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Rotavirus is the major cause of paediatric severe diarrhoea worldwide. The virus is antigenically variable, with diversity arising from immune driven drift and reassortment of its segmented RNA genome during superinfections of human and animal strains. In Africa in particular the occurrence of unusual variant combinations of the immunodiminant G and P types is very high. Live attenuated vaccines, shown to be highly effective where they have been so far trialed, are increasingly being implemented within universal infant immunization schedules. Uncertainty as to the possible outcome of population intervention includes (i) impefect heterotypic immunity to non-vaccine types, leading to strain replacement (ii) emergence of new strains from reassortment with non-human strains, (iii) lower immunogenicity due to malnutrition and high exposure to enteric pathogens. In response to this we are conducting longitudinal genetic surveillance of disease causing rotaviruses prior to and after the introduction of wide- scale vaccine introduction in Kenya.