Researchers detected, using genomic surveillance methods, 25 cases of the recombinant strain XQ in Rio Grande do Sul between March and May. The virus presents a mixture of the genome of two strains of the Omicron variant of the coronavirus: BA.1 and BA.2. The data were released by the Oswaldo Cruz Institute (IOC/Fiocruz) this Thursday (2).
The XQ strain had already been detected in isolated cases in Santa Catarina, São Paulo and Minas Gerais. However, sequencing data indicate that Rio Grande do Sul is the first state where there is a cluster of local transmission of the virus.
Cases were identified through the analysis of samples from March to May, with gradual growth: in March, two cases were detected, representing 0.3% of the 324 sequenced genomes; in April, eight cases, corresponding to 8% of the 98 sequences; and in May, 15 detections, which represented 7% of the 109 cases analyzed.
“The identification took place in different municipalities in the state of Rio Grande do Sul, which suggests a local transmission of the XQ recombinant in the state,” says Paola Resende, researcher at the Laboratory of Respiratory Viruses and Measles at the Oswaldo Cruz Institute (IOC/Fiocruz), in a statement.
The data found by the Fiocruz Laboratory were reported to the Ministry of Health and the State Health Department of RS.
Cases of the XQ recombinant have already been detected worldwide, especially in the United Kingdom, with genome data included in the international Gisaid database. The genetic sequences of the samples decoded in RS are also now available on the platform.
According to Paola, so far, there is no indication that the virus is associated with greater severity of cases since the population has good vaccination rates and many have already been exposed to previous infections. However, according to her, it is still necessary to monitor the viral evolution.
“We still have very little genomic data available for April and May. The genome of the XQ strain presents a stretch of the genetic code of the BA.1 lineage of the Ômicron variant and a stretch of the BA.2 lineage. They are two strains of the same variant of concern, so we need to monitor what will happen”, says the virologist.
Detected in Brazil in November 2021, Ômicron currently accounts for almost 100% of cases in the country, with a predominance of BA.1 and BA.2 strains and their sublines.
real-time investigation
According to Fiocruz, the intensified action of genomic surveillance in Rio Grande do Sul began in February, when Lacen-RS detected a case of another recombinant strain: XS, which presents a combination of the genomes of the Delta and Ômicron variants of concern. .
The initial objective was to investigate the possible spread of the XS recombinant, but the monitoring ended up identifying the transmission of XQ.
Between February and May, 824 coronavirus genomes referring to cases registered in RS were sequenced. The analyzes detected 25 cases associated with the XQ recombinant strain and only one linked to the strain XS recombinant .
Furthermore, the researchers observed the gradual replacement of the BA.1 lineage (or BA.1 substrains) by the BA.2 lineage of the Ômicron variant – a movement that has also been noticed internationally and in other Brazilian states.
In February, 97.3% of the cases in RS were attributed to BA.1, against 2.4% for BA.2. In May, BA.1 accounted for 13.8% of infections, compared to 72.5% for BA.2.
According to Paola, cases of coronavirus genetic recombination have been identified more frequently since January of this year, when the simultaneous circulation of two variants of SARS-CoV-2, Delta and Ômicron, was recorded in several countries.
At the time, the possibility of the emergence of a recombinant lineage was considered, which was popularly called “Deltacron”. However, global genetic monitoring showed the existence of multiple genetic combinations between variants and strains of the pathogen, which came to be named with the letter X.
“Coronavirus has brought surprises at every moment. THE recombination can occur when a person is infected simultaneously by two strains . In this situation, during the replication process of the virus, a genome can be assembled with pieces of the genetic code from different lineages. This recombination can result in strains with a potential for dissemination greater, less or equal to the original strains”, says the scientist.
In addition to strains XQ and XS, specific cases of recombinant strains XF, XE and XG have already been recorded in Brazil. “At this point, we are still unable to say whether XQ was introduced from another country or originated from a local recombination. We need to expand the analyzes to investigate this issue”, says Paola.
scientific collaboration
The first cases were identified in genetic sequencing carried out by the State Health Surveillance Center of the State Health Department of Rio Grande do Sul (CEVS/SES-RS), published in the state genomic bulletin on May 24.
The other sequences were conducted by Fundação Oswaldo Cruz (Fiocruz) in partnership with the Central Laboratory of Public Health of Rio Grande do Sul (Lacen-RS). Feevale University, which integrates the Corona-Ômica BR-MCTI Network, linked to the Ministry of Science, Technology and Innovation, also contributed genomes generated in the state of RS. The work had the collaboration of the Covid-19 Diagnosis Support Unit in Rio de Janeiro (Unadig-RJ), operated by Fiocruz.
Source: CNN Brasil
