Speaking in parliament on Wednesday morning, Prime Minister Mario Draghi said that in Italy “at least until today we have a relatively favorable situation” with respect to the spread of the omicron variant of the coronavirus: “The cases of the omicron variant are less than 0.2 per one hundred “, while in other European countries such as Denmark and the United Kingdom the variant” is very widespread “.
Draghi's statements have been taken up by the newspapers, but various observers have pointed out that in Italy omicron is searched occasionally and in an unsystematic way through sequencing (as happened previously with other variants), and that therefore its prevalence is probably more high compared to what was communicated in official reports.
The scarcity of data on the circulation of the new variant, apparently much more contagious than the delta variant still prevalent in much of the world, makes it difficult to assess the current trend of the pandemic in Italy and its future developments. Experts agree that we will in all likelihood see a marked acceleration in the increase in infections, but without an adequate amount of sequencing it is difficult to predict.
Omicron up to here
After its diffusion in some areas of southern Africa at the end of November, the omicron variant is now present in more than sixty countries, with an increasing incidence of cases in different parts of Europe. Analyzes conducted so far in the United Kingdom have found a doubling rate of omicron infections of about 2-3 days. It means that if one day the omicron cases are 10, three days later (in the most optimistic scenario) they become 20 and three days later still 40.
The doubling time is quite high when compared with that of the delta variant, now averaging around two weeks. This indicates a high contagiousness of the new variant, while offering fewer clues about the danger in terms of the severity of the disease. From the first data from South Africa, omicron would appear to cause less severe symptoms, but the South African cases have mostly concerned young individuals and therefore less at risk.
Things to know about the coronavirus The Coronavirus Post newsletter updates you on breaking news: it's free and arrives every Thursday at 6pm. To receive it, write your email address here and press the button below. Having read the information, I agree to send the Newsletter Omicron also seems to have the ability to more easily evade the defenses that our immune system produces upon completion of the vaccination cycle. The protection offered by vaccines appears to be generally lower than previous versions of the coronavirus, but remains high in the case of severe forms of COVID-19. The recall also seems to restore, at least in part, the general protection also from infection.
Sequencing
To understand which variants are in circulation in a given period, some particular analyzes are carried out on samples, taken with a swab, tested positive for coronavirus. Simplifying, “sequencing” means analyzing a sample to detect the characteristics of the genetic material of the coronavirus. It is a subsequent step to that of the molecular test, which in its basic form is limited to detecting the presence of the genetic material of the virus, but without analyzing all its characteristics.
Thanks to sequencing it is possible to distinguish the type of variant that led to the positive case, and it is possible to reconstruct the family tree of the virus in order to evaluate the mutations that affected it.
Some European countries, such as the UK and Denmark, have the ability to sequence large numbers of samples, both because they were already better equipped to do so before the pandemic, and because they have upgraded their laboratories in the last couple of years. The data deriving from the sequencing are valuable not only for individual countries, but also for others thanks to various platforms that allow you to share the results obtained.
One of the main systems for sharing genetic information on viruses is called GISAID: it was born in 2008 with the aim of better tracking the evolution of influenza viruses, but after the start of the pandemic it has become a precious resource for keeping track of evolution coronavirus.
Denmark and the United Kingdom are among the countries to have shared more sequences on GISAID, indicating the high number of sequencing they perform, while other countries such as Italy have uploaded a more limited number of analyzes to GISAID. In the last 30 days alone, for example, Denmark has sequenced and shared 24 per cent of the positive cases detected, while the UK has shared around 12 per cent (in absolute terms it has sequenced many more samples). Italy sequenced and shared just over 1 percent of the positive cases detected.
Rapid survey
The 0.2 per cent figure on the prevalence of omicron cited by Draghi does not derive from sequencing in general carried out in Italy, but from a survey rapid recently published by the Istituto Superiore di Sanità (ISS) and referred to last December 6. The survey was carried out on a sample basis, trying to create one that was as representative as possible of the current epidemiological situation in Italy, where there are regions with a higher incidence of positive cases than others.
2,127 sequences were considered, resulting in a crude national estimate of the omicron variant at 0.19 percent, with a confidence interval between 0 and 0.9 percent. The delta variant showed a prevalence of 99.72 percent, with a confidence interval between 66.7 and 100 percent.
The estimates vary slightly taking into consideration “the average prevalence in the various Regions / PA weighted by the number of regional cases notified”. In this case, the estimate for omicron reaches 0.32 percent, while maintaining the same confidence interval.
In absolute terms, 4 cases of omicron emerged from the sample survey, a number that is hardly representative of the actual situation. On such low values it is in fact difficult to select a statistical sample that adequately reflects the real situation. It should also be remembered that the data refers to the day of last December 6 and that therefore 10 days have elapsed, in which omicron has continued to spread with doubling times that seem to be rather tight even in Italy.
Detection
A greater quantity of daily sequencing could offer some more solid data to evaluate the diffusion of the omicron variant in our country, but as happened in recent months with the delta variant and even earlier with the alpha one, at the moment there does not seem to be any acceleration in the analyzes.
In addition to sequencing, which require time and resources to perform, the omicron variant can also be identified through normal molecular tests (PCR). These tests look for three genes related to some parts of the coronavirus, if one of these (gene S) is not detected it is likely that it is omicron. In order to confirm this, sequencing is still necessary, but the information can immediately be precious for making more accurate statistical models of the diffusion of the variant. This technique also allows you to carry out sequencing in a more specific way, dedicating yourself to the samples that are most likely to be related to the omicron variant.
