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

By Andrew Rambaut, Edward C. Holmes, Á. O'toole, V. Hill, J. McCrone, C. Ruis, L. du Plessis, Oliver George Pybus. Nature Microbiology, 2020

2,454 citations recorded by the source corpus.

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. The authors propose a nomenclature of SARS-CoV-2 lineages to assist research on epidemiology and decision-making during the COVID-19 pandemic. This nomenclature is based on the SARS-CoV-2 phylogeny and designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide. The authors develop a set of rules to produce a hierarchical four-level nomenclature of labels that is flexible and dynamic.

Subfields: Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5d418e2f494942fef4584a2ce4f7ac8caa866e1e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Infectious Diseases

1. Kwok-Yung Yuen
2. K. To
3. V. Cheng
4. Kwok-Hung Chan
5. Shuofeng Yuan
6. Andrew Rambaut
7. Philippe Lemey
8. H. Tsoi

In Molecular Biology

1. Philippe Lemey
2. Marc A. Suchard
3. Andrew Rambaut
4. Edward C. Holmes
5. Oliver George Pybus
6. Zhen Yang
7. Michael S. Diamond
8. Gideon Schreiber

Citations in the corpus

• Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022 (2021, background): “More importantly, it provides the hierarchical epidemiological lineage browser to easily capture the leading edge of pandemic transmission (38).”
• Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein (2021, positive): “The emergence of mutations at E484K in South African strains is concerning, because this change can impact the neutralizing activity of many RBD-specific mAbs and immune serum generated from convalescent subjects (Avanzato et al., 2020; Greaney et al., 2021; Liu et al., 2020b; Oude Munnink et al., 2”
• IQ-TREE 3: phylogenomic inference software using complex evolutionary models (2026, neutral): “…to more recent divergences among plants (Puttick et al. 2018), animals (Redmond and McLysaght 2021), birds (Stiller et al. 2024), gum trees (Crisp et al. 2024), and primates (Vanderpool et al. 2020); and even viral divergences such as SARS-CoV-2 virus (Rambaut et al. 2020; Holmes et al. 2021).”
• Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil (2021, methodology): “Viral lineages were classified using the Pangolin (26) software tool (http://pangolin.”
• SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses (2022, positive): “These observations agree with the Pango classification (Rambaut et al., 2020), which places Omicron at a substantial distance from all other variants.”
• Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool (2021, methodology): “Using the lineage designation criteria outlined in Rambaut et al. (2020), lineages are curated by hand and annotated onto the global phylogeny in the tree visualisation software, FigTree (http://tree.”
• mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant (2021, positive): “Emergence of SARS-CoV-2 Omicron as a novel and highly mutated VOC Over the course ofmore than 270million confirmed SARS-CoV-2 infections worldwide, the virus has undergone remarkable diversification, producing >1,500 uniquely identified Pango lineages (Rambaut et al., 2020) (coronavirus.”