A strain of the Sars-CoV-2 virus that has spread around the world has been discovered in Brazil. The strain called XEC, which belongs to the Omicron variant, has been identified in Rio de Janeiro, São Paulo and Santa Catarina. The first finding was made by the Oswaldo Cruz Institute (IOC/Fiocruz) in samples from two patients living in the capital of Rio de Janeiro, who were diagnosed with Covid-19 in September. The identification was carried out by the IOC Laboratory of Respiratory Viruses, Parasitology, Enteric Viruses and Viral Emergencies, which serves as the Sars-CoV-2 reference for the Ministry of Health and the World Health Organization (WHO).
The discovery of XEC in Brazil was made based on a surveillance strategy that sequenced Sars-CoV-2 genomes in the capital, Rio de Janeiro, between August and September.This finding was reported to the Ministry of Health and the state and municipal health departments of Rio de Janeiro. The decoded genetic sequences were deposited on Gisaid's online platform on September 26 and October 7. After depositing the Rio de Janeiro sequences, other groups of researchers also deposited the genomes of the decoded XEC strain in São Paulo, from samples collected in August, and in Santa Catarina, from two samples collected in September.
The alternative is under supervision
On September 24, the World Health Organization classified the XEC virus as a variant under surveillance. This occurs when a strain exhibits mutations in the genome that are suspected to affect the behavior of the virus and the first signs of a “growth advantage” are observed in relation to other circulating variants. This variant began to attract attention between June and July 2024, due to increased detection in Germany. It quickly spread throughout Europe, the Americas, Asia and Oceania. At least 35 countries have identified the strain, with more than 2,400 genetic sequences deposited on the Gisaid platform as of October 10 this year.
According to virologist Paula Resende, a researcher at the IOC's Laboratory of Respiratory Viruses, Parasitology, Enteric Viruses and Viral Emergencies, data from abroad suggest that XEC may be more transmissible than other strains, but it will be necessary to evaluate its behavior in Brazil. “In other countries, this variant has shown signs of greater transmissibility, leading to increased spread of the virus. It is important to note what will happen in Brazil. “The impact of the arrival of this variant may not be the same here because the immune memory of the population is different in each country, This is because lineages have already spread in the past,” explains Paula, who also works at the Fiocruz Genomic Network.
The discovery of XEC in Brazil was made based on a surveillance strategy that sequenced Sars-CoV-2 genomes in the capital, Rio de Janeiro, between August and September. This action was done in partnership with the Municipal Health Department of Rio de Janeiro. For three weeks, a nasal swab sample was collected to be sent to the IOC/Fiocruz reference laboratory in Sars-CoV-2 positive cases diagnosed by rapid tests in basic health units. Although it indicated the presence of XEC, monitoring confirmed the dominance of the JN.1 strain, which has been the majority in Brazil since the end of last year.
“We did this procedure to understand what was happening in Rio in real time, as there was a slight increase in Covid-19 diagnoses in the city. This was very important for detecting the XEC variant, which will need to be monitored from now on,” Paola explains.
Current data from Rio de Janeiro's Municipal Health Department and Infogripe, from Fiocruz, do not indicate an increase in COVID-19 cases in the city. The virologist warns of the weak genomic surveillance of SARS-CoV-2 in Brazil and reinforces the need to continue surveillance throughout the national territory.
“Currently, we do not have genomic data from several states because samples have not been collected and sent for genetic sequencing. It is very important to maintain this surveillance homogeneously in the state to monitor the impact of the arrival of the XEC variant and detect other variants that can change the Covid-19 scenario,” he said.
The researcher also reinforces that data on circulating Sars-CoV-2 genomes are relevant to adjusting the formulation of Covid-19 vaccines. The World Health Organization has a technical advisory group on this topic, which meets twice a year. In April, the committee recommended formulating immunization drugs based on the JN.1 strain. The next meeting is scheduled for December.
Alternative XEC
The analysis suggests that XEC arose through genetic recombination between previously circulating strains. This phenomenon occurs when an individual is infected with two different viral strains at the same time. In this case, the genomes of the two pathogens may mix during the virus replication process. The XEC genome contains excerpts from the genomes of strains KS.1.1 and KP.3.3. Furthermore, the strain introduces additional mutations that may confer advantages for its dissemination.
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