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

  title={A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology},
  author={Andrew Rambaut and Edward C. Holmes and {\'A}ine Niamh O'toole and Verity Hill and John T. McCrone and Christopher Ruis and Louis du Plessis and Oliver G. Pybus},
  journal={Nature microbiology},
  pages={1403 - 1407}
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… 
SARS-CoV-2 Lineages and Sub-Lineages Circulating Worldwide: A Dynamic Overview
A concise characterization of all the lineages and sub-lineages circulating and co-circulating across the world has been presented in order to determine the magnitude of the SARS-CoV-2 threat and to better understand the virus genetic diversity and its dispersion dynamics.
Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages
A set of genomic surveillance tools from population genetics which can be used to better understand the evolution of this virus in humans are presented and could be applied to any pathogen that threatens the health of populations of humans and other organisms.
Geographical Distribution of Genetic Variants and Lineages of SARS-CoV-2 in Chile
This work presents the occurrence of genetic variants and lineages of SARS-CoV-2 in Chile during March to April 2020 and revealed a predominance of variant D614G like in Europe and the USA and the major presence of lineage B.
No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2
This work formally test whether any of the recurrent mutations that have been observed in SARS-CoV-2 are significantly associated with increased viral transmission, and develops a phylogenetic index to quantify the relative number of descendants in sister clades with and without a specific allele.
Following the Trail of One Million Genomes: Footprints of SARS-CoV-2 Adaptation to Humans
It is concluded that adaptive mutations have emerged early, rapidly, and constantly to dominate SARS-CoV-2 populations despite clonal interference and purifying selection and underscores a need for genomic surveillance of mutation trajectories at the local level for early detection of adaptive and immune-escape variants.
Data-driven approaches for genetic characterization of SARS-CoV-2 lineages
A set of computational tools that span phylogenomics, population genetics and machine learning approaches are presented that are useful for real-time genomic surveillance of SARS-CoV-2 and could be applied to any pathogen that threatens the health of worldwide populations of humans and other organisms.
An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic
The likely most recent common ancestor of SARS-CoV-2 is reported, reconstructed through a novel application and advancement of computational methods initially developed to infer the mutational history of tumor cells in a patient, and reveals that the same coronavirus lineage has dominated North America for most of the pandemic in 2020.
Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations
This study provides an imperative framework and baseline data upon which further analysis could be built as newer variants of SARS-CoV-2 continue to appear, and recorded a striking balance between stabilizing and destabilizing mutations, therefore leading to well-maintained protein structures.


An emergent clade of SARS-CoV-2 linked to returned travellers from Iran
Potential viral diversity driving the epidemic in Iran is highlighted, and the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases is underscored.
A new coronavirus associated with human respiratory disease in China
Phylogenetic and metagenomic analyses of the complete viral genome of a new coronavirus from the family Coronaviridae reveal that the virus is closely related to a group of SARS-like coronaviruses found in bats in China.
Genomic characterization and phylogenetic analysis of SARS‐COV‐2 in Italy
This report describes the isolation, the molecular characterization and the phylogenetic analysis of the first three complete genomes of SARS-CoV-2 isolated from three patients involved in the first
Expanded Classification of Hepatitis C Virus Into 7 Genotypes and 67 Subtypes: Updated Criteria and Genotype Assignment Web Resource
This study represents a major update to the previous consensus HCV classification, incorporating additional sequence information derived from over 1,300 (near‐)complete genome sequences of HCV available on public databases in May 2013.
Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)
This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9
Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)
This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication.
Continued evolution of highly pathogenic avian influenza A (H5N1): updated nomenclature
The WHO/OIE/FAO (2012) Continued evolution of highly pathogenic avian influenza A(H5N1): Updated nomenclature is published.
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Some notable features of IQ-TREE version 2 are described and the key advantages over other software are highlighted.
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites, and one of them uses several categories of rates to approximate the gamma distribution, with equal probability for each category.