RNA viruses, such as SARS-CoV2, undergo many mutations. Some could lead to its own extinction, and others make it more efficient in its goals of entering the cell to generate an infection or resisting treatments. Recently, they were confirmed new variants of the coronavirus in the United Kingdom, South Africa and Brazil. This Tuesday, Argentine researchers determined that the last of these new variants, the so-called Rio de Janeiro, is also present in Argentina.
The mutations corresponding to the Rio de Janeiro variant were found in a sample by scientists from ANLIS-Malbrán (National Administration of Laboratories and Health Institutes), who carried out a active surveillance of genomes of the strains circulating in the country.
As part of this surveillance, the ANLIS-Malbrán Genomics and Bioinformatics Platform had evaluated 135 complete genomes in which it had not found the presence of these three mentioned variables, to which scientists are paying special attention since their confirmation. Recently 40 more samples were added, and in one of them the finding occurred.
“Of the last genomes we sequenced between November and December, we found one in which we were able to identify all six mutations corresponding to the Rio de Janeiro variant, “Josefina Campos, coordinator of the Platform, confirmed to the Telam agency.” We were also able to identify the clonal relationship, which means that it has the same origin as the Rio de Janeiro variant, “Campos explained. and noted that “this variant was also found in England and Canada.”
This week, researchers from the PAIS network had reported a mutation in a region of the SARS-CoV-2 genome. In the case of ANLIS-Malbrán, what was studied is the complete sequencing of the genome, “which is the gold standard to define the presence of variants ”, points out Claudia Perandones, technical scientific director of the organization.
First, to understand, a variant is not the same as a strain. In this case it is not a new strain, but a new variant that was already circulating in Rio de Janeiro. The sample in which it was identified is from a person who had not traveled, but most likely, researchers believe, is that originated in an “imported case” and from there it began to circulate.
Variants group a large number of mutations. That of the United Kingdom groups 23 mutations, of which nine are in the spicule (also called protein spike) and it is believed that this may be associated with a higher transmissibility. The South African one has eight mutations, all of which cluster in the spicule. This one from Rio de Janeiro has six mutations, of which five are located in different regions of the viral genome and one in the spicule. But that of the spicule is the same as one of the South African variant.
Why is that relevant? That protein, Perandones explains to Clarion, “Is what interacts with the ACE2 receptor of the human cell and allows you to enter the virus”. Could that mutation make this variable more transmittable, like the one in the UK?
“This is not known. It is under study. We do not yet know the implication in transmissibility or in the severity of the clinical picture or in mortality”, Clarifies the specialist, who details that the researchers from the University of Rio de Janeiro who sequenced this variant in October are currently conducting studies to determine whether in that area of Brazil there is a higher rate of infections that can be attributed to it.
What is also being studied in the laboratory, based on hypotheses that emerged in statistical modeling work, is whether this mutation in the spike of the Rio variant could allow the virus evade neutralizing antibodies found, for example, in convalescent plasma.
The other question that many of us ask ourselves is whether these mutations can affect the effectiveness of vaccines. Perandones explains that these changes “do not affect vaccine effectiveness” because vaccines cause our body to generate an immune response to the virus that is prior to the interaction of the protein with the receptor.
He reassures saying that “it is difficult” that a new variant of the virus can reduce the effectiveness of vaccines because “it would have to be a combination of mutations, a very large change so that none of the antibodies produced could have a neutralizing effect”. He remarks that, in any case, the vaccine developers they have been evaluating for months in statistical models these possible mutations detected now. And he adds that, since vaccines were developed by genetic engineering, if it were necessary to modify a vaccine development due to the appearance of some set of mutations, “the change would require a short period of time.”
“Every time we describe a variant do not panic. Not all of them are going to be worrisome because they are part of natural evolution. In the case of the United Kingdom, for example, identifying the N501Y mutation was relevant because it allowed restrictive measures to be taken according to that situation ”, adds the researcher and therefore remarks the importance of deepening active genomic surveillance, which the ANLIS-Malbrán has been doing since the pandemic began.
In this sense, a new next-generation sequencer has already been acquired that will be able to analyze 3,000 genomes in 24 hours. “The possibility of having a state-of-the-art equipment will make it possible to massively sequence complete SARS-CoV-2 genomes, and this implies quickly knowing the strain type, lineage, and circulation of the virus. With this information, added to others of an epidemiological nature, health actions can be defined, a key scenario in the context of a pandemic, “said Pascual Fidelio, director of ANLIS-Malbrán.