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

Between November 2023 and March 2024, coastal Kenya experienced a new 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 (total 185 positive samples) residing in the Kilifi Health and Demographic Surveillance (KHDSS) area ([~]900 km2). Sixteen SARS-CoV-2 lineages within three sub-variants (XBB.2.3-like (58.4%), JN.1-like (40.5%) and XBB.1-like (1.1%)) were identified. 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 sub-variants (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%) and one case succumbed to the infection. Genomic analysis of the virus from serial positives samples confirmed repeat infections among five participants under follow-up (median interval 21 days, range 16-95 days); in four participants, the same virus lineage was responsible in both the first and second infections, while one participant had a different lineage in the second infection compared to the first. Phylogenetic analysis including >18,000 contemporaneous global sequences estimated that at least 38 independent virus introduction events occurred into the KHDSS area during the wave, the majority likely originating in North America and Europe. Our study highlights coastal Kenya, like most other localities, continues to face new SARS-CoV-2 infection waves characterized by the 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 risk populations. Author summarySevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has transitioned to an endemic respiratory pathogen causing seasonal outbreaks. We examined the epidemiological and genomic patterns of a wave of SARS-CoV-2 infections in coastal Kenya that occurred between November 2023 and March 2024. By analyzing genetic and epidemiological data from positive cases in Kilifi, we inferred the origins of the new strains, documented repeat infections and the virus ongoing evolution. Our data revealed several variants circulating in the community, indicating multiple new virus introductions probably before and during local outbreaks. Many infected individuals were asymptomatic, highlighting unnoticed transmission within the population. Despite low vaccination rates among the cases ([~]7.0%), high population immunity has previously been reported locally. The common symptoms among those who were symptomatic included cough, fever, and sore throat. A few participants experienced repeat infections during the wave, often involving closely related strains. The virus lineages detected were most closely related to those sampled in Europe. Our findings emphasize that, despite the end of the emergency phase, SARS-CoV-2 remains a significant public health issue, necessitating ongoing monitoring and responsive measures e.g. target vaccinations, masking and good hygiene practices to protect those at risk of severe infection.