< Variants

Which variants of the SARS-CoV-2 coronavirus have attracted attention?

Text updated on 2021-06-23

VoC 202012/01 variant, also called B1.1.7 or UK variant or Alpha variant: see question What is known about the UK variant?.

The D614G mutation which is found at the origin of the B.1 line.

D614G is the mutation of SARS-CoV-2 which is most widespread in Europe (except Iceland). This mutation affects the Spike protein and appears to increase the affinity of the Spike protein for ACE2 receptors. This variant is different from the original coronavirus sequence identified in Wuhan, China in December 2019. It appears to have emerged in China and then spread to Italy in January 2020 and throughout the rest of Europe, USA, Canada, and Australia. In January 2021, this variant became the dominant form of the coronavirus, the pandemic form. This mutation, described in April 2020, has been the subject of much press coverage about its potential effect in increasing the transmissibility of the variant compared to the original form. To date, the cause of the spread of this variant, which is probably a mixture of chance and natural selection, is not known with certainty.

The Cluster 5 variant

This variant was detected in November 2020 in Denmark. It contains four mutations that affect the Spike protein, including Y453F and 69-70del mutations. This variant has been identified in mink which then infected humans working on mink farms. The discovery of this variant led to the euthanasia of all Danish minks for fear that this variant would render vaccines under development ineffective and to prevent mink from being a potential reservoir for variants.

The 501v2 or B.1.351 or Beta variant

This variant would have emerged in August 2020, in South Africa in the south-east of the country before spreading towards Cape Town, to the west and north towards Durban. This variant has eight mutations affecting the Spike protein, including E484K, K417N and N501Y which are key points in the protein. These mutations could increase transmissibility and reduce vaccine-induced immune response.

The P.1 or B.1.1.248 or Gamma variant

This variant was first described in Brazil in December 2020. It has 10 mutations on the Spike protein, including the N501Y and E484K mutations.

The B.1.617.2 or Delta, and B.1.617.1 or Kappa variants

These variants were first described in India in October 2020. They contain several mutations on the Spike protein, including the L452R and E484Q mutations.

How to limit the spread of more transmissible variants?

To slow the spread of COVID-19 and to limit the transmission of variants that may be even more transmissible, it is very important for everyone to be extremely vigilant. A well-fitting, well-filtering mask should be worn on the face (see question Why wear a mask? and the question Surgical mask or cloth mask: which one to choose?). Safety distances must be respected, hands must be washed regularly, the premises must be ventilated as often as possible with outside air, and of course crowds must be avoided.

Sources

This study traces the propagation of the variant that is at the origin of B.1 line with the D614G mutation that modifies the Spike protein. This mutation was initially detected in China and Germany at the end of January 2020. As of March 2020, both the mutated form (variant B.1) and the non-mutated form were present in Europe. By April 2020, variant B.1 had become dominant in Europe and was present in 78% of the sequenced genomes of SARS-CoV-2 . The appearance of the variant has occurred in a non-synchronous manner in different regions of the world starting in Europe (except Iceland), then in North America, Oceania, and finally in Asia. The study of 999 patients (including 756 variant carriers) in the United Kingdom showed that variant was associated with higher viral loads but had no effect on the severity of COVID-19. To examine whether this variant was more transmissible, the authors created pseudoviruses with the Spike protein with or without the D614G mutation. They showed that the pseudovirus containing the mutation was associated with greater infectivity.

Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., ... & Montefiori, D. C. (2020). Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell, 182(4), 812-827.

Study of the spread and prevalence in the United Kingdom of the variant of SARS-CoV-2 with the D614G mutation on more than 25,000 sequenced genomes. The results do not allow us to provide a conclusion on the mechanisms responsible for the spread of the variant: selective advantage or chance effect. The researchers found no clinical differences in disease severity or mortality between people infected with either form of coronavirus. Variant D614G is associated with a higher viral load and a lower age of patients than the non-mutated form.

Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O'Toole, Á., ... & Allan, J. (2020). Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. Cell.

Hamsters infected with the SARS-CoV-2 virus carrying the D614G mutation produce higher infectious titers in nasal and tracheal washings but not in the lungs, which supports clinical evidence that the mutation increases viral loads in the upper respiratory tract of patients with COVID-19 and can increase transmission.

Plante, J. A., Liu, Y., Liu, J., Xia, H., Johnson, B. A., Lokugamage, K. G., ... & Shi, P. Y. (2020). Spike mutation D614G alters SARS-CoV-2 fitness. Nature, 1-6.

The overall prevalence of D614G is associated with the prevalence of loss of sense of smell (anosmia) as a symptom of COVID-19.

Butowt, R., Bilinska, K., & Von Bartheld, C. S. (2020). Chemosensory dysfunction in COVID-19Integration of genetic and epidemiological data points to D614G Spike protein variant as a contributing factor. ACS chemical neuroscience, 11(20), 3180-3184.

Preliminary analyses suggest that the variant of SARS-CoV-2 isolated from mink in Denmark, the Cluster 5 variant, may be less easily neutralized by antibodies produced by patients previously infected with the SARS-CoV-2 coronavirus that don't contain these mutations. Indeed, two of the Cluster 5 variant mutations (69-70del and Y453F) located on the Spike protein could make it more difficult for antibodies to bind to the coronavirus and allow the coronavirus to escape the immune system. The effect was small and observed in a small population. But it caused widespread concern in the media, suggesting that vaccines under development might lose effectiveness with this variant.

Lassaunière R, Fonager J, Rasmussen M et al (2020) SARS-CoV-2 Spike mutations arising in Danish mink and their spread to humans

This study describes the 501Y.V2 variant detected in South Africa and sequenced on December 14, 2020. Analysis of data acquired in routine surveillance up to December 14, 2020 (number of patients, number of deaths, etc) and of 2,589 genomes from SARS-CoV-2 collected between March 5 and November 25, 2020. Analyses suggest that the variant appeared in August 2020 and then spread. Between October 15 and November 25, 190 sequences containing the 501Y.V2 variant were detected, this variant having become the most widespread lineage in the provinces east and west of Cape Town.

Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., ... & de Oliveira, T. (2020). Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple Spike mutations in South Africa. medRxiv.

List of SARS-CoV-2

WHO