Our LIGAN platform at the heart of the sequencing of Covid19 variants in HdFs
Press release from the LIGAN medical genetic sequencing laboratory on the situation of SARS Cov 2 variants in the North of FrancePress release from the LIGAN medical genetic sequencing laboratory on the situation of SARS Cov 2 variants in the North of France
392 samples from people found positive on March 5 after screening PCR were sent to us free of charge by the Synlab HdF Medical Biology Laboratory. These positive samples come from the North, Pas de Calais with the exception of Dunkirk and the coast. We were commissioned by the Hauts de France region to sequence the entire viral genome in search of known or new variants. Good quality genomic sequences were found for 375 samples.
The results show that compared to the last sequencing operation (mid February) the proportion of English variants increased from 34% to> 60% of the samples. As we had expected, the English variant is now largely in the majority but is still not hegemonic unlike the Dunkirk (> 90%). The South African variant regressed (1%). One person was wearing the Brazilian variant: given its dangerousness, careful monitoring should be done in the coming weeks.
These results lead to the following comments:
1 / the maintenance of a base of around 40% of the initial Chinese strain of SARS Cov2 in northern France probably explains the absence of an explosion to date in incident cases of covid 19, unlike Dunkirk. But any relaxation of vigilance would lead to what we experienced in Dunkirk in February.
2 / the continued expansion of samples contaminated by the English variant is probably involved in the overloading of intensive care services in northern France, due to its higher dangerousness now well established (> 40% of severe forms). We can unfortunately expect that the English variant will continue to disseminate and therefore that the covid hospital units in Hauts de France will be in great tension at the end of March, beginning of April.
3 / at this critical stage, accelerated vaccination, in particular for the population between 50 and 65 years old who has not yet been vaccinated, would be able to slow down the hospital overload in the coming month. Indeed, the English variant leads to a rejuvenation of patients in intensive care (schematically the life risk of people 65 years of age covid becomes that of 75 years affected by the original strain). Let us recall the very high prevalence of obesity and diabetes in the North of France, which further aggravates covid19. Instead of 27,000 doses of additional vaccines this weekend it would be 100,000 doses that would be needed to hope to block the health disaster that seems to come. Vaccinate, vaccinate, vaccinate are according to us the 3 current priorities in the Hauts de France
4 / Assessing the real proportion of mutants is not easy and requires not only a total sequencing of the genome (and not a very rough screening PCR) and a very precise and professional analysis of the viral sequences. The Pangolin software used by the French virology services probably overestimates the proportion of English variants and does not easily allow the identification of emerging variants. We deposited all the viral sequences on the European EBI platform for international analysis.