The key points
- The search for the footprint
- Same instrumentation as the swabs
- The function of sequencing
With the exception of Great Britain, the whole world investigates a small amount of SARS-CoV-2 sequences, including the dreaded Delta, and so does Italy. As demanding as it is, it is in effect a crucial activity for monitoring the evolution of the virus and looking for new variants with characteristics different from those known, including greater transmissibility and virulence. Thanks to inexpensive methods and practically zero organizational impact, it is possible to have a refined picture of the circulation of variants, almost in real time. Like the one developed by Clonit, a biotech company from Siziano (Pavia) that has been active since the beginning of the pandemic with its tests for the identification of the coronavirus.
The search for the footprint
‘The variants are characterized by the presence, in specific positions of the viral genome, of mutations of the nucleotide sequence. These mutations are limited in number in a variant compared to the original strain ”, explains the president of Clonit Carlo Roccio. These specific mutations constitute the ‘signature’ or ‘imprint’ characteristic of a certain variant. Since this footprint is known, sequencing does not necessarily need to be sequenced to determine whether a positive case is a certain variant or not. There are methods that exploit the same basic technology of SARS-CoV-2 genome research in a nasopharyngeal swab, increasing the number of molecular targets in the test to include mutations characteristic of the variants. “
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Same instrumentation as the swabs
According to some estimates by the Financial Times, in the period between January and mid-June, we would be fifth in the world for the percentage of cases due to the Delta variant. Based on data obtained from Gisaid, the international database in which all countries of the world deposit the genetic sequences of the SARS-CoV-2 virus, Great Britain and Portugal have the highest concentration of Delta (respectively with 98% and 96%) followed by the United States with 31%, Italy (26%), Belgium (16%), Germany (15%) and France (6.9%). But as is known, the sequencing system is slow and has multiple system flaws, highlighted several times. This is where the method developed by Clonit in Real Time PCR (Ultra Catcher Strategy CE-IVD marked) according to Roccio could help. “It allows you to know, with a high probability, if a positive represents a variant, costs a fraction of the sequencing, requires less time and can be applied in all centers that carry out the analysis of the molecular swab, with the same instrumentation and with obvious savings in money and above all time for the NHS, making effective tracking possible ».
The function of sequencing
In the last few days there have been news almost everywhere of cases discovered of the Delta variant. An outbreak was found among logistics workers and their close contacts between the provinces of Piacenza, Cremona and Lodi. From 15 June for six days, the Piacenza Ausl has sequenced, identified and isolated 25 cases of the mutation discovered in India, dominant in England and expanding in other countries. Another cluster in Campania where the cases of the Delta variant were 82 out of 321 at the last weekly survey. A new rapid investigation has been ordered by the Ministry of Health to estimate the spread of the main variants of the coronavirus in Italy, starting with the most worrying one and which will take into consideration the samples notified on June 22, of which the genetic sequences will be obtained. For Roccio “sequencing, as the longest, most expensive and applicable method in a small number of specialized laboratories, remains the indispensable and irreplaceable method for looking for new variants. It is to this that Italy’s limited capacities in this area must be reserved, avoiding clogging them with activities for which faster and less expensive alternatives have existed for some time ».
