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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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Applications of Molecular Taxonomy01:20

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Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

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Updated: Jun 10, 2025

Author Spotlight: Understanding and Detecting Environmental Antimicrobial Resistance by Combining Culture-Based Techniques and Genomics
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Assessing different next-generation sequencing technologies for wastewater-based epidemiology.

Anika John1, David Dreifuss1, Seju Kang2

  • 1Department of Biosystems Science and Engineering, ETH Zurich, CH-4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.

Water Research
|October 10, 2024
PubMed
Summary

Wastewater epidemiology using next-generation sequencing effectively tracks SARS-CoV-2 variants. Different sequencing technologies offer trade-offs in cost, speed, and accuracy for public health surveillance.

Keywords:
BenchmarkingElement AvitiNGS technologiesONT R9.4.1 FlongleR9.4.1 MinIONWastewater-based surveillance

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Area of Science:

  • Environmental microbiology
  • Public health surveillance
  • Genomic epidemiology

Background:

  • Wastewater-based epidemiology (WBE) is a valuable tool for population-level disease monitoring, particularly for COVID-19.
  • Next-generation sequencing (NGS) is crucial for identifying and quantifying SARS-CoV-2 strains in wastewater.
  • The choice of sequencing technology impacts data quality, timeliness, and utility in WBE.

Purpose of the Study:

  • To systematically benchmark different NGS technologies for SARS-CoV-2 surveillance in wastewater.
  • To evaluate the trade-offs between sequencing platforms regarding cost, speed, and accuracy of variant detection.

Main Methods:

  • Comparative analysis of sequencing data from Illumina NovaSeq 6000, Element Aviti, and Oxford Nanopore Technologies (ONT) R9.4.1 MinION and Flongle flow cells.
  • Utilized a time series of wastewater samples from Swiss treatment plants and spike-in experiments.
  • Assessed accuracy of viral variant abundance estimates and impact of sequencing runtime.

Main Results:

  • All tested sequencing technologies enabled SARS-CoV-2 variant tracking.
  • ONT Nanopore sequencing exhibited higher error rates, affecting variant abundance accuracy but showing overall trend concordance.
  • ONT Nanopore sequencing runtime could be reduced to five hours without significant impact on variant estimate quality.

Conclusions:

  • SARS-CoV-2 variant tracking in wastewater is feasible across multiple NGS platforms.
  • ONT Nanopore sequencing offers a rapid option, though with potential accuracy trade-offs compared to Illumina.
  • Technology selection for WBE should consider specific project needs regarding cost, timeliness, and required accuracy.