How Genome Detective assigns SARS-CoV-2 (the virus that causes COVID-19 disease)

Coronavirus Typing Tool

This tool is designed to use Blast and phylogenetic methods in order to identify the Coronavirus types, genotypes and lineages of a nucleotide sequence.

The Coronavirus typing tool includes SARS-CoV-2 (2019) genomes and lineages, including sequences initially shared by Professor Yong-Zhen Zhang and colleagues via this post on Professor Yong-Zhen Zhang and colleagues ask that you communicate with them if you wish to publish results that use the sequence that they share in a journal. We gratefully acknowledge their contribution.

Updated in January 2021:

  • Analysis of SARS-CoV-2 lineages of concern, most notably 501Y.V1, 501Y.V2 and 501Y.V3. (beta test, please provide feedback)
  • Mutations are listed in the xls/csv download link at the bottom of the overview page.
Last update: 2021-22-01: changed selection of reference sequences, improved assignments

Note for batch analysis: The tool accepts up to 2000 sequences at a time.


Submit one or more FASTA sequences to be typed individually. If you have raw NGS reads (short reads or long reads), please use the Genome Detective Virus Tool to assemble first. Subtyping tools will be linked in the results.
Click here to load some sample data.

click or drop file

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