Swab pooling: A new method for large-scale RT-qPCR screening of SARS-CoV-2 avoiding sample dilution

Christoff, Ana Paula; Cruz, Giuliano Netto Flores; Sereia, Aline Fernanda Rodrigues; Boberg, Dellyana Rodrigues; de Bastiani, Daniela Carolina; Yamanaka, Laís Eiko; Fongaro, Gislaine; Stoco, Patrícia Hermes; Bazzo, Maria Luiza; Grisard, Edmundo Carlos; Hernandes, Camila; de Oliveira, Luiz Felipe Valter

To minimize sample dilution effect on SARS-CoV-2 pool testing, we assessed analytical and diagnostic performance of a new methodology, namely swab pooling. In this method, swabs are pooled at the time of collection, as opposed to pooling of equal volumes from individually collected samples. Paired analysis of pooled and individual samples from 613 patients revealed 94 positive individuals. Having individual testing as reference, no false-positives or false-negatives were observed for swab pooling. In additional 18,922 patients screened with swab pooling (1,344 pools), mean Cq differences between individual and pool samples ranged from 0.1 (Cr.I. -0.98 to 1.17) to 2.09 (Cr.I. 1.24 to 2.94). Overall, 19,535 asymptomatic patients were screened using 4,400 RT-qPCR assays. This corresponds to an increase of 4.4 times in laboratory capacity and a reduction of 77% in required tests. Therefore, swab pooling represents a major alternative for reliable and large-scale screening of SARS-CoV-2 in low prevalence populations.