Basic Info

Use Pangolin to designate the dynamic nomenclature of SARS-CoV-2 lineages

More Details

In April 2020, proposed and developed a dynamic nomenclature system to name and track global transmission lineages of SARS-CoV-2. This is called the Pango nomenclature and complements two other SARS-CoV-2 nomenclature systems (NextStrain and GISAID) that focus on broader phylogenetic ‘clades’, and which incorporate criteria for minimum prevalence and persistence. The Pango lineage nomenclature system is hierarchical and fine scaled and designed to capture the leading edge of pandemic transmission. Each Pango lineage aims to define an epidemiologically relevant phylogenetic cluster, for instance an introduction into a distinct geographic area with evidence of onward transmission. Pango lineages are particularly suited to outbreak investigations at national or regional scales.

What's New

Pangolin (Phylogenetic Assignment of Named Global Outbreak Lineages) 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.

It is available as a command line tool and a web application. The web application was developed by the Centre for Genomic Pathogen Surveillance. The command line tool is open source software available under the GNU General Public License v3.0.

Additional Information

Related links:

https://cov-lineages.org/resources/pangolin.html

Literature

Rambaut A, Holmes EC, O'Toole Á, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403-1407. doi:10.1038/s41564-020-0770-5

O'Toole Á, Scher E, Underwood A, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol. 2021;7(2):veab064. Published 2021 Jul 30. doi:10.1093/ve/veab064