Skip to main content

SARS-CoV-2 Phylogeny (Nextstrain)

Phylogenetic evolution of SARS-CoV-2 in Europe including Czech sequences — an interactive tree of variants and their geographic spread.

Public source Source: Nextstrain · sequences from GISAID Updated: Daily (Nextstrain server) SARS-CoV-2genomicsphylogenyNextstrain

This dashboard opens Nextstrain — the standard for real-time phylogenomic pathogen surveillance, developed by the Bedford Lab (Fred Hutch / WHO).

What Nextstrain shows

  • Phylogenetic tree — evolutionary relationships between SARS-CoV-2 sequences
  • Geographic spread — an animation of how variants spread across countries
  • Timeline — when each variant emerged and when it dominated
  • Czech sequences — the Czech Republic contributes sequences via GISAID

Available Nextstrain builds

BuildDescription
ncov/gisaid/europeEurope — GISAID sequences (includes CZ)
ncov/open/globalGlobal open-data build
ncov/open/europeEurope — open data
Open Nextstrain — SARS-CoV-2 Europe

Local Nextstrain build (for your own sequences)

To build from your own or local sequences, a Nextstrain/Augur Docker container is available in docker-compose.yml (profile nextstrain):

docker compose --profile nextstrain run augur --help

Required input files:

  • nextstrain/data/sequences.fasta — FASTA sequences from GISAID/ENA
  • nextstrain/data/metadata.tsv — metadata (date, source, location)

Nextstrain: open source · Bedford Lab · MIT licence

Processing of personal data

What we collect

Web server access log — IP address, time, page address, browser type and referring page. Deleted after 14 days.

Visit counts by organisation — the IP address is resolved to an organisation (for example “Charles University”) and discarded. Only counts are kept. They are not personal data.

Which pages are read — our own analytics running on our server, with no cookies and no device identifier. The data does not go to third parties.

On your device we store a single item, and only so that this notice does not appear on every visit. It is not an identifier and it goes nowhere.

Your rights

You have the right of access to your data, to rectification or erasure, to restriction of processing, to object, and to lodge a complaint with the Czech Data Protection Authority.

⚠️ In practice: we cannot find you in the access log unless you tell us the IP address and roughly when you visited — we keep nothing else to search on.

The controller is the Institute of Molecular Genetics of the Czech Academy of Sciences. Contact: hpaces@img.cas.cz