New variant of Covid: how Brazilian scientists detect BA.2 in the country

The detection of the new variants of the coronavirus happens thanks to genomic surveillance, a structure formed by laboratories, equipment and, of course, scientists capable of receiving samples from patients with Covid-19, performing the genetic sequencing of this material and determining which strain of the virus is circulating. by a particular region.

It was this work, by the way, that managed to identify the first cases of infection related to BA.2 in Brazil, a “brother cousin” variant of the omicron that seems to be even more transmissible and has become dominant in places like Denmark and India.

As far as is known, the first samples from Brazilians infected with this new strain come from Rio de Janeiro and São Paulo, with two cases in each state, according to information recently released by the Ministry of Health.

Virologist Paola Resende, a researcher at the Laboratory of Respiratory Viruses and Measles at the Oswaldo Cruz Institute (IOC/FioCruz), is one of the scientists who are part of Brazil’s genomic surveillance structure.

As the name suggests, the center where she works is a reference in the investigation of respiratory viruses for the Ministry of Health.

The expert explains that since the omicron was first detected in South Africa and Botswana in November 2021, some lineages derived from it have been discovered in other parts of the world.

“The ‘classical’ omicron is known as B.1.1.529. Within this group, we have some other lineages, such as BA.1, BA.1.1, BA.2 and BA.3”, he explains.

The emergence of new viral versions is something to be expected: as the virus “jumps” from one person to another and replicates inside our cells, it undergoes random mutations in the genetic code. Some of these modifications do nothing. Others, however, can improve the transmission capacity, immune escape or even aggressiveness of the pathogen.

Also according to the virologist, although BA.2 has gained the spotlight in recent weeks, it is still present in a minority of the analyzed samples.

“BA.1 and BA.1.1 are the ones with the greatest global spread and rapid dispersion. BA.2 has started to stand out in some countries, such as Denmark, where it is present in about 35% of the sequenced genomes” , calculates.

“But when we look at the global scenario, it is detected in about 2% of the samples”, compares Resende.

Geneticist David Schlesinger, CEO of Mendelics, a private laboratory that is also part of São Paulo’s genomic surveillance network, explains that the Omicron BA.1 was already one of the most infectious viruses that emerged in the last hundred years.

“And BA.2 is even more transmissible”, he points out.

“It could have been catastrophic if we didn’t have a contingent of people with a good level of immunity from vaccination and from previous cases, which continue to protect against more serious conditions most of the time”, he evaluates.

A Danish study released at the end of January showed that BA.2 is 33% more infectious than BA.1 — which, in turn, already had a far greater spread capacity than alpha, beta, gamma and delta variants.

And it is precisely this greater transmissibility that would help to explain how this new viral version became dominant in Denmark, surpassing the “original” omicron.

However, Resende considers that the behavior of a variant in a given place is not always repeated in other parts of the world.

“We just need to analyze what happened with the previous variants. Alpha dominated in the UK, but had limited action here. On the other hand, gamma, which was responsible for the wave that hit Brazil in the first half of 2021, was not successful outside Latin America”, he teaches.

The delta itself, which acted quickly and devastatingly in places like India and the United States, took almost three months to spread and become dominant in Brazil.

“That depends a lot on the local dynamics, on how many vulnerable people there are, what other lineages dominate”, he lists.

These previous experiences, therefore, indicate that there is not much to know about how BA.2 will behave in each scenario — which only reinforces the constant work of the genomic surveillance teams.

​A more vigilant Brazil

Schlesinger says that every week, Mendelics randomly and anonymously selects about 90 samples from Covid patients and genetically sequences them. The idea is to get an idea of ​​how the distribution of variants of the coronavirus is.

“Between the end of January and the beginning of February, we detected a case of BA.2”, he says.

The following week, around 2/7, a new round of sequencing found no cases caused by this particular strain.

In the case of BA.1, the laboratory followed an exponential growth. “In the first week of January, it was in 15% of the samples. In the second, it rose to 80%. In the third, to 94%. In early February, it was detected in 100% of the sequencing”, he compares.

Will BA.2 follow the same path here? It’s still too early to tell, experts say. “We need to follow up and see if it’s going to follow the same pattern as BA.1 or not,” Schlesinger replies.

Resende explains that the Brazilian genomic surveillance system has evolved a lot in recent months and is much more structured than at the beginning of the pandemic, which makes it possible to identify BA.2 or other variants more quickly.

“History has changed. Anyone who says that Brazil does not have good genomic surveillance is unaware of all the advances we have had recently”, he defends.

The number of sample sequencing has, in fact, greatly increased. According to the FioCruz Genomic Network website, in October 2020, Brazil placed just over 500 sequences on Gisaid, an online platform where scientists from around the world share information on the genomes of the coronavirus.

In September 2021, the country performed almost 12,000 sequencing, a 24-fold increase in the monthly frequency of such tests.

At the end of last year, this rate dropped again a little. But this has to do with the drop in Covid cases around here, justifies the virologist – in January, with the advancement of the omicron, the sequencing rose again.

Compared to genomic surveillance in other parts of the world, we still lag far behind. Since the beginning of the pandemic, Brazilian researchers have shared 110,000 sequences in Gisaid, which represents 0.41% of the total number of diagnosed cases in the country. The percentage is close to what is done in countries like Romania, Peru, Egypt and the Philippines.

The champions in this relationship between sequencing and Covid cases are New Zealand (37% of cases are sequenced), Denmark (16%), Iceland (11%) and the United Kingdom (10%).

On the other hand, it is possible to notice an advance when we analyze the absolute numbers of sequencing carried out in the current wave of the Ômicron: Brazil is the 13th country that most recently deposited information on the Gisaid platform.

Resende clarifies that there is no need to sequence all patients with Covid. “For surveillance, we need to select a meaningful sample to understand the dynamics of the variants and get an overall picture of the situation.”

Extended Capacity

The FioCruz virologist says that the 26 states and the Federal District have Central Laboratories, also known by the acronym Lacen.

“The Lacens of each federative unit detect the positive samples for coronavirus and determine a representative sample, or how many of them will be sequenced”, he says.

This representative sampling varies depending on the population of each place and also with the moment of the pandemic – if the number of Covid cases is high, it may be necessary to increase the amount of analysis, for example.

“Following, the randomly selected samples are sent to the genomic surveillance network, which FioCruz and several other institutions are part of”, he adds.

The specialist also informs that the Lacens themselves have expanded the structure and intend to start performing genetic analysis of patient samples themselves soon. The central laboratories in São Paulo, Minas Gerais and Bahia, by the way, already have this technology in use today.

“And this will certainly remain as a legacy for the future epidemics that we will face”, he predicts.

“We can use this same structure to genetically analyze cases of influenza, zika, chikungunya, dengue…”, he exemplifies.

But, after all, what will happen to BA.2?

While genomic surveillance does the monitoring and there are not many definitions as to whether BA.2 will spread across the country or not, Schlesinger speculates what might happen if it does become dominant here.

“BA.2 can cause a prolongation of the wave we are in now. With that, the number of cases would take a little longer to fall”, he evaluates.

“And there is a likelihood that this variant will go through something similar to what we saw with the delta in Brazil, which slowly replaced the gamma, but did not actually cause a wave”, he adds.

In a scenario where we still have some uncertainties, at least one thing remains the same: preventive methods continue to stop the coronavirus, regardless of the variant of the moment.

“Non-pharmacological measures are essential and continue to be valid, especially the use of good quality masks in closed places or in agglomerations”, summarizes Resende.

Keeping a physical distance whenever possible, taking care of air circulation in the environments and doing hand hygiene regularly are other attitudes that are indicated by the authorities.

And, of course, you can’t forget about the immunization campaign against Covid. “The most important measure is to vaccinate everyone as quickly as possible,” adds Schlesinger.

“There is no other advance in the history of humanity that has had as great an impact on collective health as vaccinating people”, concludes the geneticist.