Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool.
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool.
复制标题
使用PANGOLIN工具在新兴大流行中分配流行病学谱系。
DOI：
10.1093/ve/veab064
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发表时间：
2021
期刊：
影响因子：
5.3
通讯作者：
Rambaut A
中科院分区：
文献类型：
--
作者：
O'Toole Á;Scher E;Underwood A;Jackson B;Hill V;McCrone JT;Colquhoun R;Ruis C;Abu-Dahab K;Taylor B;Yeats C;du Plessis L;Maloney D;Medd N;Attwood SW;Aanensen DM;Holmes EC;Pybus OG;Rambaut A
全球病毒基因组学界对严重急性呼吸综合征冠状病毒2型（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。病毒基因组数据生产的快速增长需要开发新的分析方法，这些方法可以处理比以前更多数量级的基因组。在这里，我们提出并描述命名的全球爆发谱系（穿山甲），已开发的计算工具，分配最有可能的谱系给定的SARS-CoV-2基因组序列根据Pango动态谱系命名方案的系统发育分配。迄今为止，已经有近200万个病毒基因组提交给穿山甲的网络应用程序实现，这促进了SARS-CoV-2基因组流行病学的研究，并为研究人员提供了有关大流行病传播谱系的可操作信息。
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.
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影响因子：
5.3
作者：
Duchene, Sebastian;Featherstone, Leo;Baele, Guy
通讯作者：
Baele, Guy
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
28.3
作者：
Rambaut A;Holmes EC;O'Toole Á;Hill V;McCrone JT;Ruis C;du Plessis L;Pybus OG
通讯作者：
Pybus OG
影响因子：
64.8
作者：
Faria NR;Quick J;Claro IM;Thézé J;de Jesus JG;Giovanetti M;Kraemer MUG;Hill SC;Black A;da Costa AC;Franco LC;Silva SP;Wu CH;Raghwani J;Cauchemez S;du Plessis L;Verotti MP;de Oliveira WK;Carmo EH;Coelho GE;Santelli ACFS;Vinhal LC;Henriques CM;Simpson JT;Loose M;Andersen KG;Grubaugh ND;Somasekar S;Chiu CY;Muñoz-Medina JE;Gonzalez-Bonilla CR;Arias CF;Lewis-Ximenez LL;Baylis SA;Chieppe AO;Aguiar SF;Fernandes CA;Lemos PS;Nascimento BLS;Monteiro HAO;Siqueira IC;de Queiroz MG;de Souza TR;Bezerra JF;Lemos MR;Pereira GF;Loudal D;Moura LC;Dhalia R;França RF;Magalhães T;Marques ET Jr;Jaenisch T;Wallau GL;de Lima MC;Nascimento V;de Cerqueira EM;de Lima MM;Mascarenhas DL;Neto JPM;Levin AS;Tozetto-Mendoza TR;Fonseca SN;Mendes-Correa MC;Milagres FP;Segurado A;Holmes EC;Rambaut A;Bedford T;Nunes MRT;Sabino EC;Alcantara LCJ;Loman NJ;Pybus OG
通讯作者：
Pybus OG
影响因子：
3.7
作者：
Price MN;Dehal PS;Arkin AP
通讯作者：
Arkin AP