AUTHOR=Pacini Antonella , Paredes Franco , Heckel Sofia , Ibarra Guadalupe , Petreli Maria Victoria , Perez Marilina , Agnella Yanina , Piskulic Laura , Allasia Maria Belen , Caprile Luis , Colaneri Alejandro , Sesma Juliana 

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

JOURNAL=Frontiers in Public Health

VOLUME=Volume 11 - 2023

YEAR=2024

URL=https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2023.1340420

DOI=10.3389/fpubh.2023.1340420

ISSN=2296-2565

ABSTRACT=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. Evaluating 1200 retrospective SARS-CoV-2 positive samples, which were either negative or positive for Delta or Omicron, we demonstrated that pools of 10 samples yield 100% sensitivity, 99% specificity, and an Area Under the Curve (AUC) exceeding 0.998 in the ROC curves, utilizing distinct commercial TaqMan variant probes. 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.