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Phylogenetic Assignment of Named Global Outbreak Lineages

Phylogenetic Assignment of Named Global Outbreak Lineages
Initial release30 April 2020 (2020-04-30)
Stable release
4.3.1[1] Edit this on Wikidata / 26 July 2023 (26 July 2023)
Repositorygithub.com/cov-lineages/pangolin
Written inPython
LicenseGNU General Public License v3.0
Websitepangolin.cog-uk.io Edit this on Wikidata

The Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) is a software tool developed by Dr. Áine O'Toole[2] and members of the Andrew Rambaut laboratory, with an associated web application developed by the Centre for Genomic Pathogen Surveillance in South Cambridgeshire.[3] Its purpose is to implement a dynamic nomenclature (known as the Pango nomenclature) to classify genetic lineages for SARS-CoV-2, the virus that causes COVID-19.[4] A user with a full genome sequence of a sample of SARS-CoV-2 can use the tool to submit that sequence, which is then compared with other genome sequences, and assigned the most likely lineage (Pango lineage).[5] Single or multiple runs are possible, and the tool can return further information regarding the known history of the assigned lineage.[5] Additionally, it interfaces with Microreact, to show a time sequence of the location of reports of sequenced samples of the same lineage.[5] This latter feature draws on publicly available genomes obtained from the COVID-19 Genomics UK Consortium and from those submitted to GISAID.[5] It is named after the pangolin.

  1. ^ "Release 4.3.1". 26 July 2023. Retrieved 1 August 2023.
  2. ^ O’Toole, Áine; Scher, Emily; Underwood, Anthony; Jackson, Ben; Hill, Verity; McCrone, John T; Colquhoun, Rachel; Ruis, Chris; Abu-Dahab, Khalil; Taylor, Ben; Yeats, Corin; Du Plessis, Louis; Maloney, Daniel; Medd, Nathan; Attwood, Stephen W; Aanensen, David M; Holmes, Edward C; Pybus, Oliver G; Rambaut, Andrew (5 July 2021). "Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool". Virus Evolution. 7 (2): veab064. doi:10.1093/ve/veab064. PMC 8344591. PMID 34527285.
  3. ^ "Real-Time Epidemiology for COVID-19". www.pathogensurveillance.net. Archived from the original on 17 January 2021. Retrieved 22 January 2021.
  4. ^ Rambaut, A.; Holmes, E.C.; O’Toole, Á.; et al. (2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMC 7610519. PMID 32669681. S2CID 220544096.
  5. ^ a b c d "Pangolin web application release". virological.org. May 2020. Archived from the original on 10 February 2021. Retrieved 18 February 2021.

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