COVID-19 variant in Brazilian Amazon spreads faster

SAO PAULO, Brazil

Four Japanese travelers -- two adults and two children -- returned to Japan on Jan. 2 after an expedition through the Brazilian Amazon.

Routine tests and subsequent analyzes led to the identification of a new variant of the coronavirus that was provisionally named B.1.1.28.1 (K417N / E484K / N501Y) and became known worldwide as P.1 or simply, the "Amazon strain."

Shortly after their return to Japan, one of the adults who traveled to the Brazilian Amazon had to be hospitalized for respiratory difficulties, while the woman and one of the children showed mild symptoms. The other child was declared asymptomatic.

The discovery of the new variant of the virus was found at the Leonidas & Maria Deane Institute (ILMD, Fiocruz Amazonia), which confirmed the identification of the strain “born in the Amazon” on Jan. 12. Furthermore, according to a study led by Felipe Naveca, vice director of Research at the institute, the new variant is recent, "probably arising between December 2020 and January 2021."

The confirmation set off alarms not only in Brazil but throughout the region and the world. The new lineage was immediately linked to an increase in deaths from the coronavirus in the state of Amazonas, which skyrocketed in recent months and currently exceeds 7,000.

"We are not sure whether this new variant is circulating in the state in large numbers to be responsible for the acceleration of cases and deaths," said Naveca, who added that it may have "some influence."

“I always consider that this situation is multifactorial; we are just at the beginning of the season for respiratory viruses in the Amazon, which historically occurs from mid-November onwards. We call it ‘Amazonian winter,’ and there are other respiratory viruses, such as influenza, that are also increasing. So you have this seasonal situation, added to the new variant of COVID-19 and the decrease in a social distancing between people," he said.

Following the ILMD report, the new variant is striking for having accumulated “many mutations in a short time,” like strains found in the UK and South Africa.

"It is important to note that the mutant virus and the original virus do not pass through the masks, they do not resist handwashing with soap and water or gel alcohol, and their transmission is also prevented with social distancing," said Naveca.

In the last few hours, a scientific study led by immunologist Ester Sabino collected genomic data from COVID-19 tests in Manaus, the capital of the state of Amazonas, which yielded surprising results that found almost half of the confirmed cases, 42% were infected with the new variant.

"This frequency came out in our data for December, we have not finished January yet, but clearly this new variant is increasing," said Sabino, associate professor of the Department of Infectious Disorders of the Faculty of Medicine of the University of Sao Paulo (USP).

For Sabino, the new Brazilian variant is likely more transmissible than the current dominant strain. In their study, P.1 was detected in 13 of the 31 positive PCR test samples collected in Manaus between March and November 2020. However, the lineage was completely absent in samples from the genome analysis between March and November, which marks the speed with which it emerged and was reproduced.

Other data collected from studies in Manaus and other regions of Amazonas indicate the new lineage causes more deaths in young people. According to the latest registry of the Registry Transparency Portal, in the last 30 days, four of 10 deaths from coronavirus were those younger than 60. To be more specific, of 710 recent coronavirus fatalities in the state, 285 were younger than 60, or 40.1%.

“Without a doubt, more young people are dying from COVID-19 than recently. We are no longer talking only about those who belong to the risk group, today we are seeing deaths of babies, children, and adolescents who, at first glance, were completely healthy," said infectious diseases expert Silvia Leopoldina, who works in the public and private health network in Manaus.

“Something very different and significant is happening in Manaus. Those of us on the front lines, fighting this pandemic, are witnessing an increase in the severity of cases," said infectious diseases expert and researcher Noaldo Lucena. “We are facing an invisible being that is more pathogenic and is transmitted with greater speed. Before, the members of a family came one by one with symptoms; now they came all together," he added.

Another confirmation that set off alarms in recent days came with the confirmation from the Leonidas & María Duarte Institute, which is an alliance with the Amazonas Health Surveillance Foundation (FVS-AM) detected the second case of reinfection by coronavirus in Brazil in Manaus -- the first was in Rio Grande do Norte -- and with the new P.1 variant.

“The confirmation of the reinfection case occurred once we finished the genetic sequence of samples and compared the first infection with the second. This was the last criterion that we needed to confirm reinfection,” said Naveca.

Although the main focus of infections is in Manaus, some other regions of Brazil are already suffering from the new strain. Even in the south, in Curitiba, capital of Parana, positive cases of COVID-19 were detected in people who arrived from Amazonas, which immediately raised concerns about the entire municipality and the state about whether the new variant could be treated.

"In Manaus, there is an explosion of cases due to this new strain of the coronavirus and that is why it is very important that people who come from there and present respiratory symptoms remain isolated for at least 10 days," warned Marion Burger, infectious disease doctor of the Municipal Secretariat of Health of Curitiba.

The identification of the new variant requires a highly complex analysis, which includes the genetic sequence of the virus, for which samples from positive ones in Curitiba were referred to the National Laboratory of Fiocruz in Rio de Janeiro.

In total, nine travelers arrived from Manaus to the capital of Parana and tested positive for COVID-19. Three are hospitalized, four isolated at home and there is a couple that worries everyone since they have not been found even though both registered positive tests for coronavirus in a first aid unit (UPA) in Curitiba.

"We cannot find them with the contacts that they left us and in case they do not attend to our monitoring, we are going to resort to the courts so that they respond for being a crime against public health," said Municipal Secretary of Health Marcia Huculak.

In Brazil, the vaccination campaign began on Jan. 17, after emergency approval of the vaccine by the National Health Surveillance Agency (Anvisa) and doubt that arose with the new Amazonian strain if it would also be fought with existing immunizers.

“Indeed, the antibodies induced by the vaccine work by blocking a protein that the virus uses to enter the cell (the S protein). It also stimulates the production of T cells, which attack our cells that have already been infected. Based on that, vaccination is also an efficient mechanism against this new strain registered in the Amazon,” said Eduardo Nolasco, immunologist and university professor.

*Maria Paula Trivino contributed with this note.