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Systematic Error: Methodological and Sampling Errors01:15

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Scientists always try their best to record measurements with the utmost accuracy and precision. However, sometimes errors do occur. These errors can be random or systematic. Random errors are observed due to the inconsistency or fluctuation in the measurement process, or variations in the quantity itself that is being measured. Such errors fluctuate from being greater than or less than the true value in repeated measurements. Consider a scientist measuring the length of an earthworm using a...
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Related Experiment Video

Updated: Feb 11, 2026

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Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

Martin Hunt1,2,3,4, Angie S Hinrichs5, Daniel Anderson1

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|February 9, 2026
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Summary

This study introduces Viridian, a new tool to correct errors in SARS-CoV-2 genomes sequenced using tiled amplicons. This improves the accuracy of global phylogenetic trees, crucial for tracking virus evolution and variant spread.

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Area of Science:

  • Genomics
  • Virology
  • Bioinformatics

Background:

  • Most SARS-CoV-2 genomes were generated using tiled amplicons, a method prone to systematic errors.
  • These errors, often stemming from outdated amplicon schemes and sequencing limitations, impacted the accuracy of phylogenetic analyses.
  • The emergence of new SARS-CoV-2 variants necessitated updates to sequencing strategies, further complicating genome reconstruction.

Purpose of the Study:

  • To develop and validate a robust method for reconstructing high-quality SARS-CoV-2 genomes from amplicon sequencing data.
  • To generate an accurate global phylogenetic tree reflecting the evolutionary history of SARS-CoV-2.
  • To quantify the improvements in phylogenetic inference achieved by the new methodology.

Main Methods:

  • Utilized Viridian, a novel assembly tool designed to rigorously process amplicon sequence data.
  • Reconstructed SARS-CoV-2 genomes from public data available as of June 2024.
  • Constructed a global phylogenetic tree incorporating 4,471,579 samples.

Main Results:

  • Generated high-quality consensus sequences by addressing systematic errors inherent in amplicon sequencing.
  • Developed a comprehensive global phylogenetic tree of SARS-CoV-2, accessible via a public portal.
  • Validated the Viridian methodology through simulations and empirical data, demonstrating significant improvements in phylogenetic accuracy.

Conclusions:

  • Viridian effectively corrects amplicon sequencing errors, leading to more reliable SARS-CoV-2 genome reconstruction.
  • The improved phylogenetic tree provides a more accurate representation of viral evolution and variant dynamics.
  • This work enhances our ability to track pandemics and understand pathogen evolution through accurate genomic data.