Current understanding of the adaptive evolution of the SARS-CoV-2 genome.

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has significantly impacted human life safety and the global economy. The rapid mutation of the SARS-CoV-2 genome has attracted widespread attention, with almost every site in the genome experiencing single nucleotide variants (SNVs). Among these, the mutations in the spike (S) protein are of particular importance, as they play a more critical role in the virus's adaptive evolution and transmission. In this review, we summarize the phylogenetic relationships between SARS-CoV-2 and related coronaviruses in non-human animals, and delves into the lineage classification of SARS-CoV-2 and the impact of key amino acid variations on viral biological characteristics. Furthermore, it outlines the current challenges and looks forward to the promising application of deep mutational scanning (DMS) combined with artificial intelligence methods in predicting the prevalence trends of SARS-CoV-2 variants.