View source for Phylogenetic Assignment of Named Global Outbreak Lineages

{{Short description|SARS-CoV-2 lineage nomenclature}}
{{Infobox software
| logo = File:Pangolin logo.svg
| logo caption = PANGOLIN logo
| released = {{Start date and age|df=yes|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#Version 3|GNU General Public License v3.0]]
}}
The '''Phylogenetic Assignment of Named Global Outbreak Lineages''' ('''PANGOLIN''') is a software tool developed by Dr. Áine O'Toole<ref>{{cite journal |last1=O'Toole |first1=Áine |last2=Scher |first2=Emily |last3=Underwood |first3=Anthony |last4=Jackson |first4=Ben |last5=Hill |first5=Verity |last6=McCrone |first6=John T |last7=Colquhoun |first7=Rachel |last8=Ruis |first8=Chris |last9=Abu-Dahab |first9=Khalil |last10=Taylor |first10=Ben |last11=Yeats |first11=Corin |last12=Du Plessis |first12=Louis |last13=Maloney |first13=Daniel |last14=Medd |first14=Nathan |last15=Attwood |first15=Stephen W |last16=Aanensen |first16=David M |last17=Holmes |first17=Edward C |last18=Pybus |first18=Oliver G |last19=Rambaut |first19=Andrew |title=Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool |journal=Virus Evolution |date=5 July 2021 |volume=7 |issue=2 |pages=veab064 |doi=10.1093/ve/veab064 |pmid=34527285|pmc=8344591 }}</ref> and members of the [[Andrew Rambaut]] laboratory, with an associated web application 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 |archive-date=17 January 2021 |archive-url=https://web.archive.org/web/20210117212459/https://www.pathogensurveillance.net/resources/articles/real-time-epidemiology-for-covid-19.html |url-status=live }}</ref> Its purpose is to implement a dynamic nomenclature (known as the Pango nomenclature) to classify [[Lineage (genetic)|genetic lineages]] for [[SARS-CoV-2]], the virus that causes [[COVID-19]].<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|journal=[[Nature Microbiology]]|volume=5|issue=11|pages=1403–1407|doi=10.1038/s41564-020-0770-5|pmid=32669681|pmc=7610519|doi-access=free|s2cid=220544096}}</ref> 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).<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|archive-date=10 February 2021|archive-url=https://web.archive.org/web/20210210223250/https://virological.org/t/pangolin-web-application-release/482|url-status=live}}</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"/> It is named after the [[pangolin]].
==Context==
PANGOLIN is a key component underpinning the Pango nomenclature system.<ref>{{cite journal |title=Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology |doi=10.1038/s41564-021-00872-5 |journal=Nature Microbiology |date=15 July 2020 |last1=Rambaut |first1=Andrew |last2=Holmes |first2=Edward C. |last3=o'Toole |first3=Áine |last4=Hill |first4=Verity |last5=McCrone |first5=John T. |last6=Ruis |first6=Christopher |last7=Du Plessis |first7=Louis |last8=Pybus |first8=Oliver G. |volume=6 |issue=3 |page=415 |pmid=33514928 |pmc=7845574 |doi-access=free}}</ref>
As described in [[Andrew Rambaut]] et al. (2020),<ref name="RambautETAL." /> a Pango lineage is described as a cluster of sequences that are associated with an 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.{{cn|date=August 2022}}
Both the tool and the PANGOLIN nomenclature system have been used extensively during the [[COVID-19 pandemic]].<ref name="RambautETAL." /><ref>{{cite journal|last1=Pipes|first1=Lenore|last2=Wang|first2=Hongru|last3=Huelsenbeck|first3=John P|last4=Nielsen|first4=Rasmus|date=9 December 2020|editor-last=Malik|editor-first=Harmit|title=Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny|url=https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa316/6028993|journal=Molecular Biology and Evolution|volume=38|issue=4|pages=1537–1543|publisher=Oxford University Press (OUP)|doi=10.1093/molbev/msaa316|pmid=33295605|pmc=7798932|issn=0737-4038|doi-access=free|access-date=22 January 2021|archive-date=10 December 2020|archive-url=https://web.archive.org/web/20201210143414/https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa316/6028993|url-status=live}}</ref><ref>{{cite bioRxiv|first1=Jobin John|last1=Jacob|first2=Karthick|last2=Vasudevan|title=Evolutionary tracking of SARS-CoV-2 genetic variants highlights intricate balance of stabilizing and destabilizing mutations|date=22 December 2020|last7=Mutreja|first7=Ankur|first5=Gagandeep|first6=Balaji|last6=Veeraraghavan|last5=Kang|first4=Karthik|last4=Gunasekaran|first3=Agila Kumari|last3=Pragasam|biorxiv=10.1101/2020.12.22.423920|quote=Phylogenetic Assignment of Named Global Outbreak LINeages tool (PANGOLIN) has been the most widely used tool for lineage assignment to newly emerging variants.}}</ref>
==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.<ref>{{cite web |url=https://github.com/cov-lineages/pangoLEARN |title=pangoLEARN Store of the trained model for PANGOLIN to access |website=GitHub: cov-lineages/pangoLEARN |date= |access-date=13 February 2021 |archive-date=3 January 2021 |archive-url=https://web.archive.org/web/20210103202912/https://github.com/cov-lineages/pangoLEARN |url-status=live }}</ref><ref>{{cite web |url=https://cov-lineages.org/pangolin.html |title=PANGO lineages |website=cov-lineages.org |date= |access-date=4 March 2021 |archive-date=28 February 2021 |archive-url=https://web.archive.org/web/20210228182435/https://cov-lineages.org/pangolin.html |url-status=live }}</ref>{{explain|reason=more specific details of usage instructions would be good|date=March 2021}}
===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<ref>{{cite web |url=https://scikit-learn.org/stable/modules/generated/sklearn.tree.DecisionTreeClassifier.html |title=sklearn.tree.DecisionTreeClassifier |website=scikit-learn.org |date= |access-date=13 February 2021 |archive-date=19 February 2021 |archive-url=https://web.archive.org/web/20210219120920/https://scikit-learn.org/stable/modules/generated/sklearn.tree.DecisionTreeClassifier.html |url-status=live }}</ref> 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.<ref name=GH_pango/> This approach is fast and can assign large numbers of SARS-CoV-2 genomes in a relatively short time.<ref name=PLearn_CovLin>{{cite web |url=https://cov-lineages.org/resources/pangolin/pangolearn.html |title=pangoLEARN PANGOLIN 2.0: pangoLEARN description |website=cov-lineages.org |date= |access-date=19 November 2021 |quote=The model was trained using ~60,000 SARS-CoV-2 sequences from GISAID... training this model takes approximately 30 minutes on our hardware |archive-date=4 November 2021 |archive-url=https://web.archive.org/web/20211104125154/https://cov-lineages.org/resources/pangolin/pangolearn.html |url-status=live}}</ref>
==Availability==
PANGOLIN is available as a [[Command line|command-line]]-based tool, downloadable from [[Conda (package manager)|Conda]] and from a GitHub repository,<ref name=GH_pango>{{cite web |url=https://github.com/cov-lineages/pangolin |title=cov-lineages/pangolin |website=GitHub: cov-lineages/pangolin |date= |access-date=13 February 2021 |archive-date=15 February 2021 |archive-url=https://web.archive.org/web/20210215054819/https://github.com/cov-lineages/pangolin |url-status=live }}</ref> and as a web-application<ref name=PCLA>{{cite web|url=https://pangolin.cog-uk.io/|title=Pangolin COVID-19 Lineage Assigner|website=pangolin.cog-uk.io|date=|access-date=13 February 2021|archive-date=10 February 2021|archive-url=https://web.archive.org/web/20210210104229/https://pangolin.cog-uk.io/|url-status=live}}</ref> with a drag-and-drop graphical user interface. The PANGOLIN web application has assigned more than 512,000 unique SARS-CoV-2 sequences as of January 2021.{{citation needed|date=March 2021}}
==Creators and 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.<ref name="Vir482" />
The PANGOLIN web application was developed by the Centre for Genomic Pathogen Surveillance,<ref name="PCLA" /> namely Anthony Underwood, Ben Taylor, Corin Yeats, Khali Abu-Dahab, and David Aanensen.<ref name="Vir482" />
==See also==
* [[Colloquial names of COVID-19 variants]]
* [[Variants of SARS-CoV-2]]
* [[Nextstrain]]
* [[INSDC]]
==References==
{{Reflist}}
== External links ==
* {{GitHub|cov-lineages/pangolin}}
* {{Official website}}
* [https://www.pango.network pango.network] — information on the Pango system rules, governance committee, and lineage designation committee
{{Bioinformatics}}
[[Category:Phylogenetics software]]
[[Category:Genome databases]]
[[Category:Medical software]]
[[Category:Medical responses to the COVID-19 pandemic]]