Lolli-Method in schools and daycare facilities, SIR-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 as well as with a school social deprivation index. Moreover, in comparison with the alpha variant, statistical modeling revealed a 31% increase for multiple (>1 child) 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 infection control in schools and daycare facilities.

Implementing the Lolli-Method and pooled RT-qPCR testing for SARS-CoV-2 surveillance in schools: a pilot project

“…In most schools, the testing was carried out only once a week per student. To minimize the number of missed infections, it is conceivable that testing should be performed more often [ 12 ].…”

“…On the other hand, RT-qPCR-pool testing reduces stigmatization as a student’s positive tests results are not immediately disclosed to their classmates leading to an increased acceptance of this surveillance method. In addition, we have recently compared the sensitivity of RADTs with that of the Lolli-Method obtained by RT-qPCR pool tests [ 12 , 22 , 23 ]. The Lolli-Method has proven to be more sensitive and therefore has the potential to detect SARS-CoV-2-positive individuals before they become highly infectious [ 12 , 22 ].…”

“…In addition, we have recently compared the sensitivity of RADTs with that of the Lolli-Method obtained by RT-qPCR pool tests [ 12 , 22 , 23 ]. The Lolli-Method has proven to be more sensitive and therefore has the potential to detect SARS-CoV-2-positive individuals before they become highly infectious [ 12 , 22 ]. Furthermore, handling of RADTs appears to be more difficult than the Lolli-Method, especially for young children that may need help from school staff.…”

“…We were able to demonstrate that the Lolli-Method as a screening strategy for SARS-CoV-2 in the daily school routine is feasible and can be applicable on a large scale. Based on the experience gained from the pilot project, the test concept was implemented as a SARS-CoV-2 screening program at elementary schools and special needs schools in North-Rhine Westphalia [ 12 ]…”

Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for SARS-CoV-2 RT-qPCR screening purposes

“…Pooled testing of samples presents itself as a valid strategy to overcome these hurdles and to realize rapid, large-scale testing at lower cost and lower dependence on test reagents. By now, 1D pooling strategies have been widely applied for SARS-CoV-2 infection surveillance 1 – 3 .…”