Safe and effective pool testing for SARS-CoV-2 detection

Background / Objectives: The global spread of SARS-CoV-2 is a serious public health issue. Large-scale surveillance screenings are crucial but can exceed diagnostic test capacities. We set out to optimize test conditions and implemented high throughput pool testing of respiratory swabs into SARS-CoV-2 diagnostics. Study design: In preparation for pool testing, we determined the optimal pooling strategy and pool size. In addition, we measured the impact of vortexing prior to sample processing, compared pipette- and swab-pooling method as well as the sensitivity of three different PCR assays. Results: Using optimized strategies for pooling, we systematically pooled 55,690 samples in a period of 44 weeks resulting in a reduction of 47,369 PCR reactions. In a low prevalence setting, we defined a preferable pool size of ten in a two-stage hierarchical pool testing strategy. Vortexing of the swabs increased cellular yield by a factor of 2.34, and sampling at or shortly after symptom onset was associated with higher viral loads. By comparing different pooling strategies, pipette-pooling was more efficient compared to swab-pooling. Conclusions: For implementing pooling strategies into high throughput diagnostics, we recommend to apply a pipette-pooling method, using pool sizes of ten samples, performing sensitivity validation of the PCR assays used, and vortexing swabs prior to analyses. Our data shows, that pool testing for SARS-CoV-2 detection is feasible and highly effective in a low prevalence setting.