New Strain of SARS-CoV-2 and Vaccines

Now that the vaccination campaigns against the coronavirus causing the COVID-19 pandemic are beginning, a new strain that has emerged, or detected for the first time, in the British country is coming to the fore. The alarms have jumped from the English government and have communicated that a new strain with several mutations in the spike protein of the virus is beginning to circulate and that it has already been detected in other countries. In fact, this variant has been known since September, when it accumulated 14 mutations, since then it has been monitored in which it has been found that mutations have been added in different key regions, such as the spike protein. The accumulation of these mutations has two important implications.

On the one hand, the spike is the protein that intervenes in the interaction between the virus and the ACE2 protein of the host cells. Mutations in said viral protein can alter the efficiency of the interaction, as in fact seems to have happened in this case. According to the English sources, these mutations cause the virus to be transmitted 70% more than the ordinary strains that we had until now. This means that if before each infected person infected another person, now it will infect 1.7 people. In epidemiological terms, it was considered that COVID-19 spread at a rate of 1.5 infected per patient. So if we add 70%, patients with this strain are more likely to infect up to 2.55 people. This already represents a new challenge for global health. Although the studies carried out in this regard do not show that although it spreads more quickly, its fatality rate has varied, it must be said that infecting more people will increase the mortality rate, not because of a more harmful virus but because of greater number of infected.

On the other hand, spike protein is the preferred target of vaccines that are being developed against the virus. By mutating this region, it is possible that the target of the genetic material that the vaccines marked has disappeared or changed and is no longer recognizable. For now it appears that no vaccine has lost its efficacy due to these mutations, although live tests have yet to be performed to corroborate these indications on paper. So far the tests carried out in this regard are only theoretical. 3D molecular studies of proteins and the necessary software for this have been greatly developed in recent years. Thanks to them we can make estimates of how mutations will change the shape of proteins. It is thanks to them that it seems that these mutations in the spike protein will not alter the different methods of action of the vaccines against the virus. In hindsight we know that many times the vaccines that are synthesized can fight against one strain, but are ineffective against another. As is the case that we can see year after year for the flu, which each season must be studied to develop a new vaccine.


Strain b.1.17 has multiple mutations, or rather it must be said that the cluster of SARS-CoV-2 strains that we call b.1.17 or VUI-202012/01 have mutations in several locations. Specifically, in the spike, we find the following base deletions at position 69-70, also at position 144, and the following base changes that affect amino acids N501Y, A570D, D614G, P681H, T716I, S982A, D1118H. Of all of them, the most important mutation is at position 501, the change produces a variation in the spike protein that alters the ability to bind with the entry receptor, the ACE2 protein. This mutation is similar in effect to another located in the 614 region, which also alters the ability of the virus to interact with ACE2. This second mutation is very frequent in other strains, as in the majority strain in the south of the American continent. The number of mutations present in b.1.17 is very high and it is believed that so many have been accumulated in a single genome due to the fact that it has been reproduced within a single patient who should have been immunosuppressed and has suffered from the disease for a long time. chronicle. Although this is only a hypothesis, that of the single host, up to 3 different substrains have already been cataloged.

One of the problems with this new strain, and others that will arise, is the immediacy we need to be able to act correctly against the pandemic. At the beginning of 2021 there are no scientific articles published on the b.1.17 strain. This is not surprising if we understand that it is a very modern strain. Studies on its infective capacity, the mutations that characterize it or the probability that vaccines affect it have been carried out by the British health authorities who have given the information directly to the World Health Organization (WHO). In turn,  WHO has issued a statement to warn about the new strain and to track its evolution. The actual efficacy of vaccines against this and other new strains will have to be done in the field to verify theoretical estimates.

Biblio:

European Centre for Disease Prevention and Control. Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom. Dec 2020. ECDC: Stockholm; 2020.

Andrew Rambaut, Nick Loman, Oliver Pybus, Wendy Barclay, Jeff Barrett, Alesandro Carabelli, Tom Connor, Tom Peacock, David L Robertson, Erik Volz, on behalf of COVID-19 Genomics Consortium UK (CoG-UK). Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Dic, 2020.

Avanzato, Victoria A., M. Jeremiah Matson, Stephanie N. Seifert, Rhys Pryce, Brandi N. Williamson, Sarah L. Anzick, Kent Barbian, et al. 2020. “Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer.” Cell, Nov 2020.

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