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 summary Severe 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. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was funded by Wellcome through (a) a Career Development Award to CNA (Ref. #226002/A/22/Z & Ref. #226002/Z/22/Z) and (b) 226130/Z/22/Z from the Wellcome Covid19: understanding the biological significance of SARS CoV 2 variants application to IO. SD acknowledges support from the Fonds National de la Recherche Scientifique (F.R.S.FNRS, Belgium; grant nF.4515.22), from the Research Foundation, Flanders (Fonds voor Wetenschappelijk Onderzoek, Vlaanderen, FWO, Belgium; grant nG098321N), and from the European Union Horizon 2020 projects MOOD (grant agreement n874850) and LEAPS (grant agreement n101094685). E.C.H. is supported by a National Health and Medical Research Council (Australia) Investigator Grant (GNT2017197). AWL was supported by the Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE) which is funded by the Science for Africa Foundation [Del22007] with support from Wellcome Trust and the UK Foreign, Commonwealth & Development Office and is part of the EDCPT2 programme supported by the European Union; the Bill & Melinda Gates Foundation [INV033558]; and Gilead Sciences Inc., [19275]. All content contained within is that of the authors and does not necessarily reflect positions or policies of any SANTHE funder. For the purpose of Open Access, the author has applied a CC-BY public copyright license to any author accepted manuscript version arising from this submission. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee/IRB of KEMRI Scientific Ethics and Research Unit (SERU), Nairobi Kenya gave ethical approval for this work. Each surveillance platform (community, outpatient, and inpatient) that provided samples analysed here had a dedicated research protocol. The protocols consenting and sample collection process were reviewed and approved by KEMRI Scientific Ethics and Research Unit (SERU), Nairobi Kenya (protocol numbers #3178, #3103 and 4724). Samples were collected following consent from a parent or guardian for participants aged <18 year olds (with assent for children aged between 13 to 18 year olds). Individual written informed consent was sought for participants aged >18 years. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The final consensus genomes from the SARS-CoV-2 samples sequenced in this study have been deposited in the Global Initiative on Sharing all Influenza Data (GISAID) database and can be accessed at <https://doi.org/10.55876/gis8.250116pz>. Epidemiological data and scripts for data analysis are available on the Harvard dataverse <https://doi.org/10.7910/DVN/BMCJTI>.