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Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or infection spreads to susceptible subpopulations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model, we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of higher-transmissibility variants. Reopening schools led to a minor increase in transmission between the second and third waves. Socioeconomic and urban–rural population structure are critical determinants of viral transmission in Kenya.

Original publication




Journal article


Science (New York, N.Y.)

Publication Date





989 - 994


Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya.


Humans, Incidence, Seroepidemiologic Studies, Communicable Disease Control, Models, Biological, Social Class, Socioeconomic Factors, Kenya, Epidemics, COVID-19, COVID-19 Nucleic Acid Testing