Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool

By Á. O'toole, Emily Scher, A. Underwood, B. Jackson, V. Hill, J. McCrone, R. Colquhoun, C. Ruis, K. AbuDahab, Ben Taylor and 9 more. Virus Evolution, 2021

1,013 citations recorded by the source corpus.

Abstract The response of the global virus genomics community to the SARS-CoV-2 pandemic has been unprecedented, with significant advances made towards the ‘real-time’ generation and sharing of SARS-CoV-2 genomic data. The rapid growth in virus genome data production has necessitated the development of new analytical methods that can deal with orders of magnitude more genomes than previously available. Here we present and describe pangolin (Phylogenetic Assignment of Named Global Outbreak Lineages), a computational tool that has been developed to assign the most likely lineage to a given SARS-CoV-2 genome sequence according to the Pango dynamic nomenclature scheme described in Rambaut et al. (2020). To date, nearly two million virus genomes have been submitted to the web-application implementation of pangolin, which has facilitated the SARS-CoV-2 genomic epidemiology and provided researchers with access to actionable information about the pandemic’s transmission lineages.

Subfields: Ecology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/b8ad1ee6c7c9d0875348f5a69b8aa7b770e2811c

Citations in the corpus

• Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants (2022, neutral): “1 were greatly or completely resistant to all RBD class 1 and class 3 mAbs tested as well as 92 to one RBD class 2 mAb (XGv051), a class 4 mAb (10-40), and an NTD-SD2 mAb (C1717).”
• The UCSC Genome Browser database: 2023 update (2022, neutral): “A minimized version of the tree is included in the pangolin tool (30), used by public health departments worldwide to assign lineages to new sequences.”