Related Experiment Video

Updated: Sep 9, 2025

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
09:26

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Published on: June 30, 2023

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A Benchmark of methods for SARS-CoV-2 whole genome sequencing and development of a more sensitive method

Anthony Bayega1,2, Sarah J Reiling1,2, Ju Ling Liu1,2

  • 1McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC, Canada.

Frontiers in Genetics
|September 2, 2025
PubMed

Insights

Comparing SARS-CoV-2 sequencing methods, ARTIC protocols excelled in yield and lineage accuracy. A new ARTIC-Amp method improved genome coverage, especially for low-RNA samples like wastewater.

Area of Science:

  • Virology
  • Genomics
  • Molecular Biology

Background:

  • The COVID-19 pandemic, caused by SARS-CoV-2, necessitates robust viral surveillance due to ongoing mutations impacting public health interventions.
  • Whole genome sequencing is crucial for tracking virus evolution and transmission patterns.

Purpose of the Study:

  • To compare the efficiencies of different SARS-CoV-2 whole genome sequencing approaches.
  • To evaluate sequencing performance across various viral loads and sample types.

Main Methods:

  • Comparative analysis of ARTIC and Entebbe protocols using synthetic and cell-cultured SARS-CoV-2 variants.
  • Assessment of PCR amplicon yield, genome completeness, and lineage calling accuracy.
  • Development and testing of a novel ARTIC-Amp method utilizing rolling circle amplification.

Main Results:

  • ARTIC protocols demonstrated superior PCR amplicon yield and lineage identification accuracy compared to the Entebbe protocol.
  • The SNAP protocol achieved high genome completeness with synthetic genomes, while ARTIC protocols excelled with cell-cultured variants across different viral loads.
  • The novel ARTIC-Amp method achieved 100% gene coverage, outperforming the standard ARTIC protocol in proof-of-principle experiments.

Conclusions:

  • The ARTIC protocol is a robust method for SARS-CoV-2 whole genome sequencing.
  • The ARTIC-Amp method offers improved amplicon yield and coverage, particularly beneficial for samples with limited viral RNA, such as wastewater samples.
Keywords:
COVID-19SARS-CoV-2articbenchmarkingnanopore sequencingrolling circle amplificationwastewater

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