Spain tries to shield itself from the new omicron variant of the coronavirus. The mutations detected a week ago in South Africa and Botswana have already been identified in half a dozen European countries, including Spain, whose hospitals are already actively looking for it and where the first positive occurred this Monday. Meanwhile, the Ministry of Health has reinforced this Monday the controls for all travelers arriving from southern Africa: those from South Africa, Botswana, Swaziland (Eswatini), Lesotho, Mozambique, Namibia and Zimbabwe must keep a 10-day quarantine.
In addition, the Ministry of Health has strengthened health controls for countries at risk given the uncertainty about the effects of this new variant: at the moment it is not known that it is more transmissible, that it causes more serious disease or that it escapes vaccines, But scientists need more time to rule out these hypotheses. Until now, everyone who came to Spain from a country with a great growth in diagnoses or in which worrisome mutations circulated had to show the certificate of having been vaccinated, having passed the covid or having a negative test. From now on, according to one order published this Saturday in the BOE, “They will be required, regardless of their vaccination status or having previously passed the disease, the presentation of a diagnostic certificate of active infection of covid-19 with a negative result.”
To this rule, this Monday another order has been added to quarantine travelers from the aforementioned seven southern African countries who arrive in Spain “with or without intermediate stopovers.” “During the quarantine period [los viajeros] must remain at their home or accommodation, and must limit their travels, as well as the access of third parties to the home or accommodation, to those essential for carrying out the following activities: purchase of food, pharmaceuticals and basic necessities, assistance to centers , health services and establishments or causes of force majeure or situation of need ”, reads the order. The text allows the isolation to be shortened from 10 to 7 days if after a week a test is negative.
At the same time, hospital laboratories are already actively looking for the new variant. The European Union asked member countries to sequence between 5% and 10% of diagnoses. It is the amount that is considered sufficient to detect a mutation that is already circulating in a territory. Since August 9, Spain has sequenced 5.9% of positive samples, according to data from the Ministry of Health. Depending on the weeks, it has ranged from 2.5% to 8.5%. In a context of few diagnoses, as has been the case for most of that period, it is easier to sequence a high number of samples, since it is a process that takes days. When the wave of infections rises, the capacities of hospitals allow a smaller portion of cases to be sequenced.
Because the sequencing process can take up to two days to complete due to its complexity, current PCR tests can advance work by detecting the presence (or absence) of certain mutations in the sample analyzed in just a few hours. This allows us to suspect that a new case detected corresponds to the variant detected a week ago in South Africa and Botswana.
Inmaculada Casas, coordinator of the laboratory network that sequence the virus (called Relecov) from the National Center for Microbiology (CNM), explains that they are already looking for suspected cases of mutation by these simpler techniques and then confirm them with sequencing, something that has already been done. “Very effective” in locating the alpha variant.
Thermo Fisher brand PCR, for example, looks for mutations in three different parts of the virus. Juan Carlos Galán, head of virology at Hospital Ramón y Cajal, 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 tests positive for this gene , then surely you are not facing the omicron variant. But if you are negative in the S gene and positive in the other two targets, then it is possible to suspect that it is. This is a warning, an alert, although it cannot be ruled out that other variants can give the same results, so genetic sequencing will always be necessary ”.
Not all hospitals use Thermo Fisher PCRs, as this is just one more brand available on the market. Other large centers use other systems and some use several of them at the same time. But the accumulated experience and knowing how the mutations are combined in each variant allows us to approach a reliable result. The San Cecilio Hospital in Granada, whose Microbiology service is a reference for Eastern Andalusia, developed another system that made it possible to identify the delta variant by focusing on two parts of the virus.
Federico García, head of microbiology at the Granada hospital, details: “The results we obtain with the delta variant, which currently represents more than 90% of the positives, would be different with the omicron, which lacks the mutations used as a target for the delta . This would allow us to suspect a case of omicron, although it should be confirmed by genetic sequencing, which is still the reference test ”.
#Spanish #hospitals #seek #omicron #variant #Health #imposes #quarantine #travelers #arriving #southern #Africa