The Omicron variant has prevailed at 87% in Attica, while at the same time the respective genetic indicators of the Delta strain have significantly decreased, according to EKPA analysis in the wastewater, during the period 27-12-2021 to 1-1-2022.
The analysis of the data further shows that there are several combinations of different mutations of the virus that may prevail each time with different clinical behavior, which requires vigilance and faithful implementation of protection measures.
The analysis of wastewater was done with the application of a new methodology developed by EKPA that detects in time, even from 50ml of wastewater or any environmental sample, new mutations and strains / variants that have just begun to enter the population.
EKPA has even submitted an application for the grant of National and International Patents.
The entire announcement of EKPA:
At the National and Kapodistrian University of Athens (EKPA), through the collaboration of Research Units of the Departments of Biology, Medicine and Chemistry, in the framework of research with Professor Andreas Skorilas and an interdisciplinary team of EKPA consisting of Nikolaos Athimaridis, , Evi Lianidou, Dimitrios Gourgiotis, Theodora Psaltopoulou, Panagiotis Adamopoulos, Mario Diamantopoulos, Lambros Dimitrakopoulos, Katerina Galani, Mario Kostakis, Katerina Kontou, Vassilis Kape, Anachopis and Nikolaos Voulithos identification of mutant strains / variants of SARS-CoV-2 in wastewater samples using a series of molecular methods and Next Generation Sequencing / NGS.
This hypersensitive methodology is particularly important because it shows the presence and percentage of mutants in the total population of a city. In addition, it detects in time, even from 50ml of wastewater or any environmental sample, new mutations and strains / variants that have just begun to enter the population. This makes genomic surveillance of new strains / variants of SARS-CoV-2, as well as other viruses or bacteria, easier and more reliable, providing the necessary information for epidemiological surveillance as well as the redesign of new vaccines and drug protocols. . The relevant article was published in the prestigious international scientific journal “International Journal of Molecular Sciences”, while an application for the grant of National and International Patents has been submitted by EKPA.
The methodology meets the requirements of the relevant recommendation of 15-3-2021 of the European Commission for the common approach in establishing systematic monitoring of SARS-CoV-2 and its variants in wastewater. In addition, it detects new strains / variants in time that begin to enter the community.
With the application of the new methodology, the analysis of mutant strains of SARS-CoV-2 in wastewater samples of the Attica Regional Unit, completed on a daily basis during the period 27-12 / 2021 to 1-1-2022 by the Wastewater Treatment Center has been completed. of Psyttalia (KELD). The specific samples were tested for specific mutations – genetic markers (genetic markers) of the entire S gene (Spike) (> 100 genetic markers) for the variants of special interest (Variants of Concern – VOC) and the variants under investigation (Variants of Interest – VOI).
The results of the analysis showed the predominance, at a rate of 87% with significant diversity, of the Omicron variant (B.1.1.529 lineage) and the simultaneous significant reduction of the corresponding genetic markers of the Delta strain (B.1.617.2 lineage).
More specifically, the presence of specific mutations (genetic markers) of the S gene (Spike) of the Omicron variant (B.1.1.529 lineage) was detected:
– in the section “receptor-binding domain / RBD” at a rate of 87% (genetic markers: G339D, S371L, S373P, S375F, K417N, N440K, G446S)
– in the section “receptor-binding motif / RBM” at a rate of 29% (genetic markers: S477N, E484A, Q493R, G496S, Q498R, N501Y, Y505H)
– excluding RBD / RBM components by 45% (genetic markers: T547K, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F)
At the same time, for the first time, the presence of two strains of the Omicron variant was detected, which carry (co-record) additional mutations, namely:
– the mutation R346K (B.1.1.529 + R346K), at a rate of 27%, which has been reported in the Mu variant (B1.621)
– the mutation A701V (B.1.1.529 + A701V), at a rate of 5%, which has been reported in the Beta variant (B1.351)
Based on the above results, the predominance of the Omicron variant is established in Attica (at a rate of 87% from <40% 2 weeks ago) as well as the corresponding reduction of the Delta variant.
At the same time, the sequencing of the virus genome reveals significant variability in the percentage of specific mutations in the S gene, which encodes the Spike protein, emphasizing their different importance and significance in the behavior of the virus, as well as in its reliable and specific determination.
The analysis of the next generation sequencing data with the above method also shows that in addition to variability there are several combinations of different mutations of the virus, which may prevail each time with different clinical behavior, which requires vigilance and faithful application of protection measures.
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