Abstract
The response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (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 of more genomes than previously available. Here, we present and describe Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin), 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 lineage nomenclature scheme. 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.
Highlights
The response of the global virus genomics community to the coronavirus disease 2019 (COVID-19) (severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)) pandemic has been unprecedented, with a concerted and cooperative effort toward the generation and timely sharing of large numbers of SARS-CoV-2 genomes
The response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards the ‘real-time’ generation and sharing of SARS-CoV-2 genomic data
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
Summary
The response of the global virus genomics community to the coronavirus disease 2019 (COVID-19) (severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)) pandemic has been unprecedented, with a concerted and cooperative effort toward the generation and timely sharing of large numbers of SARS-CoV-2 genomes. The rapid sharing of high volumes of virus genomes has given public health bodies potential access to actionable data as the pandemic has unfolded. This contrasts with the generation and application of virus genomes during some previous global health public emergencies, such as the West African Ebola virus epidemic and Zika virus in the Americas, during which sequencing was more retrospective and undertaken on a smaller scale (Rota et al 2003; Dudas et al 2017; Faria et al 2017; Worobey, Cox, and Gill 2019). In April 2020, Rambaut et al (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 (Rambaut et al 2021) 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. Each Pango lineage aims to define an epidemiologically relevant phylogenetic
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