Is Italy really ready to sequence the variants of the coronavirus?

The first investigation by the Higher Institute of Health and the establishment of a consortium for monitoring circulating viruses helps us shed light on the evolution of viruses underway, adopting containment strategies

(illustration: Pixabay) It is an imperative repeated by many and several times in recent times, institutions as well as experts: it is necessary to sequence (more) the viral samples, to understand which are the viral variants most in circulation and at the same time to proceed the most shipped possible with vaccinations. And something, after several appeals, in Italy seems to be about to change, after the announcement of a consortium for the monitoring of circulating viruses and the launch of a first investigation to map the VOC202012 / 01 variant by the Higher Institute yes health care, which has already brought the first results.

Indeed, after the first months of the pandemic in which substantially the monitoring of circulating mutant viruses did not seem to be of particular concern, today we know instead that variants are a serious problem. Attention is focused on at least three (VOC202012 / 01, 501Y.V2 and P.1, which are incorrectly referred to as English, South African and Brazilian variants) due to the danger associated with greater contagiousness and to the possible reduction of efficacy of the available medicines.

(infographic: Ecdc)

Variants: monitoring to counter

The problem of variants has become very hot in recent days, after the identification of, for example, the English and Brazilian ones in Umbria, which, together with the increase in cases, have led to the establishment of reinforced red bands in several municipalities in the region. The increase in cases - together with the increase in transmissibility or virulence in an area - is among the priority criteria identified in sequencing coronavirus samples by the European Center for Disease Prevention and Control (Ecdc) for analysis and identification of variants, especially in the presence of limited availability of analysis. Without careful monitoring, the ECDC also recalled a few days ago, the risk is that the variants in question (but also others) are underestimated. And so are their epidemiological effects and the measures to counter them. Such as enhanced contact tracing (perhaps considered partially outdated and unmanageable in the face of the spread of the epidemic in the past months) or the suspension of the end of quarantine on the tenth day. Or the surgical creation of red zones, to restrict any outbreaks of variants, Andrea Crisanti told La7, as done in Umbria.

But every action to combat the variants must start first of all with their identification, so in fact the sequencing itself is almost an action of prevention, as the ministry itself recognizes. "Once the sequence of a virus has been extrapolated and established if we are dealing with variants, the next step is to try to extrapolate the prevalence of that variant and its circulation on the territory - Massimo Ciccozzi, of Campus Bio University, comments to Wired. Doctor of Rome - in this sense the monitoring of viral flow with sequencing allows us to link genomics to epidemiology and thus the measures to be implemented, such as the possibility of reviewing vaccinations in the event that, but this is not yet the case, vaccines were less effective against a variant ".

The ISS investigation and a consortium

The widespread feeling is that even with regard to sequencing, we are proceeding slowly. Indirectly, it was the ministry itself to admit it, presenting the rapid investigation coordinated by the Higher Institute of Health (ISS) to assess the prevalence of the English variant in our territory in collaboration with regions and autonomous provinces. With the declared intention of "establishing a first mapping of the degree of diffusion of the VOC 202012/01 variant". First mapping, therefore, suggests that until now it was not clear how widespread the English variant was. Certainly, it is the most widespread worldwide of the three that concern the scientific community today, whose presence has been confirmed almost everywhere, with the exception of a large part of the African continent, at least according to the latest data collected by the WHO.

The collection of data from the ISS survey ended just a few days ago and the results, as soon as they were made known, confirm that the VOC 202012/01 variant is also quite widespread in our country: the prevalence estimate it is 17.8% (extrapolated from just over 800 samples and about eighty laboratories). But similar collections, promises from the ISS, will also be repeated in the days to come, to follow the evolution of the case.

"We were completely overdue both with respect to the pandemic and with respect to the identification of the variant problem - Ciccozzi told us - in the beginning there were also those who claimed that the virus did not mutate. And still today everything happens because there are some laboratories that sequence the virus under their own will starting from viral isolates, to conduct studies, perhaps on particular patients ". Perhaps something on the model of the British consortium Covid-19 Genomics Uk consortium, hopes Ciccozzi and to which the newborn Italian Consortium for the genotyping and phenotyping of Sars-Cov-2 and for the monitoring of the immune response to vaccination, of which we have spoken, could refer in the past few weeks. Essentially a network of laboratories scattered throughout the territory to monitor the genetic evolution of the coronavirus (and immunological responses to the vaccine), coordinated by the Higher Institute of Health. "A project still in progress, it is quite simple to set up, first of all for the allocation of funds to be disbursed to the sequencing laboratories".

Sequencing and sharing data

There is no doubt that resources are needed, but once fully operational, the consortium could make it possible to sequence tens of thousands of viruses a year, Giovanni Maga bets. director of the Institute of Molecular Genetics Luigi Luca Cavalli Sforza of Cnr: "The structures and machines for carrying out sequencing, both in hospitals and research institutes, already exist, and it is possible to estimate that the sequencing of thousands of viruses per month once the project is implemented ". So far, according to Maga, rather than proceeding slowly, we have proceeded with a minimum regime of virological surveillance, with limited numbers of sequencing, also by virtue of an effort, both technical and human resources, focused on the analysis of the swabs and the preparation then of the vaccination campaign. The spread of the variants in recent weeks had suggested increasing the virological surveillance and increasing the potential to sequence about 500 samples per week, Maga also recalls: "That the virus mutates was known: now we are aware of how important it is to keep d ' keep an eye on its evolution, not only for the three variants we are talking about but also others that could emerge ", continues the researcher:" Sustained sequencing will allow us to understand if and how the new variants are expanding, possibly supplanting others, as happened in the United Kingdom ".

It is very important to shed light on the diffusion and emergence of new variants, also the WHO reminded us, underlining the importance of sharing what has been observed on a global level, for example through databases such as Gisaid, which it also maps the occurrence of variants around the world.