The emergence of high-fitness variants accelerates the slowdown of genome heterogeneity in the coronavirus

Supplement of the paper

“The emergence of high-fitness variants accelerates the slowdown of genome heterogeneity in the coronavirus”

Since the outbreak of the COVID-19 pandemic, the SARS-CoV-2 coronavirus accumulated an important amount of genome variability through mutation and recombination. To test evolutionary trends that could inform us on the adaptive process of the virus to its human host, we compute a genome-wide measure of Sequence Compositional Complexity (SCC) in high-quality coronavirus genomes from across the globe, covering the full span of the pandemic. By using phylogenetic ridge regression, a method able to reveal both macro- and microevolutionary trends, we present evidence for a long-term tendency of decreasing genome sequence heterogeneity in SARS-CoV-2. In early samples, we find no statistical support for any trend in SCC values over time, although the virus genome appears to evolve faster than Brownian Motion expectation. However, in samples taken after the emergence of Variants of Concern with higher transmissibility, and controlling for phylogenetic and sampling effects, we detect a declining trend for SCC and an increasing one for its absolute evolutionary rate. This means that the decline in SCC itself accelerated over time, and that increasing fitness of variant genomes lead to a reduction of their genome sequence heterogeneity.

Supplementary files