Virologist Alerts to New Coronavirus Variants in Brazil

RIO DE JANEIRO, BRAZIL – “We are cooperating to create more transmissible strains”. The alert comes from virologist José Eduardo Levi, researcher of the University of São Paulo Institute of Tropical Medicine (IMT-SUP).

Levi was in charge of the December discovery of the first two cases of the British novel coronavirus variant in Latin America. The mutation features eight alterations to the Spike protein, which interacts with a human cell receptor and paves the way for the virus to invade the body and cause Covid-19.

Changes in this protein may not only affect the transmissibility of the virus – as occurred with the English mutation – but also make it more resistant to vaccines already developed by different laboratories around the world.

The virologist who is studying the behavior of the English variant (B.1.1.7) in Brazil received samples of another mutation (B.1.1.28) this week, the same detected in Japanese tourists who contracted Covid-19 in Manaus. In it, ten alterations in the Spike protein were found. Although, in this case, greater transmissibility and a possible resistance to vaccines have not been proven, the chance that the coronavirus will continue circulating and evolving sparks a warning at a decisive moment for immunization.

“This is a critical moment. The detection of variants can raise questions about the performance of diagnostic tests, and particularly of vaccines, which is the most important strategy,” alerts the virologist.

According to Levi, the current context calls for serious measures to be taken by the population and science. First, the circulation of people must be reduced – a “fertilizer” for the mutation of the virus, he says.

However, amplifying and increasing the frequency of the sequencing of the virus in activity in the country would be just as important: “Only then will we be able to know if the vaccines used will be as effective in these variants. And, should we suspect a potential loss, we would be able to update it in a timely manner.”

The researcher also points out that, with the low rate of sequencing in the country, the mutation found in the capital of Amazonas may be just the tip of the iceberg of a series of variants that would have already been created on Brazilian soil: “In the case of Manaus, everything suggests that we have created a Brazilian variant. But we are certainly creating others, however, we will only know when we sequence them,” he says.

Below is the interview with José Eduardo Levi:

Q: What is known so far about the novel coronavirus mutation found in Manaus?

A: Laboratory samples sent to the USP-Oxford consortium [which analyzes the new coronavirus sequencing in Brazil] suggest that the variant found in Japan would have actually emerged in Manaus. I am not part of the consortium, but I used the Manaus variant samples to compare with the British mutation.

Manaus is a case that interests the whole world. There were many cases right at the start of the pandemic, reaching a 60% sero-prevalence, which for many models would mean herd immunity. However, months later, cases explode again. What happened to herd immunity? Would it be a second wave infecting the remaining 40% or would it be a consequence of a new, more transmissible variant? For now, we don’t know, but it’s likely to be the second case. Some data show that the new cases in Manaus are not reinfections. It seems to be a similar situation to the United Kingdom, but this still needs to be analyzed.

Q: Could the Brazilian variant be more transmissible, as the British one?

A: The B.1.1.28 variant is still very recent. What we know is that ten mutations were found in the Spike protein, while in the British there were eight. In theory, these alterations in the protein suggest that the mutated virus can have different behaviors, given that it is the virus’ gateway. But, for now, we can’t say that any of the variants found in Brazil are more transmissible. Regarding the B.1.1.7 [British], the only evidence that it would be more transmissible is an English study finding that because it is increasingly frequent, this strain would also be more transmissible. But regarding the Brazilian B.1.1.7 samples, for the time being, we are undergoing tests, and I expect that by the end of the month we will have a better notion of whether it is indeed becoming more transmissible in Brazil.

The Manaus variant is what worries me the most today, because it is likely that we have more cases of it than the British because of the flow of people. The problem is that we can’t see it because of the low sequencing rate we have been doing here. We need better molecular monitoring to control mutations.

Q: Can the virus mutations affect the vaccine’s efficacy?

A: There is data from Pfizer showing that the vaccine was able to neutralize an artificial virus with one of the most important mutations of the British variant. This is positive, but I have not yet seen any laboratory study that has neutralized the virus itself. We have to see if those who were vaccinated were infected by the new variant. If that happens, it is an indication that the B.1.1.7 can withstand immunization.

Q: Can lower adherence to isolation in Brazil contribute to the breeding of more transmissible or resistant strains?

A: We are certainly cooperating to the creation of more transmissible strains. Just think: if you place more people clustered, some with the lowest transmission virus and others with the most transmissible variant, which one will emerge? It will be the second strain. And that must have been the case in Manaus. Isolation does not give the virus a chance. If the variant does not spread, it is easier for it to die or not to evolve to more resistant ones.

Q: What must be done to control the virus’ mutations at this time?

A: Constant monitoring is required, either to advance or to move along with the virus. All viruses will have variants, but we will only be able to recognize them, and find out where they are occurring if we do the sequencing. This is the only way to quickly see the emergence of a more aggressive variant.

The sequencing index in Brazil is low compared to developed countries, and even lower than other emerging nations, such as India and South Africa. Why can’t we better monitor the virus?

I believe that in Brazil there are as many sequencers as in the United Kingdom, but we have more impediments, such as financing, reagent import difficulties and human resources. We have a very good initiative here, which is the group led by Ester Sabino [researcher of IMT-USP]. They have a very fast sequencing technique. And that, in an epidemic, makes a huge difference.