New Sars-CoV-2 variant identified in three Brazilian states
A new strain of the Sars-CoV-2 virus, currently spreading worldwide, has been detected in Brazil. Named XEC, this sublineage of the Omicron variant has been identified in the states of Rio de Janeiro, São Paulo, and Santa Catarina.
The Oswaldo Cruz Institute (IOC/Fiocruz) made the first discovery of the variant in samples from two patients residing in Rio de Janeiro. Both were diagnosed with COVID-19 in September.
The decoded genetic sequences were uploaded to the Gisaid platform on September 26 and October 7. Following the data from Rio de Janeiro, additional XEC lineage genomes from São Paulo, based on samples collected in August, and from Santa Catarina, from two samples taken in September, were also submitted by other research groups.
Monitoring
XEC was classified as a variant under monitoring by the World Health Organization (WHO) on September 24. This classification is given when a strain shows mutations in the genome that are suspected of affecting the virus's behavior, and early signs of a "growth advantage" compared to other circulating variants are observed. The XEC variant first gained attention in June and July 2024, following a surge in detections in Germany. It has since spread rapidly across Europe, the Americas, Asia, and Oceania. As of October 10, more than 2,400 genetic sequences of this strain have been uploaded to the Gisaid platform from at least 35 countries.
According to Paola Resende, a researcher at the Oswaldo Cruz Institute, international data suggest that the XEC variant may be more transmissible than other strains, but its behavior in Brazil still needs to be assessed. "In other countries, this variant has shown signs of greater transmissibility, leading to an increase in virus circulation. It's important to monitor how it behaves in Brazil. The impact here may differ, as each country’s population has a unique immunological memory based on the strains that circulated previously," Resende explains.
Strategy
The detection of the XEC variant in Brazil resulted from a surveillance strategy that increased the sequencing of Sars-CoV-2 genomes in Rio de Janeiro during August and September. Over a three-week period, nasal swab samples from Sars-CoV-2 positive cases—diagnosed through rapid tests at local health units—were collected and sent to the IOC/Fiocruz Reference Laboratory. While the analysis revealed the presence of XEC, the monitoring confirmed that the JN.1 strain remains predominant in Brazil, as it has been since the end of last year.
“We undertook this initiative to gain real-time insights into the situation in Rio, particularly in light of the recent uptick in COVID-19 cases in the city. This effort was crucial for identifying the XEC variant, which will require ongoing monitoring,” said the virologist. She also cautioned about the diminishing genomic surveillance of SARS-CoV-2 in Brazil and emphasized the necessity of maintaining consistent monitoring across the country.
“Currently, we lack genomic data from several states due to the absence of collected samples sent for genetic sequencing. It is crucial to ensure that monitoring is consistently maintained across the country to assess the impact of the XEC variant's arrival and to detect any other variants that could alter the COVID-19 landscape,” Resende stated.
The virologist further highlighted that information on the circulating Sars-CoV-2 genomes is crucial for optimizing the composition of COVID-19 vaccines.
The WHO has established a technical advisory group that convenes twice a year. In April, the committee recommended the development of vaccines based on the JN.1 strain. The next meeting is scheduled for December.
Origin
Analysis suggests that XEC emerged through genetic recombination between previously circulating strains. This phenomenon occurs when an individual is simultaneously infected with two different viral strains, leading to a mixing of their genomes during the viral replication process. The XEC genome contains segments from the KS.1.1 and KP.3.3 strains, along with additional mutations that may provide advantages for its spread.
