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{{Infobox software
[[File:Pangolin logo.svg|thumb|right|PANGOLIN logo]]
| logo = File:Pangolin logo.svg
| logo caption = PANGOLIN logo
| released = {{Start date and age|2020|04|30}}
| latest release version = {{wikidata|property|reference|edit|P348}}
| latest release date = {{Start date and age|{{wikidata|qualifier|P348|P577}}}}
| repo = {{url|https://github.com/cov-lineages/pangolin}}
| programming language = [[Python (programming language)|Python]]
| license = [[GNU General Public License v3.0]]
}}
'''Phylogenetic Assignment of Named Global Outbreak Lineages''' (PANGOLIN) is a software tool developed by members of the Rambaut Lab, and the associated web application is developed by the [[Centre for Genomic Pathogen Surveillance]] in [[South Cambridgeshire]].<ref>{{cite web |url=https://www.pathogensurveillance.net/resources/articles/real-time-epidemiology-for-covid-19.html |title=Real-Time Epidemiology for COVID-19 |website=www.pathogensurveillance.net |access-date=22 January 2021}}</ref> Its purpose is to implement the dynamic nomenclature of [[SARS-CoV-2]] [[Lineage (genetic)|lineages]], known as the PANGO nomenclature.<ref name="RambautETAL.">{{cite journal|author1=Rambaut, A.|author2=Holmes, E.C.|author3=O’Toole, Á.|display-authors=etal|year=2020|title=A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology|url=https://www.nature.com/articles/s41564-020-0770-5|journal=[[Nature Microbiology]]|volume=5|issue=11|pages=1403–1407|doi=10.1038/s41564-020-0770-5|pmid=32669681|doi-access=free|s2cid=220544096}}</ref> A user with a full genome sequence of a sample of SARS-CoV-2 (the virus that causes [[COVID-19]]) can use the tool to submit that sequence, which is then compared with other genome sequences, and assigned the most likely lineage (PANGO Lineage).<ref name="Vir482">{{cite web|date=May 2020|title=Pangolin web application release|url=https://virological.org/t/pangolin-web-application-release/482|access-date=18 February 2021|website=virological.org}}</ref> Single or multiple runs are possible, and the tool can return further information regarding the known history of the assigned lineage.<ref name="Vir482"/> Additionally, it interfaces with Microreact, to show a time sequence of the location of reports of sequenced samples of the same lineage.<ref name="Vir482"/> This latter feature draws on publicly available genomes obtained from the [[COVID-19 Genomics UK Consortium]] and from those submitted to [[GISAID]].<ref name="Vir482"/>
'''Phylogenetic Assignment of Named Global Outbreak Lineages''' (PANGOLIN) is a software tool developed by members of the Rambaut Lab, and the associated web application is developed by the [[Centre for Genomic Pathogen Surveillance]] in [[South Cambridgeshire]].<ref>{{cite web |url=https://www.pathogensurveillance.net/resources/articles/real-time-epidemiology-for-covid-19.html |title=Real-Time Epidemiology for COVID-19 |website=www.pathogensurveillance.net |access-date=22 January 2021}}</ref> Its purpose is to implement the dynamic nomenclature of [[SARS-CoV-2]] [[Lineage (genetic)|lineages]], known as the PANGO nomenclature.<ref name="RambautETAL.">{{cite journal|author1=Rambaut, A.|author2=Holmes, E.C.|author3=O’Toole, Á.|display-authors=etal|year=2020|title=A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology|url=https://www.nature.com/articles/s41564-020-0770-5|journal=[[Nature Microbiology]]|volume=5|issue=11|pages=1403–1407|doi=10.1038/s41564-020-0770-5|pmid=32669681|doi-access=free|s2cid=220544096}}</ref> A user with a full genome sequence of a sample of SARS-CoV-2 (the virus that causes [[COVID-19]]) can use the tool to submit that sequence, which is then compared with other genome sequences, and assigned the most likely lineage (PANGO Lineage).<ref name="Vir482">{{cite web|date=May 2020|title=Pangolin web application release|url=https://virological.org/t/pangolin-web-application-release/482|access-date=18 February 2021|website=virological.org}}</ref> Single or multiple runs are possible, and the tool can return further information regarding the known history of the assigned lineage.<ref name="Vir482"/> Additionally, it interfaces with Microreact, to show a time sequence of the location of reports of sequenced samples of the same lineage.<ref name="Vir482"/> This latter feature draws on publicly available genomes obtained from the [[COVID-19 Genomics UK Consortium]] and from those submitted to [[GISAID]].<ref name="Vir482"/>


Revision as of 14:00, 24 March 2021

Phylogenetic Assignment of Named Global Outbreak Lineages
Initial releaseApril 30, 2020; 4 years ago (2020-04-30)
Stable release
4.3.1[1] Edit this on Wikidata / 26 July 2023; 15 months ago (26 July 2023)
Repositorygithub.com/cov-lineages/pangolin
Written inPython
LicenseGNU General Public License v3.0
Websitepangolin.cog-uk.io Edit this on Wikidata

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

Context

PANGOLIN is a key component underpinning the PANGO nomenclature system.[5]

As described in Andrew Rambaut et al. (2020),[3] a PANGO Lineage is described as a cluster of sequences that are associated with a epidemiological event, for instance an introduction of the virus into a distinct geographic area with evidence of onward spread. Lineages are designed to capture the emerging edge of the pandemic and are at a fine-grain resolution suitable to genomic epidemiological surveillance and outbreak investigation.

Both the tool and the PANGOLIN nomenclature system have been used extensively during the COVID-19 pandemic.[3][6][7]

Description

Lineage designation

Distinct from the PANGOLIN tool, Pango lineages are regularly, manually curated based on the current globally circulating diversity. A large phylogenetic tree is constructed from an alignment containing publicly available SARS-CoV-2 genomes, and sub-clusters of sequences in this tree are manually examined and cross-referenced against epidemiological information to designate new lineages; these can be designated by data producers, and lineage suggestions can be submitted to the Pango team via a GitHub issue request.[8][9][further explanation needed]

Model training

These manually curated lineage designations, and the associated genome sequences, are the input into the machine learning model training. This model, both the training and the assignment, has been termed 'pangoLEARN'. The current version of pangoLEARN uses a classification tree, based on the scikit learn implementation[10] of a decision tree classifier.

Lineage assignation

Originally, PANGOLIN used a maximum-likelihood-based assignment algorithm to assign query SARS-CoV-2 the most likely lineage sequence. Since the release of Version 2.0 in July 2020, however, it has used the 'pangoLEARN' machine-learning-based assignment algorithm to assign lineages to new SARS-CoV-2 genomes.[11] This approach is fast and can assign large numbers of SARS-CoV-2 genomes in a relatively short time.[12]

Availability

PANGOLIN is available as a command-line-based tool, downloadable from Conda and from a GitHub repository,[11] and as a web-application[13] with a drag-and-drop graphical user interface. The PANGOLIN web application has assigned more that 512,000 unique SARS-CoV-2 sequences as of January 2021.[citation needed]

Creators/ Developers

PANGOLIN was created by Áine O'Toole and the Rambaut lab and released on 5 April 2020. The main developers of PANGOLIN are Áine O'Toole and Emily Scher; many others have contributed to various aspects of the tool, including Ben Jackson, J.T. McCrone, Verity Hill, and Rachel Colquhoun of the Rambaut Lab.[4]

The PANGOLIN web application was developed by the Centre for Genomic Pathogen Surveillance,[13] namely Anthony Underwood, Ben Taylor, Corin Yeats, Khali Abu-Dahab, and David Aanensen.[4]

See also

References

  1. ^ "Release 4.3.1". 26 July 2023. Retrieved 1 August 2023.
  2. ^ "Real-Time Epidemiology for COVID-19". www.pathogensurveillance.net. Retrieved 22 January 2021.
  3. ^ a b c 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. PMID 32669681. S2CID 220544096.
  4. ^ a b c d e f "Pangolin web application release". virological.org. May 2020. Retrieved 18 February 2021.
  5. ^ "Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 15 July 2020. doi:10.1038/s41564-021-00872-5. Retrieved 4 March 2021.
  6. ^ Pipes, Lenore; Wang, Hongru; Huelsenbeck, John P; Nielsen, Rasmus (9 December 2020). Malik, Harmit (ed.). "Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny". Molecular Biology and Evolution. Oxford University Press (OUP). doi:10.1093/molbev/msaa316. ISSN 0737-4038.
  7. ^ Jacob, Jobin John; Vasudevan, Karthick; Pragasam, Agila Kumari; Gunasekaran, Karthik; Kang, Gagandeep; Veeraraghavan, Balaji; Mutreja, Ankur (22 December 2020). "Evolutionary tracking of SARS-CoV-2 genetic variants highlights intricate balance of stabilizing and destabilizing mutations". bioRxiv 10.1101/2020.12.22.423920. Phylogenetic Assignment of Named Global Outbreak LINeages tool (PANGOLIN) has been the most widely used tool for lineage assignment to newly emerging variants. {{cite bioRxiv}}: Unknown parameter |url= ignored (help)
  8. ^ "pangoLEARN Store of the trained model for PANGOLIN to access". GitHub: cov-lineages/pangoLEARN. Retrieved 13 February 2021.
  9. ^ "PANGO lineages". cov-lineages.org. Retrieved 4 March 2021.
  10. ^ "sklearn.tree.DecisionTreeClassifier". scikit-learn.org. Retrieved 13 February 2021.
  11. ^ a b "cov-lineages /pangolin". GitHub: cov-lineages/pangolin. Retrieved 13 February 2021.
  12. ^ "pangoLEARN PANGOLIN 2.0: pangoLEARN description". cov-lineages.org. Retrieved 3 March 2021. The model was trained using ~60,000 SARS-CoV-2 sequences from GISAID... training this model takes approximately 30 minutes on our hardware
  13. ^ a b "Pangolin COVID-19 Lineage Assigner". pangolin.cog-uk.io. Retrieved 13 February 2021.
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