Safe and Effective Pool Testing for SARS-CoV-2 Detection

Abstract

Background: 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 optimized test conditions and implemented high throughput pool testing of respiratory swabs into SARS-CoV-2 diagnostics. Methods: In preparation for pool testing, we determined the optimal pooling strategy and pool size, and evaluated aspects of pre-analytics including method and timepoint of sample collection during course of infection. 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. Findings: Using optimized strategies for pooling, we systematically pooled 16,164 samples in a period of 18 weeks resulting in a reduction of 14,170 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 swab increased cellular yield by a factor of 2·34, and sampling at or shortly after symptom onset by oropharyngeal or combined nasal/oropharyngeal swabs was associated with higher viral loads. By comparing different pooling strategies, pipette-pooling was more efficient compared to swab-pooling. Interpretation: 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. Funding: No external funding was received. Declaration of Interests: The authors declare no competing interests. Ethics Approval Statement: All samples and clinical data were collected on the wards or outpatient departments of the University Hospital of Cologne. No identifying data were used for the patient’s characterization. According to §15 subparagraph 3 (Professional Code for Physicians in Germany) ethical principles of WMA Declaration of Helsinki were respected, and no ethics committee approval and informed consent were necessary for this study.