Pango Lineages:
Latest epidemiological lineages of SARS-CoV-2

cov-lineages.org


The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern. This website documents all current Pango lineages and their spread, as well as various software tools which can be used by researchers to perform analyses on SARS-COV-2 sequence data.


For more information on the process by which these lineages are discovered and designated, visit pango.network

Pangolin
Pangolin was developed to implement the dynamic nomenclature of SARS-CoV-2 lineages, known as the Pango nomenclature. It allows a user to assign a SARS-CoV-2 genome sequence the most likely lineage (Pango lineage) to SARS-CoV-2 query sequences.

Pangolin assigns lineages to query sequences as described in Rambaut et al 2020.

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Scorpio
Serious constellations of reoccurring phylogenetically-independent origin. A tool for snp-based calling of variants of concern.

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Civet
Civet is a tool developed with 'real-time' genomics in mind.

Using a background phylogeny, such as the large phylogeny available through the COG-UK infrastructure on CLIMB, civet will generate a report for a set of sequences of interest i.e. an outbreak investigation.

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Polecat
Using a background phylogeny, such as the large phylogeny available through the COG-UK infrastructure on CLIMB, polecat will identify and flag clusters based on various configurable statistics.

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pango.network
A website documenting the Pango nomenclature as well as the policies involved with designating new lineages.

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Global Lineage Reports

Variants of Concern

Contributors

University of Edinburgh
Áine O'Toole
Emily Scher
Ben Jackson
JT McCrone
Rachel Colquhoun
Verity Hill
Isobel Guthrie
Andrew Rambaut
Centre for Genomic Pathogen Surveillance
Anthony Underwood
Ben Taylor
Corin Yeats
Khali Abu-Dahab
David Aanensen
University of Oxford
Oliver Pybus
Moritz Kraemer
Louis du Plessis
bluedot
Kamran Khan
Isaac Bogoch
Alexander Watts
University of Cambridge
Chris Ruis
University of Sydney
Eddie Holmes

Acknowledgements

GISAID data
We acknowledge the hard work and open-science of the individual research labs and public health bodies that have made their genome data accessible on GISAID.
COG-UK
We acknowledge the COG-consortium for allowing direct and immediate access to the UK SARS-CoV-2 data and all individuals involved generating the genome sequences.
GitHub Issues
We thank the users of pangolin who provided feedback on the GitHub issues page and recognise the software is much improved thanks to their patience and suggestions!

Contact Us

For Questions About Pango Lineages

Please first check that your question is not answered in the cov-lineages FAQ page or in the Pango network FAQ page.

If you are reaching out regarding a SARS-CoV-2 cluster you believe should be designated as a lineage, please file an issue in the pango-designation repository. Instructions on how to file an issue can be found here.

For Questions About Pangolin

Before reaching out, please first check the Pangolin Docs as well as the Pangolin repository previous issues to make sure that your question has not already been answered.

If not, enquiries should be posted to the panoglin repository as a new issue.