Integrated surveillance in Kilifi reveals continued SARS-CoV-2 circulation and immune escape of emerging JN.1 sublineages post-pandemic

Introduction SARS-CoV-2 has been deprioritized post-pandemic, especially in Africa. Vaccination in Kenya was conducted using the Wuhan-based vaccines only, which showed reduced neutralization efficacy against Omicron and its sublineages. Methods We performed SARS-CoV-2 immune surveillance in five health facilities within the Kilifi Health Demographic and Surveillance System from November 2024 to March 2026. Patients in the facilities presenting acute respiratory symptoms were recruited and nasopharyngeal/oropharyngeal swabs taken for SARS-CoV-2 RT-PCR. Convalescent plasma from 30 patients with confirmed SARS-CoV-2 RT-PCR positive tests and genome sequences were taken for sero-neutralization assays against the infecting variants LF.7, MV.1, and globally predominant strains, XEC.4, LP.8.1 and XFG. Results In total 5115 patients were tested and 171 patients (3.4%) were positive for SARS-CoV-2. Cough (91.7%), nasal discharge (74.5%) and fever (55.4%) were the most common symptoms while wheezing (2%) and crackles (2.8%) were rarest. Sequencing revealed circulation of JN.1 omicron sub-lineages, LF.7, MV.1 and XEF. Sera from majority of individuals infected by the dominant variants, LF.7 and MV.1 were able to neutralize infecting variants but not the recently circulating XFG variant 23% (7/30) suggesting that infection with a JN.1 lineage virus alone is not sufficient to prevent re-infection with XFG. Overlapping titer distributions was observed between vaccinated and unvaccinated sera, with no statistically significant difference observed for any variant. Conclusion Our study demonstrates that SARS-CoV-2 continues to circulate in coastal Kenya causing predominantly mild upper respiratory illness while evolution enabling immune escape. These findings emphasize the importance of integrated genomic and immunological surveillance to track emerging variants, evaluate population-level protection, and inform future vaccine update strategies and public health preparedness efforts.