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 possible designation as a WHO SARS-CoV-2 Variant of Concern of a nucleotide sequence.

Updated in May 2022:

  • The scope of the tool was changed to detect only whether a submitted nucleotide sequence is SARS-CoV-2 variant of concern:
    WHO designation Pangolin lineage(s) Nextstrain clade
    Alpha B.1.1.7 20I
    Beta B.1.351 20H
    Gamma P.1 20J
    Delta * B.1.617.2 21A, 21I, 21J
    Omicron * BA.1 21K
    Omicron * BA.2 21L
    Omicron * BA.4 22A
    Omicron * BA.5 22B
    Omicron * XE
    (* beta test, please provide feedback)

For a fine grain classification of variants other online tools are availble: nextClade and pangolin .

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

Input

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

Revisit results from a previous run

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