Swab Pooling for Large-Scale RT-qPCR Screening of SARS-CoV-2

Abstract

Background: Pool testing has been proposed as an alternative for large-scale SARS-CoV-2 screening. However, dilution factors proportional to the number of pooled samples have been a source of major concern regarding its diagnostic performance. Further, sample pooling can lead to increased laboratory workload and operational complexity. Therefore, pooling strategies that minimize sample dilution, loss of sensitivity, and laboratory overload are needed to allow reliable and large-scale screenings of SARS-CoV-2. Methods: Sample collection was performed with two nasopharyngeal swabs for each patient: one for pool testing and another for individual testing. Swabs meant for pool testing were combined into the same tube with up to 15 other swabs at the time of sample collection (swab pooling). A total of 45 pools and 613 corresponding individual samples were analyzed in parallel to assess equivalence between procedures. Additional 18,922 patients were screened using the swab pooling procedure in a total of 1,344 pools. Findings: Paired analysis of pooled and individual samples from 613 patients revealed 94 positive individual tests. Having individual testing as a reference, no false-positives or false-negatives were observed for swab pooling. A Bayesian model estimated a sensitivity of 99% (Cr.I. 96·9% to 100%) and a specificity of 99·8% (Cr.I. 99·4% to 100%) for the swab pooling procedure. Data from additional 18,922 patients screened with swab pooling were included for further quantitative analysis. Mean Cq differences between individual and corresponding pool samples ranged from 0·1 Cq (Cr.I. -0·98 to 1·17) to 2·09 Cq (Cr.I. 1·24 to 2·94). Overall, 19,535 asymptomatic and presymptomatic patients were screened using 4,400 RT-qPCR assays, resulting in 246 positive patients (positivity rate 1·26%). This corresponds to an increase of 4·4 times in laboratory capacity and a reduction of 77% in required tests.Interpretation: Swab pooling minimizes sample dilution and sensitivity issues commonly seen in another traditional sample pooling methods. Therefore, swab pooling represents a major alternative for reliable and large-scale screening of SARS-CoV-2 in low prevalence populations.Funding: BiomeHub BiotechnologiesDeclaration of Interests: Authors from BiomeHub are currently full-time employees of this research and consulting company specialized in microbiome biotechnologies. All other authors declare no conflict of interest.Ethics Approval Statement: This study was approved by the Hospital Israelita Albert Einstein Ethics Committee (number 36371220.6.0000.0071). The patient informed consent was waived off by the ethics committee as the research was performed on de-identified, anonymised samples.