Phylogenetic Assignment of Named Global Outbreak Lineages

The Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) is a software tool developed by Dr. Áine O'Toole and members of the Andrew Rambaut laboratory, with an associated web application developed by the Centre for Genomic Pathogen Surveillance in South Cambridgeshire. 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. 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). Single or multiple runs are possible, and the tool can return further information regarding the known history of the assigned lineage. Additionally, it interfaces with Microreact, to show a time sequence of the location of reports of sequenced samples of the same lineage. This latter feature draws on publicly available genomes obtained from the COVID-19 Genomics UK Consortium and from those submitted to GISAID. It is named after the pangolin.