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Updated: Sep 10, 2025
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Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
Published on: June 30, 2023
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Characterizing influenza A virus lineages and clinically relevant mutations through high-coverage wastewater
Anika John1, Seju Kang2, Lara Fuhrmann1
1Department of Biosystems Science and Engineering, ETH Zurich, CH-4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
Water Research
|August 27, 2025
Summary
Wastewater surveillance effectively tracks influenza A virus evolution, identifying key mutations for vaccine and antiviral strategies. This method provides reliable genomic data, complementing clinical monitoring for public health.
Area of Science:
- Virology
- Public Health
- Genomic Surveillance
Background:
- Influenza A virus causes significant public health issues, necessitating continuous genomic monitoring.
- Rapid viral evolution requires effective strategies for vaccine and antiviral development.
- Wastewater-based surveillance presents a cost-effective and unbiased method for genomic monitoring.
Purpose of the Study:
- To develop and validate a novel primer panel for influenza A virus genomic surveillance in wastewater.
- To assess the utility of wastewater-based surveillance for tracking influenza A virus diversity and mutations.
- To correlate wastewater genomic data with clinical surveillance data.
Main Methods:
- Development of a tiling amplicon primer panel targeting HA, NA, and M segments of Influenza A virus subtypes H1N1 and H3N2.
- Sequencing of nucleic acid extracts from 59 Swiss wastewater samples across two winter seasons (2022/2023, 2023/2024).
- Analysis of wastewater genomic data for clade abundance, lineage identification, and mutation tracking.
Main Results:
- Wastewater-based abundance estimates for dominant H1N1 clades correlated with clinical estimates in the 2023/2024 season.
- Wastewater sequencing identified mutations in vaccine and drug target sites, aligning with clinical findings.
- Successful lineage identification and mutation tracking were achieved through wastewater surveillance.
Conclusions:
- Wastewater-based genomic surveillance is an effective tool for monitoring influenza A virus.
- This approach aids in identifying circulating strains and tracking genetic changes relevant to public health.
- Findings support the use of wastewater surveillance to inform influenza vaccine and antiviral strategies.
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