Genetic variability of SARS-CoV-2 XFG lineage and its parental lineages

SARS-CoV-2 XFG (nicknamed Stratus), a recombinant lineage arising from LP.8.1.2 and LF.7, is currently the most prevalent circulating lineage. Although most recombinant lineages do not pose a significant public health concern, some have shown the capacity to emerge and spread, highlighting the importance of their investigation. In this context, we performed a genome-based analysis to assess the genetic variability of XFG and to identify its recombination breakpoint. The breakpoint was mapped to approximately position 1507 within the spike (S) gene, in the distal region of the receptor-binding domain. This configuration suggests that LP.8.1.2 contributed the genomic backbone as the acceptor, whereas LF.7 acted as the donor. Phylodynamic survey suggests that XFG originated in early 2024, approximately 10 months before its first genomic detection. Bayesian Skyline Plot revealed a transient expansion phase beginning in August 2024, followed by a plateau, indicating limited and non-sustained growth. The estimated evolutionary rate of XFG (2.90 × 10−4 subs/site/year) was comparable to those of its parental lineages, supporting a relatively low level of genetic variability. Overall, these findings suggest that the widespread prevalence of XFG is more likely driven by lineage turnover rather than increased transmissibility, highlighting the importance of continuous genomic surveillance for monitoring emerging SARS-CoV-2 lineages.