A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

被引：1699

作者：

Rambaut, Andrew ^{[1
]}

Holmes, Edward C. ^{[2
,3
]}

O'Toole, Aine ^{[1
]}

Hill, Verity ^{[1
]}

McCrone, John T. ^{[1
]}

Ruis, Christopher ^{[4
]}

du Plessis, Louis ^{[5
]}

Pybus, Oliver G. ^{[5
]}

机构：

[1] Univ Edinburgh, Inst Evolutionary Biol, Edinburgh, Midlothian, Scotland

[2] Univ Sydney, Marie Bashir Inst Infect Dis & Biosecur, Sch Life & Environm Sci, Sydney, NSW, Australia

[3] Univ Sydney, Sch Med Sci, Sydney, NSW, Australia

[4] Univ Cambridge, Dept Med, Cambridge, England

[5] Univ Oxford, Dept Zool, Oxford, England

来源：

NATURE MICROBIOLOGY | 2020年 / 5卷 / 11期

基金：

澳大利亚研究理事会; 英国惠康基金; 欧洲研究理事会;

关键词：

D O I：

10.1038/s41564-020-0770-5

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. Here, we present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and delabelling virus lineages that become unobserved and hence are probably inactive. By focusing on active virus lineages and those spreading to new locations, this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.

引用

页码：1403 / 1407

页数：5

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