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

Nature Microbiology
Andrew RambautOliver G Pybus

Abstract

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.

References

Apr 15, 2000·Science·D L RobertsonB Korber
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Nov 1, 2011·Influenza and Other Respiratory Viruses·UNKNOWN WHO/OIE/FAO H5N1 Evolution Working Group
Feb 19, 2013·Molecular Biology and Evolution·Bui Quang MinhArndt von Haeseler
Oct 12, 2013·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Donald B SmithPeter Simmonds
Apr 7, 2017·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Yuelong Shu, John McCauley
Jan 25, 2020·The New England Journal of Medicine·Na ZhuUNKNOWN China Novel Coronavirus Investigating and Research Team
Feb 6, 2020·Molecular Biology and Evolution·Bui Quang MinhRobert Lanfear
Mar 31, 2020·Journal of Medical Virology·Gianguglielmo ZehenderMassimo Galli
Apr 17, 2020·Virus Evolution·John-Sebastian EdenUNKNOWN 2019-nCoV Study Group

❮ Previous
Next ❯

Citations

Jul 30, 2020·Viruses·Alessia LaiGianguglielmo Zehender
Sep 9, 2020·The Indian Journal of Medical Research·Priya AbrahamVarsha Potdar
Aug 8, 2020·Journal of Medical Virology·Juan David RamírezAlberto Paniz-Mondolfi
Sep 12, 2020·Science·Trevor BedfordKeith R Jerome
Sep 20, 2020·International Journal of Molecular Sciences·Arun Samidurai, Anindita Das
Jul 22, 2020·Nature Reviews. Microbiology·Stephanie W Lo, Dorota Jamrozy
Jul 25, 2020·Science·Darlan S CandidoNuno Rodrigues Faria
Aug 15, 2020·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Erik AlmUNKNOWN WHO European Region sequencing laboratories and GISAID EpiCoV group*
Sep 11, 2020·Nature Genetics·Jason D FernandesMaximilian Haeussler
Sep 30, 2020·Open Forum Infectious Diseases·Linda HuestonMatthew V N O'Sullivan
Aug 26, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Kelvin Kai-Wang ToKwok-Yung Yuen
Sep 24, 2020·Journal of Medical Virology·Matías J PeresonFederico A Di Lello
Nov 1, 2020·Nature Communications·Pengcheng DuChen Chen
Oct 14, 2020·Journal of Medical Virology·María Teresa Hernández-HuertaCarlos Alberto Matias-Cervantes
Oct 29, 2020·ELife·Yiska WeisblumPaul D Bieniasz
Dec 3, 2020·Emerging Infectious Diseases·Nadine MullerVictor M Corman
Nov 19, 2020·Journal of Medical Virology·Daniele MercatelliFederico M Giorgi
Dec 1, 2020·Military Medicine·John Mark VelascoStefan Fernandez
Nov 19, 2020·Transboundary and Emerging Diseases·Fangfeng YuanLeyi Wang
Dec 1, 2020·PLoS Neglected Tropical Diseases·Yoong Min ChongYoke Fun Chan
Dec 22, 2020·Briefings in Bioinformatics·Anna BernasconiStefano Ceri
Dec 30, 2020·Expert Review of Anti-infective Therapy·Seyed MohammadReza HashemianAli Akbar Velayati
Jan 6, 2021·Emerging Infectious Diseases·Tara SwadiJoep de Ligt
Jan 10, 2021·Science·Louis du PlessisOliver G Pybus
Jan 9, 2021·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Kathy LeungJoseph T Wu
Oct 10, 2020·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Edgar SimulunduNathan Kapata
Jan 9, 2021·Briefings in Bioinformatics·Tao HuWeifeng Shi
Jan 9, 2021·Microbiology Resource Announcements·Franklin Rómulo Aguilar-GamboaJuan P Cárdenas

❮ Previous
Next ❯

Software Mentioned

IQ
MAFFT
TREE
GISAID

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.