Effects of genomic recombination on SARS-CoV-2 evolution and the growth of the recombinant variant XFG in Germany

In recent several years, multiple predominant SARS-CoV-2 variants that spread worldwide were derived from genomic recombination between SARS-CoV-2 lineages with diversified genetic backgrounds. However, the current understanding about the effects of recombination on SARS-CoV-2 evolution and functional aspects is limited. In this study, to achieve one overview regarding the evolution of SARS-CoV-2 recombinant variants, phylogenetic analyses have been performed to evaluate the divergence of representative Omicron recombinant variants from the predicted original Omicron lineage as well as the phylogenetic distances among these variants. As one example of predominant recombinant variants, we also investigated the growth of XFG in Germany by means of virus genomic epidemiology approaches. The results of the evolutionary relationship analyses indicate that recombination between evolutionarily distant lineages or closely related lineages can both drive SARS-CoV-2 evolution, and has the potential of resulting in a novel predominant strain, indicating that recombination plays one important role in SARS-CoV-2 evolution. Furthermore, this study provided information about the growth of XFG in Germany, and revealed a clear relative growth advantage of XFG over co-circulating lineages, such as LP.8.1 and NB.1.8.1. The information acquired from these investigations underlines the need for continuous efforts to detect recombination events and track recombinant variants, which is important for evaluating the long-term effects of recombination on SARS-CoV-2 evolution and of significance for public health.