Track and identify Covid-19 mutations through genome sequencing. A ‘simple’ and fast method, all Italian. The new types of SARS-CoV-2 are identified on the basis of the simultaneous presence, in the same type of genomic sequence, of two or more characteristic and prevalent mutations.
These are the results of a study conducted by the Cnr-Ibiom of Bari together with the University of Bari and the State University of Milan, with the support of the bioinformatics platform Elixir Italia, which has developed a new and simple methodology for the classification of virus variants. The study conducted on the sequences of over 180,000 viral genomes isolated from different centers around the world allowed to characterize the evolutionary dynamics of SARS-CoV-2. The study is published in Molecular Biology and Evolution.
The researchers, based on the characteristics of the genomes, propose a method for the innovative and effective typing of those viral genomes, both to monitor the current spatio-temporal distribution of the virus and to predict its spread.
“The authors have identified, at different time intervals during the course of the pandemic, a set of mutations in the viral genome that are highly prevalent and remain stable. According to the proposed method, the new types of SARS-CoV-2 are identified on the basis of the simultaneous presence, in the same type of genomic sequence, of two or more characteristic and prevalent mutations, the concept that takes the name of “haplotype” . By extension, the different types of viral genomes have been defined as “haplogroups”, explains coordinator Graziano Pesole. “Comparative analyzes of viral genomes – isolated in China between December 26, 2019, when the virus first appeared, and January 20, 2020 – showed that the mutation rate of SARS-Cov-2 is slightly lower than other viruses of the same family and identified genetic variants of different subtypes, each of which is associated with a certain geographic prevalence. More up-to-date analyzes, based on more than 800,000 available genomes, suggest that at least 119 haplogroups are currently in circulation worldwide. The study also made it possible to confirm the hypothesis that the spread of the virus is to be pre-dated between September and November 2019 “.
The authors point out that these observations are based solely on comparative analysis of viral genomes and are not associated with epidemiological or clinical data. “Taking this into account, it should be noted that the comparison of viral subtypes prevalent in different regions of the world and emerged at different times suggests that the large part of the genetic diversity observed in SARS-CoV-2, over 72,000 mutations compared to the viral genome of reference, should not be associated with particular changes in the dynamics of contagion or sensitivity to vaccines ”, continues the associate researcher Cnr-Ibiom.
Finally, the study suggests that a very limited number of variants of the viral genome, even recently emerged, could be the result of a ‘adaptive evolution. At the present time it cannot be ruled out that these variants are associated with more “efficient” forms of the virus. “Given our current and limited knowledge of SARS-CoV-2, which will continue to evolve and mutate its genome, it appears necessary to start a genomic sequencing campaign repeated over time of a significant sample, as is already the case in the UK, Denmark and Australia. , sharing the data according to the Open Science principles supported by the portal (www.covid19dataportal.it) recently set up by the ELIXIR Italia project. The monitoring and identification of new viral subtypes in different geographical areas is a crucial source for countering the spread of the pandemic ”, Pesole concludes.