A strain of the SARS-CoV-2 virus that has been spreading around the world has been detected in Brazil. The strain called XEC, which belongs to the Omicron variant, was identified in Rio de Janeiro, São Paulo and Santa Catarina.
The first discovery was made by the Oswaldo Cruz Institute (IOC/Fiocruz) in samples from two patients residing in the capital of Rio de Janeiro, diagnosed with Covid-19 in September.
Identification was carried out by Laboratory of Respiratory Viruses, Exanthematics, Enteroviruses and Viral Emergencies do IOC, which acts as a reference for SARS-CoV-2 with the Ministry of Health and the World Health Organization (WHO).
The discovery 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 the Gisaid online platform on September 26 and October 07.
After the deposit of the sequences from Rio de Janeiro, genomes of the XEC lineage decoded in São Paulo, from samples collected in August, and in Santa Catarina, from two samples collected in September, were also deposited by other groups of researchers.
On September 24, XEC was classified by the WHO as a variant under monitoring. This occurs when a lineage presents mutations in the genome that are suspected of affecting the behavior of the virus and the first signs of a “growth advantage” over other variants in circulation are observed.
This variant began to attract attention between June and July 2024, due to increased detections in Germany. It quickly spread across Europe, the Americas, Asia and Oceania.
At least 35 countries have identified the strain, which totals more than 2,4 genetic sequences deposited on the Gisaid platform as of October 10 of this year.
According to virologist Paola Resende, researcher at the Laboratory of Respiratory Viruses, Exanthematous, Enteroviruses and Viral Emergencies at IOC, data from abroad indicate 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, increasing the circulation of the virus. It is important to observe what will happen in Brazil. The impact of the arrival of this variant may not be the same here because the population’s immunological memory is different in each country, due to the strains that have already circulated in the past”, explains Paola, who also works in Genomic Network Fiocruzi.
The detection of XEC in Brazil was carried out based on a surveillance strategy that expanded the sequencing of SARS-CoV-2 genomes in the capital of Rio de Janeiro between August and September.
This action was carried out in partnership with the Municipal Health Department of Rio de Janeiro. Over a three-week period, nasal swab samples were collected and sent to the Reference Laboratory of the IOC/Fiocruz in positive cases for SARS-CoV-2 diagnosed by rapid tests in basic health units.
Although it pointed out the presence of XEC, monitoring confirmed the predominance of the JN.1 lineage, which has been the majority in Brazil since the end of last year.
“We carried out this action to understand in real time what was happening in Rio, since there was a slight increase in Covid-19 diagnoses in the city. This was very important to detect the XEC variant, which will need to be monitored from now on,” explains Paola.
Current data from the Rio Municipal Health Department and Infogripe, from Fiocruz, do not indicate an increase in Covid-19 cases in the city.
The virologist warns of the weakening of SARS-CoV-2 genomic surveillance in Brazil and reinforces the need to maintain monitoring 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 that this monitoring is maintained in a homogeneous manner across the country to monitor the impact of the arrival of the XEC variant and detect other variants that may change the Covid-19 scenario,” Paola emphasizes.
The researcher also emphasizes that data on SARS-CoV-2 genomes in circulation are relevant for adjusting the composition of Covid-19 vaccines.
The WHO has a technical advisory group on the subject, which meets twice a year. In April, the committee recommended the formulation of vaccines based on the JN.1 lineage. The next meeting is scheduled for December.
Analysis indicates that XEC arose through genetic recombination between previously circulating strains. The phenomenon occurs when an individual is infected by two different viral strains simultaneously. In this situation, the genomes of the two pathogens may mix during the viral replication process.
The XEC genome presents excerpts from the genomes of the KS.1.1 and KP.3.3 lineages. In addition, the lineage presents additional mutations that may confer advantages for its dissemination.
A strain of the SARS-CoV-2 virus that has been spreading around the world has been detected in Brazil. The strain called XEC, which belongs to the Omicron variant, was identified in Rio de Janeiro, São Paulo and Santa Catarina.
The first discovery was made by the Oswaldo Cruz Institute (IOC/Fiocruz) in samples from two patients residing in the capital of Rio de Janeiro, diagnosed with Covid-19 in September.
Identification was carried out by Laboratory of Respiratory Viruses, Exanthematics, Enteroviruses and Viral Emergencies do IOC, which acts as a reference for SARS-CoV-2 with the Ministry of Health and the World Health Organization (WHO).
The discovery 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 the Gisaid online platform on September 26 and October 07.
After the deposit of the sequences from Rio de Janeiro, genomes of the XEC lineage decoded in São Paulo, from samples collected in August, and in Santa Catarina, from two samples collected in September, were also deposited by other groups of researchers.
On September 24, XEC was classified by the WHO as a variant under monitoring. This occurs when a lineage presents mutations in the genome that are suspected of affecting the behavior of the virus and the first signs of a “growth advantage” over other variants in circulation are observed.
This variant began to attract attention between June and July 2024, due to increased detections in Germany. It quickly spread across Europe, the Americas, Asia and Oceania.
At least 35 countries have identified the strain, which totals more than 2,4 genetic sequences deposited on the Gisaid platform as of October 10 of this year.
According to virologist Paola Resende, researcher at the Laboratory of Respiratory Viruses, Exanthematous, Enteroviruses and Viral Emergencies at IOC, data from abroad indicate 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, increasing the circulation of the virus. It is important to observe what will happen in Brazil. The impact of the arrival of this variant may not be the same here because the population’s immunological memory is different in each country, due to the strains that have already circulated in the past”, explains Paola, who also works in Genomic Network Fiocruzi.
The detection of XEC in Brazil was carried out based on a surveillance strategy that expanded the sequencing of SARS-CoV-2 genomes in the capital of Rio de Janeiro between August and September.
This action was carried out in partnership with the Municipal Health Department of Rio de Janeiro. Over a three-week period, nasal swab samples were collected and sent to the Reference Laboratory of the IOC/Fiocruz in positive cases for SARS-CoV-2 diagnosed by rapid tests in basic health units.
Although it pointed out the presence of XEC, monitoring confirmed the predominance of the JN.1 lineage, which has been the majority in Brazil since the end of last year.
“We carried out this action to understand in real time what was happening in Rio, since there was a slight increase in Covid-19 diagnoses in the city. This was very important to detect the XEC variant, which will need to be monitored from now on,” explains Paola.
Current data from the Rio Municipal Health Department and Infogripe, from Fiocruz, do not indicate an increase in Covid-19 cases in the city.
The virologist warns of the weakening of SARS-CoV-2 genomic surveillance in Brazil and reinforces the need to maintain monitoring 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 that this monitoring is maintained in a homogeneous manner across the country to monitor the impact of the arrival of the XEC variant and detect other variants that may change the Covid-19 scenario,” Paola emphasizes.
The researcher also emphasizes that data on SARS-CoV-2 genomes in circulation are relevant for adjusting the composition of Covid-19 vaccines.
The WHO has a technical advisory group on the subject, which meets twice a year. In April, the committee recommended the formulation of vaccines based on the JN.1 lineage. The next meeting is scheduled for December.
Analysis indicates that XEC arose through genetic recombination between previously circulating strains. The phenomenon occurs when an individual is infected by two different viral strains simultaneously. In this situation, the genomes of the two pathogens may mix during the viral replication process.
The XEC genome presents excerpts from the genomes of the KS.1.1 and KP.3.3 lineages. In addition, the lineage presents additional mutations that may confer advantages for its dissemination.
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