Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes

Comandatore, Francesco; Chiodi, Alice; Gabrieli, Paolo; Biffignandi, Gherard Batisti; Perini, Matteo; Ricagno, Stefano; Mascolo, Elia; Petazzoni, Greta; Ramazzotti, Matteo; Rimoldi, Sara Giordana; Gismondo, Maria Rita; Micheli, Valeria; Sassera, Davide; Gaiarsa, Stefano; Bandi, Claudio; Brilli, Matteo

The SARS-CoV-2 pandemic that we are currently experiencing is exerting a massive toll both in human lives and economic impact. One of the challenges we must face is to try to understand if and how different variants of the virus emerge and change their frequency in time. Such information can be extremely valuable as it may indicate shifts in aggressiveness, and it could provide useful information to trace the spread of the virus in the population. In this work we identified and traced over time 7 amino acid variants that are present with high frequency in Italy and Europe, but that were absent or present at very low frequencies during the first stages of the epidemic in China and the initial reports in Europe. The analysis of these variants helps defining 6 phylogenetic clades that are currently spreading throughout the world with changes in frequency that are sometimes very fast and dramatic. In the absence of conclusive data at the time of writing, we discuss whether the spread of the variants may be due to a prominent founder effect or if it indicates an adaptive advantage.