Assessing Mass Screening as an Effective Tool for Pandemic Management: An Experimental Study of SARS-CoV-2 Diagnosis

Abstract

SARS-CoV-2 infection has emerged worldwide. To reduce the number of cases and limit the transmission of the virus, health and local authorities have implemented several strategies. Mass screening is a key strategy for mitigating the damage caused by this pandemic. This strategy is based on the use of qRT-PCR and pooling to diagnose SARS-CoV-2 infection. The present work explores the performance and limitations of this strategy for the molecular diagnosis of SARS-CoV-2 infection. Three important technical aspects were retained: the comparison of two commercial extraction kits (BIGFISH and BIOER), the simulation of a non-compliant nasopharyngeal swab, and the evaluation of the pooling strategy. A total of 97 SARS-CoV-2-positive nasopharyngeal samples were used. The comparison of the two extraction kits was based on threshold cycles (Ct) values. The results showed a significant difference (IC = 95%) in the Ct of the nucleocapsid gene (N; p = 0.0000384) and RNA-dependent RNA polymerase (RdRp; p = 0.0254). However, no significant difference was observed between the Internal Control gene (IC; p = 0.0723) and Envelope gene (E; p = 0.150). The Ct values resulting from the BIGFISH extraction kit were generally lower than those obtained from BIOER. In terms of sensitivity, the RT-qPCR technique allows for the detection of viral RNA up to 10−3 as a dilution factor. This study demonstrated that the pooling strategy is an effective diagnostic technique. Positive samples remained detectable even in pools of 1000 or even 10,000 samples. However, the size of the pool under diagnostic conditions should not exceed a limit that must be dynamically adapted to prevalence to ensure economic and analytical viability.