PT  - JOURNAL ARTICLE
AU  - José L. Oliver
AU  - Pedro Bernaola-Galván
AU  - Francisco Perfectti
AU  - Cristina Gómez-Martín
AU  - Silvia Castiglione
AU  - Pasuale Raia
AU  - Miguel Verdú
AU  - Andrés Moya
TI  - Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus
AID  - 10.1101/2021.11.06.467547
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2021.11.06.467547
4099  - http://biorxiv.org/content/early/2022/10/25/2021.11.06.467547.short
4100  - http://biorxiv.org/content/early/2022/10/25/2021.11.06.467547.full
AB  - During the spread of the COVID-19 pandemic, the SARS-CoV-2 coronavirus underwent mutation and recombination events that altered its genome compositional structure, thus providing an unprecedented opportunity to check an evolutionary process in real time. The mutation rate is known to be lower than expected for neutral evolution, suggesting purifying selection and convergent evolution. We begin by summarizing the compositional heterogeneity of each viral genome by computing its Sequence Compositional Complexity (SCC). To analyze the full range of SCC diversity, we select random samples of high-quality coronavirus genomes covering the full span of the pandemic. We then search for evolutionary trends that could inform us on the adaptive process of the virus to its human host by computing the phylogenetic ridge regression of SCC against time (i.e., the collection date of each viral isolate). In early samples, we find no statistical support for any trend in SCC values, although the viral genome appears to evolve faster than Brownian Motion (BM) expectation. However, in samples taken after the emergence of high fitness variants, and despite the brief time span elapsed, a driven decreasing trend for SCC and an increasing one for its absolute evolutionary rate are detected, pointing to a role for purifying selection in the evolution of SCC in the coronavirus. The higher fitness of variant genomes leads to adaptive trends of SCC over pandemic time in the coronavirus.Competing Interest StatementThe authors have declared no competing interest.