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Related Experiment Video

Updated: May 10, 2025

Large-Scale SARS-CoV-2 Testing Utilizing Saliva and Transposition Sample Pooling
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SARS-CoV-2 genomic surveillance using self-collected saliva specimens during occupational testing programs.

Andrew T Schnaubelt1, David M Brett-Major2, Janet Williamson1

  • 1Department of Pathology, Microbiology, and Immunology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States.

Frontiers in Public Health
|April 23, 2025
PubMed
Summary

This study shows self-collected saliva is effective for SARS-CoV-2 screening and genomic surveillance, enabling real-time variant monitoring in occupational settings. Optimized PCR cutoff values improve sequencing efficiency for public health interventions.

Keywords:
COVID-19SARS-CoV-2genome sequencingsalivasurveillancevariant

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Area of Science:

  • Virology
  • Public Health
  • Genomic Surveillance

Background:

  • Emerging SARS-CoV-2 variants necessitate continuous monitoring for effective public health strategies.
  • Real-time variant surveillance is crucial for adapting clinical and public health interventions.

Purpose of the Study:

  • To evaluate a SARS-CoV-2 screening and surveillance program utilizing self-collected saliva specimens for variant monitoring.
  • To demonstrate the utility of sequencing-based variant determination in occupational settings.

Main Methods:

  • Conducted saliva-based SARS-CoV-2 screening in occupational settings (December 2021-November 2022).
  • Utilized extraction-free PCR for RNA testing and whole-genome sequencing for variant analysis.
  • Assessed program utilization, quality metrics, and sequencing outputs across different sites.

Main Results:

  • High specimen quality from self-collected saliva suitable for PCR and genomic surveillance.
  • Successfully determined SARS-CoV-2 variant strains in 83% and 67% of positive samples via sequencing.
  • Demonstrated successful integration of sequencing into occupational screening programs using self-collected saliva.

Conclusions:

  • Self-collected saliva is a viable, non-invasive method for SARS-CoV-2 screening and genomic surveillance.
  • Optimizing PCR cycle threshold (Ct) cutoffs enhances variant analysis sensitivity and efficiency.
  • Community-based saliva testing programs offer scalable, resilient approaches for respiratory infection monitoring.