Fiocruz works on detecting new variant of Sars-CoV-2 virus in Brazil 

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, has been identified in the states of Rio de Janeiro, São Paulo and Santa Catarina. It was first detected by the Oswaldo Cruz Institute (IOC/Fiocruz) in samples from two patients living in the capital of Rio de Janeiro, diagnosed with COVID-19 in September. The identification was conducted by the IOC's Respiratory, Exanthematous, Enterovirus and Viral Emergencies Laboratory, which serves as a reference for Sars-CoV-2 with the Ministry of Health and the World Health Organization (WHO).

The detection of XEC in Brazil was carried out through a surveillance strategy that expanded the genomic sequencing of SARS-CoV-2 in the city of Rio de Janeiro between August and September

The finding was reported to the Ministry of Health and the State and Municipal Health Secretariats of Rio de Janeiro. The decoded genetic sequences were deposited in the online platform Gisaid on September 26th and October 7th. After the sequences from Rio de Janeiro were deposited, other groups of researchers also deposited genomes of the XEC strain decoded in São Paulo, from samples collected in August, and in Santa Catarina, from two samples collected in September 

Variant under monitoring 

On September 24th, XEC was classified by the WHO as a variant under monitoring. This occurs when a strain presents mutations in the genome that are suspected of affecting the behavior of the virus and the first signs of a "growth advantage" are observed in relation to other variants in circulation. This variant began to attract attention between June and July 2024, due to the increase in detections in Germany. It quickly spread across Europe, the Americas, Asia and Oceania. At least 35 countries have identified the strain, which has over 2,400 genetic sequences deposited in the platform Gisaid as of October 10th of this year. 

According to virologist Paola Resende, a researcher at the IOC's Respiratory, Exanthematous, Enterovirus and Viral Emergencies Laboratory, data from abroad indicates that XEC may be more transmissible than other strains, but it will be necessary to assess 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 watch what happens in Brazil.  "The impact of the arrival of this variant may not be the same here as the immune memory of the population differs from country to country, due to the strains that have circulated in the past," explains Paola, who also works with the Fiocruz Genomic Network.

The detection of XEC in Brazil was made through 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 Secretariat of Rio de Janeiro. For three weeks, nasal swab samples were collected and sent to the IOC/Fiocruz Reference Laboratory in cases positive for Sars-CoV-2 diagnosed by rapid tests in basic health units. While the presence of XEC was detected, the monitoring confirmed the predominance of the JN.1 strain, responsible for the majority of cases in Brazil since the end of last year.  

"We carried out this action to understand in real time what was happening in Rio, 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," details Paola. 

Current data from the Municipal Health Secretariat of Rio de Janeiro and Infogripe, from Fiocruz, do not point to an increase in COVID-19 cases in the city. The virologist warns about the weakening of genomic surveillance of SARS-CoV-2 in Brazil and emphasizes the need to maintain monitoring throughout the entire country. 

"We are currently lacking 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 homogeneously throughout the country to monitor the impact of the arrival of the XEC variant and detect other variants that could alter the COVID-19 scenario," Paola emphasizes. 

The researcher further emphasizes that the data on the circulating Sars-CoV-2 genomes are important for adjusting the composition of COVID-19 vaccines. The WHO has a technical advisory group on the subject that meets twice a year. In April, the committee recommended formulating immunizers based on the JN.1 strain. The next meeting is scheduled for December. 

The XEC variant 

Analyses indicate that XEC emerged from 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 contains parts of the genomes of the KS.1.1 and KP.3.3 strains. Additionally, the strain has additional mutations that may confer advantages for its dissemination.