Coronavirus: Along with the United States and Italy, Argentina is one of the first countries in which the two most worrying variants have been detected

The report of the PAIS collaboration (Interinstitutional Consortium for Genome Sequencing and Genomic Studies of SARS-CoV-2) in which, out of a total of 20 samples analyzed from the city of Olavarría, province of Buenos Aires, 11 with the variant of the United Kingdom and three with that of Manaus triggered the alarms of the health authorities.

From the British variant, it is already established that there is community circulation. If something equivalent is confirmed for Manaus (of which detections are added without epidemiological link), and taking into account that there are dozens of countries for which there is no information, Argentina would be part of a small group in which the co-circulation of the two highly transmissible variants was found, along with the United States and Italy.

“The UK has already been detected in 130 countries and Manaus in 45,” explains Humberto Debat, Conicet virologist at INTA and researcher for the PAIS consortium. There are probably many that both are in. Ours is one of the few for which there is evidence that these variants circulate simultaneously at a significant frequency ”.

The PAIS consortium was created to follow the evolution of the coronavirus and track the most worrying variants. “The Ministry of Health wants to know if they are, and is studying individual cases of vaccinated or of unusual severity across the country,” explains project coordinator Mariana Viegas. Our collaboration aims to do evolutionary genetic studies to understand how the virus evolves, and to understand how it moves and how it spreads, but we can’t do that in real time. So, in December, we proposed the strategy of taking “sentinel” labs from certain places and seeing what had happened in the last few days. It’s kind of like taking a snapshot of what happened the week before. “

For this, the entire genome is not sequenced, but a fragment of the protein of interest (Spike or “S”, which is where the changes are recorded and the one used in many vaccines) which allows to identify if what they see is one of the three current variations of concern. “With this strategy, we can confirm that it is that of South Africa, Manaus or the United Kingdom, but we cannot say which line it is: we do it with genomic studies, “says Viegas.

Surveillance centers report the total number of samples taken in the previous week, randomly choosing between 5 and 10% of positive samples, which scientists sequence using the “Sanger” method. So far a surveillance of the city of Buenos Aires, Greater Buenos Aires, Cordoba, Santa Fe and Neuquén is about to begin.

In the last weeks of February, it began to be seen that there was already a constant presence of unrelated epidemiologically linked cases of the British variant. This sampling allows extrapolations and statistical estimation of the incidence. “What we can see is the tip of the iceberg,” Viegas says. During the last two weeks of February, there were already systematic cases of the British variant; During the first two months of March, this frequency increased from 1 or 2% to 6 or 7%. At the moment, it is circulating in CABA and sporadically in Greater Buenos Aires ”.

In Cordoba, for the moment, the only thing that is done is the analysis of travelers and their close contacts, which is why the community circulation of one of the variants cannot yet be confirmed there. Studies with the sentinel laboratory strategy will begin shortly.

Concerning that of Manaus, the researchers had looked for it and in one week they detected two cases without epidemiological link. “These two that we have identified”, emphasizes Viegas, “represent a percentage of the total that should circulate. Since then, we have seen it systematically. The percentages have not yet been calculated because we want to divide between AMBA and CABA ”. A new report will be published tomorrow.

Although there is still a lack of “clean” epidemiological studies (without variables that cloud the results) to estimate the severity of cases generated by the Manaus variant, the increase in relative frequency is very similar to that observed in various parts of the country world. The concern stems from the fact that, according to calculations, an increase in the number of cases will eventually lead to more deaths.

Regarding the co-circulation of the two variants, Viegas believes: “We must understand the gravity of the situation: it is established that that of Manaus has a higher transmissibility and can re-infect, although we still cannot say that it is more deadly ”.

The experience of the British variant in different countries, such as Israel, Portugal, Denmark and the United States, suggests that it is 50% to 70% more transmissible and 60% to 65% more severe.

To the PAIS project information, that of the Malbrán Institute is added, which processes around 200 samples per week. “We are seeing this number increase,” says Analía Rearte, director of epidemiology at the Nation’s Ministry of Health. We received a machine that could analyze around 3,000 per week, but some things are missing to complete its installation ”.

According to the official, what already exists, an important consensus is that the variants are more transmissible and cause high viral loads in patients. Whether they affect young people the most or are deadliest, there are only case reports and it is not possible to deduce from what is happening in a collapsed health system. . “This is clearly something that worries us,” he says. So far, the age groups had no variation from what we had seen. Neither in severity nor in number of cases ”.

What has been attempted since December with the border restrictions and the rest of the measures has been to delay their massive release, Rearte says. “Sequencing allows us to follow the epidemiological situation. If traffic increases in a town, you can put in place stricter strategies, ”he explains. It would not be at all surprising if they started to be detected more and more. And we will do everything we can to ensure that this does not lead to an explosive increase in cases. If there is one variant that we don’t want to happen, it’s the one from South Africa. [la única de la que se sospecha con bastante fundamento que neutralizaría las vacunas]”.

For Debat, longitudinal studies are needed where samples are taken at random from the positives of different regions to infer not only their presence, but also their potential implantation and the increase in relative frequency. “We know that some have a great capacity to replace the rest of the viruses in circulation, so that once a certain threshold of frequency has been reached, they can become dominant in a few weeks, that is to say that they represent more than 50% of cases, and therefore favor this chance of a new pandemic with a more transmissible virus, and in certain cases more severe, and associated with an immune escape or escape. We have noted with concern that the UK variant is increasing in frequency and could become dominant in AMBA within a matter of weeks. It is important to point out that there are a large number of provinces in our country where these longitudinal studies are not carried out, so we do not know what their situation is ”.

With the entry of the already consolidated variants, it is worth asking whether they are responsible for the skyrocketing increase in cases the Nation’s Ministry of Health’s Covid report shows every day. For now, however, The The researchers attribute this to the fact that a drop in temperature of around four degrees in a few days prompted most to spend more time indoors.

“This coincides perfectly with the increase in the prevalence of the British variant, both according to the curve predicted in February from European data, and by the estimates of the PAIS project and the Olavarría report”, explains analytical chemist Roberto Etchenique , of the Faculty. of Exact Sciences of the UBA–. The variant has only just begun. I would say a lot of the increase is due to social behavior and the “variant effect” will add up ”.

According to the scientist, “the trajectory of the increase in cases is very stable. It seems to have exploded because the increase is exponential, but the growth rate has been constant since March 23. As it increases the same percentage per day, it grows more and more; this is precisely the basis of exponential behavior. It is expected that within a week, if the restrictive measures are respected, the rate will drop a bit. Or that nothing comes down, if they are not fulfilled. The increase in these variants is pushing up contagion rates ”.