Pango Lineages:
Latest epidemiological lineages of SARS-CoV-2
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 assigns lineages to query sequences as described in Rambaut et al 2020.
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.
Scorpio
Serious constellations of reoccurring phylogenetically-independent origin. A tool for snp-based calling of variants of concern.
Civet 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.
Civet is a tool developed with 'real-time' genomics in mind.
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.
pango.network
A website documenting the Pango nomenclature as well as the policies involved with designating new lineages.
Global Lineage Reports
Variants of Concern
How to Cite
Citing the Pango Nomenclature
Citing a Cov-Lineages.org Lineage Report
Citing Pangolin
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
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!