Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR

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dc.citation.titleFrontiers in Public Health
dc.citation.volume11
dc.creatorPacini, Antonella
dc.creatorParedes, Franco
dc.creatorHeckel, Sofía
dc.creatorIbarra, Guadalupe
dc.creatorPetreli, María Victoria
dc.creatorPerez, Marilina
dc.creatorAgnella, Yanina
dc.creatorPiskulic, Laura
dc.creatorAllasia, María Belén
dc.creatorCaprile, Luis
dc.creatorColaneri, Alejandro
dc.creatorSesma, Juliana
dc.date.accessioned2024-10-03T17:51:26Z
dc.date.available2024-10-03T17:51:26Z
dc.date.issued2024-01-11
dc.description.abstractIntroduction: The declaration of the end of the Public Health Emergency for COVID-19 on May 11th, 2023, has shifted the global focus led by WHO and CDC towards monitoring the evolution of SARS-CoV-2. Augmenting these international endeavors with local initiatives becomes crucial to not only track the emergence of new variants but also to understand their spread. We present a cost-effective digital PCR-based pooled sample testing methodology tailored for early variant surveillance. Methods: Using 1200 retrospective SARS-CoV-2 positive samples, either negative or positive for Delta or Omicron, we assessed the sensitivity and specificity of our detection strategy employing commercial TaqMan variant probes in a 1:9 ratio of variant-positive to variant-negative samples. Results: The study achieved 100% sensitivity and 99% specificity in 10-sample pools, with an Area Under the Curve (AUC) exceeding 0.998 in ROC curves, using distinct commercial TaqMan variant probes. Discussion: The employment of two separate TaqMan probes for both Delta and Omicron establishes dual validation routes, emphasizing the method’s robustness. Although we used known samples to model realistic emergence scenarios of the Delta and Omicron variants, our main objective is to demonstrate the versatility of this strategy to identify future variant appearances. The utilization of two divergent variants and distinct probes for each confirms the method’s independence from specific variants and probes. This flexibility ensures it can be tailored to recognize any subsequent variant emergence, given the availability of its sequence and a specific probe. Consequently, our approach stands as a robust tool for tracking and managing any new variant outbreak, reinforcing our global readiness against possible future SARS-CoV-2 waves.
dc.description.filFil: Pacini, Antonella. Hospital Provincial de Rosario. Molecular Biology Department; Argentina.
dc.description.filFil: Pacini, Antonella. Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET); Argentina.
dc.description.filFil: Paredes, Franco. Hospital Provincial de Rosario. Molecular Biology Department; Argentina.
dc.description.filFil: Paredes, Franco. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario; Argentina.
dc.description.filFil: Heckel, Sofía. Hospital Provincial de Rosario. Molecular Biology Department; Argentina.
dc.description.filFil: Heckel, Sofía. Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET); Argentina.
dc.description.filFil: Heckel, Sofía. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas
dc.description.filFil: Ibarra, Guadalupe. Hospital Provincial de Rosario. Molecular Biology Department; Argentina.
dc.description.filFil: Ibarra, Guadalupe. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario; Argentina.
dc.description.filFil: Petreli, María Victoria. Hospital Provincial de Rosario. Molecular Biology Department; Argentina.
dc.description.filFil: Petreli, María Victoria. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario; Argentina.
dc.description.filFil: Perez, Marilina. Hospital Provincial de Rosario. Molecular Biology Department; Argentina.
dc.description.filFil: Agnella, Yanina. Hospital Provincial de Rosario. Molecular Biology Department; Argentina.
dc.description.filFil: Agnella, Yanina. Universidad Nacional de Rosario. Facultad de Ciencias Veterinarias; Argentina.
dc.description.filFil: Piskulic, Laura. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área Estadística y Procesamiento de Datos; Argentina.
dc.description.filFil: Allasia, María Belén. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Área Estadística y Procesamiento de Datos; Argentina.
dc.description.filFil: Caprile, Luis. Hospital Provincial de Rosario. Molecular Biology Department; Argentina.
dc.description.filFil: Colaneri, Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Argentina.
dc.description.filFil: Sesma, Juliana. Hospital Provincial de Rosario. Molecular Biology Department; Argentina.
dc.description.filFil: Sesma, Juliana. Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET); Argentina.
dc.description.filFil: Sesma, Juliana. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; Argentina.
dc.description.sponsorshipMinisterio de Ciencia, Tecnología e Innovación: SF 06-COVID FEDERAL: IF-2020-37418385-APN-SSFCTEI#MCT
dc.format.extent01-09
dc.identifier.issn2296-2565
dc.identifier.urihttps://hdl.handle.net/2133/27925
dc.language.isoen
dc.publisherFrontiers Media
dc.relation.publisherversionhttps://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2023.1340420/full
dc.relation.publisherversionhttps://doi.org/10.3389/fpubh.2023.1340420
dc.rightsopenAccess
dc.rights.holderPacini, Antonella
dc.rights.holderParedes, Franco
dc.rights.holderHeckel, Sofía
dc.rights.holderIbarra, Guadalupe
dc.rights.holderPetreli, María Victoria
dc.rights.holderPerez, Marilina
dc.rights.holderAgnella, Yanina
dc.rights.holderPiskulic, Laura
dc.rights.holderAllasia, María Belén
dc.rights.holderCaprile, Luis
dc.rights.holderColaneri, Alejandro
dc.rights.holderSesma, Juliana
dc.rights.holderUniversidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas
dc.rights.textAttribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectCOVID-19
dc.subjectPolymerase Chain Reaction
dc.subjectRetrospective Studies
dc.subjectSARS-CoV-2
dc.titleReady for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR
dc.typearticulo
dc.type.collectionarticulo
dc.type.versionpublishedVersion

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