Abstract
<title>Abstract</title> <p> The evolution of coronaviruses is generally rapid, facilitated by the plasticity of their RNA genomes, and its understanding is essential for interpreting viral diversification and informing evolutionary surveillance. However, the contributions of recombination and the gain and loss of genomic fragments to the evolution of the <italic>Coronaviridae</italic> family remain incompletely characterized. Here, we investigated the evolutionary history of this family, within and among its diverse genera, with a focus on the effects of recombination and insertion-deletion (indel) events. The analyses of representative whole genomes from all genera of the family, using curated genome- and gene-based sequence alignments, showed that genomic recombination and indel events are frequent and influence <italic>Coronaviridae</italic> evolution and diversification. These events occurred both within and across genera and included key gene losses and gains in ancestral <italic>Coronaviridae</italic> lineages, highlighting their influence on genomic organization, diversification, phylogeny, and ultimately, molecular epidemiology of this viral family. Our findings also suggest that forecasting the future evolution of these viruses, which was proposed as a strategy to anticipate the emergence of novel pathogenic variants, is inherently challenging due to the complexity of modeling these evolutionary processes. </p>