Covid-19 in Spain: First case of omicron variant detected in Spain, in a traveler from South Africa

Covid-19 in Spain: First case of omicron variant detected in Spain, in a traveler from South Africa

Spain is seeking to protect itself from the new variant of the coronavirus, which has been designated an omicron. Mutations in the virus detected a week ago in South Africa and Botswana have been identified in half a dozen European countries, and Spanish hospitals are already looking for them.

On Monday, the microbiology department at Gregorio Marañón Hospital in Madrid confirmed the first case detected in Spain so far of the new variant. It was found in a traveler from South Africa. “We have managed to use a super-fast procedure that allows us to get the result the same day,” explained the hospital laboratory via its Twitter account. “The patient is fine. “

As the search for this variant progresses, the Ministry of Health has today tightened checks on all passengers arriving in Spain from southern Africa: those traveling from Africa from South Africa. South, Botswana, Eswatini, Lesotho, Mozambique, Namibia and Zimbabwe will have to quarantine for 10 days. .

Given the uncertainty about the effects of this new variant – for the moment it is not confirmed that it is more transmissible, causes more serious diseases or could escape the protection offered by vaccines – the ministry of Health has also strengthened controls for countries at risk. Until now, anyone arriving in Spain from a country where the number of infections is increasing or where variants of concern are circulating had to present a certificate proving that they had been vaccinated, had recovered from Covid-19 or had tested negative. From now on, according to a decree published on Saturday in the Official Journal of the State (BOE), newcomers “will be required, regardless of their vaccination status or if they have already had the disease, to present a certificate of diagnosis of Covid-19 active. infection with a negative result.

On Monday, another decree was issued to quarantine travelers from the seven aforementioned countries upon arrival in Spain, “with or without intermediate stops”. “During the quarantine period, [travelers] must remain in their home or accommodation, limiting their movements, as well as access by third parties to the home or accommodation, to those essential for the exercise of the following activities: purchase of groceries or pharmaceutical and essential products, frequentation health centers, services and establishments, and for reasons of force majeure or emergency situations ”, we read in the text. The order reduces the quarantine from 10 to seven days if a test comes back negative after a week.

Tedros Adhanom Ghebreyesus, WHO Director-General, speaking from Switzerland.PHOTO: LAURENT GILLIERON (AP) | VIDEO: REUTERS

At the same time, Spanish hospital laboratories are actively trying to locate the new variant. The European Union has called on member states to start sequencing between 5% and 10% of diagnostic test results. This is the proportion that they consider sufficient to detect a mutation that is already circulating in a territory. Since August 9, Spain has sequenced about 5.9% of positive results, according to data from the Ministry of Health. Depending on the week, the figure fluctuates between 2.5% and 8.5%. In the context of weak diagnostic tests, as has been the case over this period, it is easier to sequence a high number of samples, since this is a process that can take a few days. When the wave of infections increases, hospitals can sequence a smaller proportion of cases.

Due to its complexity, the sequencing process can take up to two days, current PCR tests can get ahead of this work by detecting the presence (or absence) in just a few hours of particular mutations in the analyzed sample. This suggests that a new case detected could correspond to the variant identified a week ago in South Africa and Botswana.

The Thermo Fisher-branded PCR test, for example, looks for mutations in three different parts of the virus. Juan Carlos Galán, head of the virology service at Ramón y Cajal Hospital, explains: “The first information we have indicates that a mutation in the new variant means that the PCR test does not detect the S gene. If a sample is positive for this gene, it is clear that it is not the omicron variant. But if you get a negative result for the S gene and a positive result for the other two targets, there is a suspicion that this is the case. This is a warning, an alert, although it is not excluded that other variants may give the same result, which means that genetic sequencing will always be necessary.

However, not all Spanish hospitals use the Thermo Fisher PCR test, as it is only one of those available on the market. Other large health centers use other systems and some use more than one at the same time. But the accumulated experience and knowledge of how the mutations of each variant are combined makes it possible to obtain a result close to a trustworthy result. The San Cecilio Hospital in Granada, which has the main microbiology department in eastern Andalusia, has developed another system to identify the delta variant by focusing on two parts of the virus.

Federico García, head of microbiology at San Cecilio, explains: “The results we get with the delta variant, which currently represent over 90% of positive cases, will be different with omicron, which does not have the target mutations used for delta. . This would allow us to suspect a case of omicron, even if it would have to be confirmed by genetic sequencing, which remains the gold standard test.


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