A joint research by Cnr-Ibiom together with the University of Bari and the University of Milan, with the support of Elixir Italy's bioinformatics and genomics platform, has developed a novel methodology for the computational assessment of the pathogenicity and potential pathological relevance of novel variants of the SARS-CoV-2 virus. Recently published in Nature Communications Biology, the study bears important implications for public health and pathogen’s surveillance. The developed methodology is easily extendable to tackle any novel pathogen which might emerge in the future.
A team of researchers from the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council of Bari (Cnr-Ibiom), the University of Bari "Aldo Moro", and the University of Milan, with the support of the genomics and bioinformatics platforms made available by the Italian node of Elixir, the European research infrastructure for life sciences, has developed a computational system for the automated identification and flagging of viral variants of SARS-CoV-2 which might pose a threat for public health. In their study the researchers compared the genomes of more than 11 million SARS-CoV-2 isolates sampled throughout the COVID-19 pandemic.
The study, published in Nature Communications Biology, examined the numerous "variants" of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and their classification by International Health Authorities. Based on their epidemiological relevance, SARS-CoV-2 viral variants can be classified as VOC (variant of concern), VOI (variant of interest) and VUM (variant under monitoring) according to their degree of infectivity, the ability to evade the immune response, and the severity of the disease caused.
"To face a pandemic crisis and minimize its social and health impact, the ability to immediately recognize the most dangerous variants (VOC) is crucial: the retrospective analysis presented in this study demonstrates how the time elapsed between the first observation of the critical variants (e.g. alpha, delta, omicron), and their acknowledgment by International Health Authorities, equals t two months or more, and is not compatible with the implementation of adequate containment practices", explains Graziano Pesole of the Cnr-Ibiom and of the University of Bari. "Through this new study it was possible, through a comparative analysis of a large number of characteristics derived from the analysis of viral genomes, to elaborate an index of "dangerousness" which can be calculated in a few seconds as soon as the new variant is observed".
This innovative methodology makes it possible to characterize and flag new variants as soon as they begin to spread in the population. The new method can be easily applied to assess the potential pathogenic and epidemiological impact of any new emerging pathogen , and hence can ideally lead to significant improvement in the efficiency of public health response.
"The study demonstrates the importance of genomic surveillance to homogeneously sample viral genomes in different time intervals and at regular time intervals", concludes Pesole.
Cnr - Ibiom
Francesca De Leo, Cnr-Ibiom, email: firstname.lastname@example.org
Cnr Press Office