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Maximizing viral nucleic acid yield from passive samplers: Evaluating elution and extraction protocols.
Madison Gouthro1, Emalie K Hayes1, Graham A Gagnon1
1Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3H 4R2, Canada.
The Science of the Total Environment
|December 1, 2024
Summary
Optimized protocols for granular activated carbon (GAC) passive sampling enhance viral detection in freshwater. This method improves recovery of viral nucleic acids, crucial for monitoring viruses like SARS-CoV-2 in aquatic environments.
Area of Science:
- Environmental Virology
- Water Quality Monitoring
- Molecular Biology Techniques
Background:
- Effective viral surveillance in freshwater is critical, especially for non-enteric viruses, but faces challenges with traditional sampling methods.
- Wastewater-based epidemiology has advanced, yet freshwater viral monitoring remains limited.
- Granular Activated Carbon (GAC) offers potential for passive viral sampling in aquatic systems.
Purpose of the Study:
- To optimize extraction and elution methods for GAC-based passive samplers to improve viral nucleic acid recovery in freshwater.
- To identify the most effective combination of total nucleic acid (TNA) extraction kits and elution buffers for GAC sampling.
- To validate optimized protocols for field-scale viral surveillance in freshwater ecosystems.
Main Methods:
- Evaluated three commercial TNA extraction kits and four elution buffers for recovering SARS-CoV-2 and bacteriophage MS2 from GAC samplers.
- Determined optimal extraction and elution conditions to maximize viral nucleic acid recovery efficiency.
- Applied optimized protocols in field studies to assess GAC passive sampler performance for various viruses.
Main Results:
- The Promega Wizard® Enviro Total Nucleic Acid Kit combined with a Tween®20-based buffer yielded the highest virus recovery efficiency from GAC.
- Optimized GAC passive samplers successfully captured SARS-CoV-2, Influenza A (INFA), Respiratory Syncytial Virus (RSV), and Measles Virus (MeV).
- Optimized passive sampling showed higher detection frequencies compared to grab samples, highlighting improved sensitivity.
Conclusions:
- Selection of appropriate TNA extraction kits and elution buffers is crucial for maximizing virus recovery from passive samples.
- Optimized GAC-based passive sampling protocols significantly enhance the sensitivity and reliability of viral surveillance in freshwater.
- This study provides a refined methodology for effective viral monitoring in diverse aquatic environments.
