SARS-CoV-2 detection in multi-sample pools in a real pandemic scenario: A screening strategy of choice for active surveillance

ANDRÉS MARCOS CASTELLARO; PABLO VELEZ; GUILLERMO GIAJ MERLERA; JUAN RONDAN DUEÑAS; FELIZ CONDAT; JESICA GALLARDO; AYLEN MAKHOUL; CAMILA CINALLI; LORENZO ROSALES CAVAGLIERI; GUADALUPE DI COLA; PAOLA SICILIA; LAURA LOPEZ; FACULTAD DE CIENCIAS QUÍMICAS UNC GROUP: PILAR CRESPO; GABRIELA FURLÁN; LAURA GATICA; MARÍA SOLEDAD MIRÓ; RUBÉN MOTRICH; ANA CRISTINA RACCA AND LUCIANA REYNA; JOSE LUIS BOCCO; MARIA GABRIELA BARBÁS; DIEGO HERNAN CARDOZO; MARIA BELEN PISANO; VIVIANA RE; ANDREA BELAUS; GARBARINO-PICO E

PLOS ONE

PUBLIC LIBRARY SCIENCE

Lugar: San Francisco; Año: 2022

1932-6203

Background: The current COVID-19 pandemic has overloaded the diagnostic capacity of laboratories by the gold standard method rRT-PCR. This disease has a high spread rate and almost a quarter of infected individuals never develop symptoms. In this scenario, active surveillance is crucial to stop the virus propagation.Methods: Between July 2020 and April 2021, 11,580 oropharyngeal swab samples collected in closed and semi-closed institutions were processed for SARS-CoV-2 detection in pools, implementing this strategy for the first time in Córdoba, Argentina. Five-sample pools were constituted before nucleic acid extraction and amplification by rRT-PCR. Comparative analysis of cycle threshold (Ct) values from positive pools and individual samples along with a cost-benefit report of the whole performance of the results was performed.Results: From 2,314 5-sample pools tested, 158 were classified as positive (6.8%), 2,024 as negative (87.5%), and 132 were categorized as indeterminate (5.7%). The Ct value shift due to sample dilution showed an increase in Ct of 2.6±1.53 cycles for N gene and 2.6±1.78 for ORF1ab gene. Overall, 290 pools were disassembled and 1,450 swabs were analyzed individually. This strategy allowed correctly identifying 99.8% of the samples as positive (7.6%) or negative (92.2%), avoiding the execution of 7,806 rRT-PCR reactions which represents a cost saving of 67.5%.Conclusion: This study demonstrates the feasibility of pooling samples to increase the number of tests performed, helping to maximize molecular diagnostic resources and reducing the work overload of specialized personnel during active surveillance of the COVID-19 pandemic.