Genomic and clinical epidemiology of SARS-CoV-2 in coastal Kenya: insights into variant circulation, reinfection, and multiple lineage importations during a post-pandemic wave.

Publication date: Sep 09, 2025

Between November 2023 and March 2024, coastal Kenya experienced another wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections detected through our continued genomic surveillance. Herein, we report the clinical and genomic epidemiology of SARS-CoV-2 infections from 179 individuals (a total of 185 positive samples) residing in the Kilifi Health and Demographic Surveillance System (KHDSS) area (~ 900 km). We analyzed genetic, clinical, and epidemiological data from SARS-CoV-2 positive cases across pediatric inpatient, health facility outpatient, and homestead community surveillance platforms. Phylogenetic analyses were performed using maximum-likelihood and Bayesian frameworks. Temporal trends were summarized, comparisons conducted using Kruskal-Wallis and Wilcoxon tests, and associations examined using univariate and multivariable logistic regression models. Sixteen SARS-CoV-2 lineages within 3 subvariants [XBB. 2.3-like (58. 4%), JN. 1-like (40. 5%), and XBB. 1-like (1. 1%)] were identified. The symptomatic infection rate was estimated at 16. 0% (95% CI, 11. 1-23. 9%) based on community testing regardless of symptom status and did not differ across the subvariants (p = 0. 13). The most common infection symptoms in community cases were cough (49. 2%), fever (27. 0%), sore throat (7. 3%), headache (6. 9%), and difficulty in breathing (5. 5%). One case succumbed to the infection. Genomic analysis of the virus from serial positive samples confirmed repeat infections among 5 participants under follow-up (median interval 21 days, range 16-95 days); in 4 participants, the same virus lineage was responsible in both episodes, whereas 1 participant had a different lineage in the second compared with the first episode. Phylogenetic analysis including > 18,000 contemporaneous global sequences provided evidence for at least 38 independent virus introduction events into the study area (KHDSS) during the wave, the majority likely originating in North America and Europe. Our study highlights that coastal Kenya, like most other localities, continues to face new SARS-CoV-2 infection waves characterized by circulation of new variants, multiple lineage importations, and reinfections. Locally, the virus may circulate unrecognized, as most infections are asymptomatic in part due to high population immunity after several waves of infection. Our findings highlight the need for sustained SARS-CoV-2 surveillance to inform appropriate public health responses, such as scheduled vaccination for populations at risk of severe infection.

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