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A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees.

Jakob McBroome1,2, Bryan Thornlow1,2, Angie S Hinrichs2

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Molecular Biology and Evolution
|September 1, 2021
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Summary

A new database of SARS-CoV-2 phylogenetic trees, encoded in the mutation-annotated tree (MAT) format, offers a comprehensive view of the virus's evolution. This resource, updated daily, aids in analyzing the vast scale of sequencing data.

Keywords:
COVID-19SARS-CoV-2 phylogeneticsgenomic surveillance

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Area of Science:

  • Virology
  • Computational Biology
  • Genomics

Background:

  • The exponential growth of SARS-CoV-2 sequencing data presents significant analytical challenges.
  • Existing tools and file formats struggle to manage and interpret the massive volume of viral genomic information.
  • Understanding SARS-CoV-2 evolution is critical for public health responses.

Purpose of the Study:

  • To develop an efficient and scalable database for analyzing SARS-CoV-2 phylogenetic trees.
  • To provide a comprehensive and daily-updated resource for tracking the virus's evolutionary history.
  • To introduce a novel command-line utility for manipulating and querying phylogenetic data.

Main Methods:

  • Inference of phylogenetic trees using unrestricted public SARS-CoV-2 sequences.
  • Implementation of the mutation-annotated tree (MAT) format for efficient data encoding.
  • Daily updates to incorporate new sequence data and associated metadata (Nextstrain clades, Pango lineages).
  • Development of `matUtils`, a command-line tool for data manipulation and querying.

Main Results:

  • Creation of a SARS-CoV-2 MAT database containing over 834,521 sequences as of June 9, 2021.
  • The database provides a daily-updated, comprehensive view of SARS-CoV-2 evolutionary history.
  • The `matUtils` tool enables rapid querying and interpretation of the MAT database.

Conclusions:

  • The developed SARS-CoV-2 MAT database and `matUtils` offer a powerful solution for analyzing large-scale viral sequencing data.
  • This resource facilitates a deeper understanding of SARS-CoV-2 evolution and adaptation.
  • The MAT format and associated tools represent a significant advancement in viral phylogenetics.