O'Toole Áine, Scher Emily, Underwood Anthony, Jackson Ben, Hill Verity, McCrone John T, Colquhoun Rachel, Ruis Chris, Abu-Dahab Khalil, Taylor Ben, Yeats Corin, du Plessis Louis, Maloney Daniel, Medd Nathan, Attwood Stephen W, Aanensen David M, Holmes Edward C, Pybus Oliver G, Rambaut Andrew
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH93FL, UK.
The Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, Oxfordshire OX3 7LF, UK.
Virus Evol. 2021 Jul 30;7(2):veab064. doi: 10.1093/ve/veab064. eCollection 2021.
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.
全球病毒基因组学界对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）大流行的反应是前所未有的，在SARS-CoV-2基因组数据的“实时”生成和共享方面取得了重大进展。病毒基因组数据产量的快速增长使得有必要开发新的分析方法，这些方法能够处理比以前多几个数量级的基因组。在此，我们展示并描述命名全球暴发谱系的系统发育分配工具（Pangolin），这是一种计算工具，已开发用于根据Pango动态谱系命名方案为给定的SARS-CoV-2基因组序列分配最可能的谱系。迄今为止，已有近200万个病毒基因组提交给Pangolin的网络应用程序，这促进了SARS-CoV-2基因组流行病学研究，并为研究人员提供了有关大流行传播谱系的可操作信息。
