What is a variant of the SARS-CoV-2 coronavirus?
Text updated on 2021-01-14
A variant of coronavirus is a viral strain characterized by the presence of certain specific sequences within its genetic material. When a new variant becomes prevalent, researchers usually give it a name.
Variant is a term used to describe a form of SARS-CoV-2 that has one or more specific letters at certain positions in its genome sequence and is different from the original form but not so different that it can be called another coronavirus. At the start of the epidemic in December 2019, there were very few variants of the SARS-CoV-2 coronavirus: the genomes taken from the first patients in Wuhan were all identical within a few letters. (See the question What is a mutation for the SARS-CoV-2 coronavirus?). There are now several thousand variants of SARS-CoV-2 that can be grouped into mutation lines. Some variants are more widespread than others. Nomenclature systems have been proposed to name these lines.
How do we detect the different variants?
To detect variants, coronaviruses collected from patients with COVID-19, this means identifying the particular sequence of letters in their genome and then comparing the sequences of the genomes with each other in order to reconstruct the order and timing of the mutations (See the question on notable variants, Which variants of the SARS-CoV-2 coronavirus have attracted attention?). Beware of the magnifying glass effect: depending on the country, sequencing is done differently. Some countries such as the United Kingdom or Denmark sequence the samples of nearly 10% of infected patients, and are therefore more likely to discover variants than other countries such as France which conducts very little sequencing (only 0.1% of samples are sequenced in France) (See the question on the Variant VoC 202012/01, also called B1.1.7, What do we know about the British variant?). The discovery of a variant thus depends on the presence of the variant but also on its research!
When the epidemic began in December 2019, the genomes taken from the first patients in Wuhan were all identical within a few letters. By April 2020, there were an average of 9.6 mutations between two genomes of the coronavirus SARS-CoV-2 randomly selected from all those available. This shows that the epidemic started with an initial virus corresponding to a single sequence and then mutations accumulated over time in the different branches.van Dorp, L., Acman, M., Richard, D., Shaw, L. P., Ford, C. E., Ormond, L., ... & Balloux, F. (2020). Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infection, Genetics and Evolution, 104351.
The analysis in July 2020 of 10,022 genomes from SARS-CoV-2 patients from 68 countries identified 5,775 variants. The three most common variants were: 3037C > T (synonymous mutation, i.e., mutation that does not change the protein, 6,334 samples), P4715L (mutation that changes the 1ab protein, 6,319 samples) and D614G (mutation that affects the Spike protein, 6,294 samples). Six major clades have been identified: the basal clade responsible for the first detected cases of COVID-19, D614G, L84S, L3606F, D448del, and G392D. A clade is a group of variants. Lineage is also used to describe a group of variants. The clade, D614G, has become the most common variant since December 2019.Koyama, T., Platt, D., & Parida, L. (2020). Variant analysis of SARS-CoV-2 genomes. Bulletin of the World Health Organization, 98(7), 495.
The countries that have published the most sequences from SARS-CoV-2 are the United Kingdom (38.9% of total sequences) and the United States (22.7% of total sequences).Furuse, Y. (2020). Genomic Sequencing Effort for SARS-CoV-2 by Country during the Pandemic. International Journal of Infectious Diseases.
Currently there is no internationally agreed consensus method for naming the different variants of SARS-CoV-2. This paper presents a rational and dynamic nomenclature that uses a phylogenetic framework to identify the lines that contribute most to the active spread of coronavirus.Rambaut, A., Holmes, E. C., O'Toole, Á., Hill, V., McCrone, J. T., Ruis, C., ... & Pybus, O. G. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature microbiology, 5(11), 1403-1407.