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Pacini A, Paredes F, Heckel S, Ibarra G, Petreli MV, Perez M, Agnella Y, Piskulic L, Allasia MB, Caprile L, Colaneri A, Sesma J. Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR. Front Public Health 2024; 11:1340420. [PMID: 38298257 PMCID: PMC10829044 DOI: 10.3389/fpubh.2023.1340420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
Introduction 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.
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Affiliation(s)
- Antonella Pacini
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, Argentina
| | - Franco Paredes
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sofia Heckel
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guadalupe Ibarra
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Maria Victoria Petreli
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Marilina Perez
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
| | - Yanina Agnella
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Veterinarias, Universidad Nacional de Rosario, Casilda, Argentina
| | - Laura Piskulic
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Maria Belen Allasia
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luis Caprile
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
| | - Alejandro Colaneri
- Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Juliana Sesma
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
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