> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/sars-cov-2-notable-mutations.md).

# SARS-CoV-2 Notable Mutations

## About

Genomes identified by Pathogenwatch as SARS-CoV-2 are searched against the Type Mutations database to identify mutations of significance to public health researchers. A full description of the database and software can be found here: <https://cgps.gitlab.io/cog-uk/type_variants/>.

## Method

{% hint style="warning" %}
This tool hasn't been updated since it was released and there are now likely to be many new mutations of interest.
{% endhint %}

A modified version of the ["type\_variants"](https://github.com/cov-ert/type_variants) program is used to search against a curated database of variants. For each tested position, there are four possible outcomes: (1) wildtype; (2) mutation present; (3) another mutation; (4) sequence error - if the position is missing or contains one or more non-ATCG characters. If the mutation description contains a "\*" that any mutation at that site is considered as "(2) mutation present".

## Viewing the results

### Genome Reports

Notable mutations are reported in individual genome reports with links to descriptions of the mutations in the Type Mutations website (e.g. for A222V view <https://cgps.gitlab.io/cog-uk/type_variants/#A222V>).

![Genome report showing notable mutations](/files/-MVaax9uLfLvSd1wbf9y)

### Collection Viewer

Notable mutations are shown for SARS-CoV-2 collections in a metadata table that can be accessed using the table switcher. Found mutations are shown as a red circle, while other mutations at those positions are shown in yellow. Question marks indicate sequence errors, while a blank cell indicates that location has the wild type/reference sequence. Mutations can be selected by clicking on the header and corresponding tree leaves and map markers will update to red, yellow, or white.

![D614G highlighted in the Notable Variants table and collection tree](/files/-MVacTKdIBsN1bq0m_M7)

## Browsing genomes with a mutation

It's possible to select genomes with a specific mutation in the Genome Browser by selecting "*Betacoronavirus*" in the "Genus" filter, "*Severe acute respiratory virus*" in the "Species" filter, and then "*subsp. SARS-CoV-2*". This enables the "Notable Mutations" filter, allowing genomes with a specific mutation to be selected.

## How to cite

This tool has not been published and is currently not under development. Please contact us if you need any further information about it.