Three Spanish experts in sequencing and genomic surveillance of the new coronavirus answer our questions about the new variant detected in South Africa, in statements to the international trusted information portal Covid-19 Vaccine Media Hub, where SINC is the Spanish node. They agree in pointing out that it is important to monitor its evolution, but without alarming the population.

What is known about this new variant?

Iñaki eats

Co-director of the SeqCovid-Spain consortium, researcher at the Instituto de Biomedicina de Valencia (IBV) CSIC

At the moment, not much. On the one hand, it accumulates a large number of mutations at the peak, including some that we believe are associated with increased transmissibility and others associated with reduced antibody efficacy. However, never seeing each other together, we cannot know whether that is really the case or not. For this, experiments are already being carried out that allow us to say whether the response to antibodies is similar or not, and at the same time we are looking at its epidemiological growth rate, which will allow us to know whether it has greater or lesser transmissibility than delta. .

The fact that South Africa has seen rapid growth so far, displacing the delta, does not necessarily indicate an advantage in transmissibility.

Iñaki Comas, CSIC

The fact that South Africa has seen rapid growth so far, displacing the delta, does not necessarily indicate an advantage in transmissibility. We have to wait to see which direction it will take in South Africa and, above all, compare it with other countries, to see whether or not there is a gap. For example, beta was something that we were very concerned about at the time, but it never left South Africa. Therefore, it is necessary to see what trajectory it follows in countries with different epidemiological situations (vaccination, increasing or decreasing cases, etc.). It is true that in South Africa a rapid identification test is being used (the genomic sequencing takes a while) and seems to be growing at high speed in the regions where it is present.

Maria Iglesias-Caballero

Researcher at the National Center for Microbiology Reference Laboratory for Influenza and Respiratory Viruses, Carlos III Health Institute

The variant was detected in Botswana this month and acquires special relevance due to the large number of alterations its spike acquired. It is related to the increase in cases in South Africa, estimating that 90% of cases detected by PCR in Gauteng province may be due to this variant. According to what was published by Túlio de Oliveira, director of the Center for Response to Epidemics and Innovation in Durban, in less than two weeks it became the dominant bloodline in circulation, displacing the majority delta variant so far in that province.

Fernando Gonzalez Candelas

Professor of Genetics. Co-director of the SeqCovid-Spain consortium. Researcher at FISABIO-Universitat de Valencia

It is a variant linked to an outbreak in an area where there was very little circulation of the virus and a large unvaccinated population. This variant appears to be growing disproportionately immediately, mainly because being associated with an outbreak, almost all cases that test positive are related to it and its relative frequency is immediately very high. This apparently makes its growth rate spectacular.

It is a variant linked to an outbreak in an area where there was very little virus circulation and a large unvaccinated population

Fernando González-Candelas, FISABIO

On the other hand, and this shouldn’t be forgotten, it’s true that it has many more mutations than the variants we’ve seen so far. In the S protein alone, at the peak, there are already 32 mutations in relation to the original Wuhan virus. Many of these spike mutations have also been seen in variants of interest and variants of interest before, but this is the first where, so to speak, it assembles many, many of them into a single genome.

What is still unclear and will take some time to be known with reliable ​​and reliable ​​data is whether the accumulation of all these mutations actually has the effect of increasing transmissibility, possible escape from vaccine immunity or previous infection, or if it is more virulent and infected people have a worse evolution. There is no data on all of this and all we can do at the moment is speculate about it.

Francisco Díez Fuertes, researcher at the National Center for Microbiology at the Carlos III Health Institute

It is too early to evaluate this new variant of the B.1.1.529 strain. It is true that it has many mutations in the spike protein that were found in other variants of interest and concern, such as the alpha and delta variants, associated in some studies with a possible higher transmission capacity and a possible different response to antibodies. neutralizers, but we must wait for surveillance and have more data.

ECDC already recognizes this variant as a variant of interest, pending evaluation of its designation as a variant of concern based on its epidemiological impact in the European Union.

Does this deserve special attention in your opinion?

Iñaki eats

Yes, you deserve it. Not so much for what we know it does, which for now is little, but for the potential of the combination of mutations we see. Many of them we’ve seen in other variants of concern. So, without falling into alarm, we should go with it and see if we are in a scenario like the delta of a few months ago or if it is a false alarm.

The important thing is that we have the ability around the world to identify these potential threats, track them and assess them

Iñaki Comas, CSIC

What is important is having the global capacity to identify these potential threats, track them and assess them. The vast majority come to nothing, but some, like delta, have displaced the previous variants, making epidemiological control a little more difficult.

In any case, now more than ever, remember that prevention is based on multiple layers, all imperfect but very good together. The best layer we have is vaccines, but with delta we’ve seen that they don’t interrupt transmission enough. However, this happens when we add masks, distance and ventilation. And this lesson is valid for any variant of the past, present and future.

Maria Iglesias-Caballero

In my opinion it is important to monitor the circulation of this variant and characterize its changes. The phenotypic characterization of this set of changes in the spike is very important, as among the numerous changes described are changes that can improve affinity for the receptor, such as changes in N440K and S477N, changes that can impact the neutralizing activity of antibodies, such as changes in E484A, T478K and Q493K, and changes that can affect protein processing and hence its transmission, such as changes in N679K and P681H. Therefore, the phenotypic study of this combination of alterations is very relevant to know its real impact.

Until a better dataset is available, it would be remiss to make claims about vaccine transmission or protection

Maria Iglesias-Caballero, ISCIII

Since we do not have a better set of data, both epidemiological and virological, it would be difficult to make statements about transmission and protection of the vacunas, even though for the people we work in the surveillance systems, each appearance of a new variant deserves all our attention and work.

Fernando Gonzalez Candelas

It deserves attention, but this: attention. We have to see what happens to it in more environments and, if it reaches other countries, what happens. For this it is necessary to watch, but it is one thing to watch and another to raise alarm. It doesn’t seem that the situation requires an alarm, but surveillance similar to what was done previously with the other variants.

Vaccines remain as effective as they are. We have seen that over time the effectiveness of vaccines decreases, hence the booster doses, and this variant cannot be expected to be any different. So watch but don’t alarm.

In light of what is known, could this affect the effectiveness of vaccines?

Iñaki eats

We don’t know yet, we’ve already seen some of the most worrying mutations in this respect in other variants, but we also know that it’s the combination of all the mutations, how they combine into a specific variant, that determines its behavior. Some mutations of this variant we know will reduce the neutralization by antibodies because we’ve seen them before, it’s not good news, but the immune response is much more complex that it is mediated by antibodies, including the cell response that we all have, but it’s rarely measured because it’s not is easy.

What we do know is that the variants carrying some of the mutations reduced effectiveness a little, but not much, and there was still good protection against hospitalization and death.

Maria Iglesias-Caballero

Serological studies are needed to show the impact of this variant in vaccinated people. Theoretically, this set of changes has the potential to affect the protection provided by vaccines. In addition, infection with this variant has been described in some full-scheme vaccinates by Pfizer, Janssen, and Astra Zeneca. The reality is that, at the moment, the studied sample is small, which is why we do not have complete information about it.

Serological studies are needed to show the impact of this variant in vaccinated people.

Maria Iglesias-Caballero, ISCIII

Fernando Gonzalez Candelas

As far as we know, we have no evidence that this could affect it. We know that it has some mutations that decrease the neutralizing capacity of specific antibodies, but vaccines do not trigger the production of a single antibody, but of many antibodies (possibly dozens of them).

It does not appear that this virus has the ability to simultaneously evade all the antibodies produced when a person is vaccinated. Decrease yes, but not that we have to think that there will be a serious increase in the incidence in people infected with this variant despite being vaccinated, which does not mean that it should not be monitored if it occurs. Take the necessary measures to control, revaccinate or formulate new vaccines to correct this undesirable deviation.

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