Virus genome sequencing disaster in Italy (unlike Britain)
Italy is among the last countries in the world for sequencing rate. Here is what the European Molecular Biology Laboratory (EMBL), the most important European institute in the sector, says
In December, Great Britain found itself facing a new surge in infections, from 10 thousand infections a day to 70 thousand. The culprit was the new coronavirus strain, whose scientific name is B117, renamed the "English variant". Among the weapons deployed by the United Kingdom to deal with the second wave of mutated covid-19 is sequencing, or the study of all the individual units that make up the DNA of the virus. Sequencing is extremely useful for finding out if the virus has mutated and new variants are in circulation. Presa Diretta , broadcast by Rai 3 , has dedicated an investigation to this activity by comparing what is happening in Italy with what is happening across the Channel. The revelations of the leaders of the European Molecular Biology Laboratory (EMBL), the most important European institute in the sector, are relevant .
Here are all the details.
The English variant: EMBL sequencing work
“We found the so-called 'English variant' for the first time in September in a patient but only in December did we realize how dangerous it was – says Ewan Birney , Deputy Director of EMBL – to Direct Intake microphones. So we notified the health authorities and shared the data with the scientific community ”. From London, the B117 variant soon spread to other European countries, the Netherlands, Ireland, Portugal, Germany and Denmark. In Italy the first cases are recorded in Umbria and Abruzzo , but in a short time it will be present throughout the national territory. “After a long time that the virus has been in circulation sooner or later combinations of mutations appear that give the virus different characteristics – explained prof. Francesco Lescai (Department of Biology and Biotechnology, University of Pavia) -. The English variant has 17 mutations in a genome of about 30 thousand letters that increase the efficiency with which it binds to human cells ”.
English variant: more contagious and more lethal
“The English variant makes the virus 50% more contagious , so in a month we have an increase in infections from 8 to 10 times – continues Ewan Birney -. An alarming aspect because when the contagion curve rises it becomes impossible to control the pandemic. The B117 variant is not only more contagious but also more lethal, some studies speak of 15-20% more deaths than the original virus ". A very difficult client to deal with. The way not to be surprised is to increase surveillance by studying the sequencing of the virus. “Sequencing means taking the entire viral genome and reading it in its entirety – adds prof. Francesco Lescai -. This is to determine what kind of virus has infected the person. Italy sequences only 1 per thousand of positive swabs. So very little ".
Italy among the last in the class for sequencing
Our country is among the last in the world for sequencing rate. In the ranking shown by Presa Diretta , our country is after Bangladesh, Sri Lanka and Oman. In one year we managed to sequence only 4 thousand swabs against the 250 thousand of the United Kingdom , the sentinel of Europe. “I think Italy can do more – says the deputy director of EMBL -. We as EMBL are a European institution ready to help other countries to promptly collect and share the genetic data of the virus and its variants ”. Italy is also far behind on the reporting of variants in the international database. “We have an average deposit of 70 days, there are data deposited even after 300 days from the collection of the sample – admits prof. Lescai -. It's a lot. England has an average of 24 days of deposit ”.
In Italy, one out of 5 infected has the English variant
The first cases of 'English variant' in Italy are certified on 21 December 2020. The Ministry of Health issues the first circular only on 31 January. Recommendations include reestablishing contact tracing and sequencing at least 500 swabs per week . “The United Kingdom sequences no less than 10 thousand swabs a week – adds Ewan Birney -. I think each country should sequence at least 5% of positive crampons, preferably 10%. It is feasible and there are excellent genomics scientists in Italy who can do it ”. Today among the Italian positives, 1 in 5 presents the English version of the virus. Sequencing is very important because it allows us to understand which strains circulate in the country and to equip ourselves to stem the spread before hospitals fill up. It is also useful for keeping an eye on vaccine-resistant mutations.
Vaccine resistance: the other side of variants
Vaccine resistance is the reason why the South African and Brazilian variant deprive doctors and scientists of sleep. “The South African variant is the most worrying at the moment, not only because it is transmitted more but also because it is able to evade antibodies – concludes the deputy director of the EMBL -. This means that if a person has already caught Covid-19 they could get sick again. All vaccines are less effective with the South African variant , at least in preventing mild forms. We expect more variants to arrive because mass vaccination increases the pressure on the virus and the ability to evade antibodies. We vaccinate as many people as possible and in the shortest possible time. But let's take into account having to make a third recall designed for the most recent variants ”. The vaccines were designed on the first Sars-cov2 virus, that of Wuhan. However, vaccines can be modified very quickly, thanks to messenger RNA technology. “There must be vaccine surveillance in all countries. It is necessary to monitor how many people are becoming infected and to verify that the safety profile is confirmed – says Armando Genazzani (Medicines Committee for Human Use EMA) at the end of the report. The EMA will see this data and can take action. A vaccine is all the stronger the stronger its data is ”.
This is a machine translation from Italian language of a post published on Start Magazine at the URL https://www.startmag.it/primo-piano/disastro-sequenziamento-del-genoma-del-virus-in-italia-a-differenza-della-gran-bretagna/ on Thu, 25 Feb 2021 08:39:49 +0000.