Low Transmission of the Globally Dominant Recombinant SARS-CoV-2 XFG variant in Kenya, May-July 2025

ObjectiveThe ongoing SARS-CoV-2 evolution has produced over 5,200 genetically distinct PANGO lineages whose epidemiological trajectories differ across regions. In early 2025, a new recombinant SARS-CoV-2 variant named XFG emerged, predominating in most global regions by June 2025. Here we describe XFG introduction and molecular epidemiological patterns in Kenya, May-July 2025. ResultsOf 7,564 nasopharyngeal/oropharyngeal swabs sampled across three surveillance platforms (a community cohort and two outpatient ARI) and tested by quantitative PCR, only 23 (0.03%) were positive. From these, we recovered six near-complete genomes that mapped to PANGO lineages XFG.12, XFG.4.1, XFG.7 and XFG.21. The median age of the positive cases was 18 years (IQR 10.0-21.8) and presented mainly with runny nose (47.6%), cough (42.9%), sore throat (33.3%) and fever (33.3%). Phylogenetic analysis including 14 sequences from Nairobi deposited on GISAID suggested at least 13 introduction events of the XFG variant into Kenya. Amino acid differences were observed between the Kenyan XFG.12 and XFG.4.1 in the ORF1a (H45Y) and ORF1b (D1848X/Y) proteins respectively. We confirm introduction but limited transmission of the XFG variant in Kenya during May-July 2025. This observation underlines the importance of regional genomic surveillance for appropriate and optimized intervention design.