Norovirus GII.17 Predominates in Selected Surface Water Sources in Kenya

In this study, the prevalence and genotypes of noroviruses (NoVs) in selected water sources from rural, urban and refugee settings in Kenya were investigated. Ten litres each of river, household and borehole water was collected in rural (Mboone River), urban (Nairobi and Mutoine River) and refugee (Dadaab refugee camp) settings. NoVs were recovered from the water samples by a glass wool adsorption-elution technique and/or PEG/NaCl precipitation. Nucleic acid was extracted using the automated MagNA Pure platform. NoVs were detected with singleplex real-time reverse transcription-polymerase chain reaction assays and characterised by nucleotide sequence analysis. NoVs were detected in 63% (25/40) of the selected water samples comprising GII (42.5%), GI (2.5%) and mixed GI/GII (17.5%) positive samples. The prevalence of NoVs in the Mutoine River (urban area) was higher than in the Mboone River (rural area) (P = 0.0013). Noroviruses GI.1, GI.3, GI.9, GII.4, GII.6, GII.12, GII.16 and GII.17 were identified, with GII.17 accounting for 76% (16/21) of the typed strains. The NoV GII.17 predominance differs to other studies in Africa and further surveillance of NoVs in clinical and environmental settings is required to clarify/elucidate this observation. As information regarding NoVs in Kenyan water sources is limited this report provides valuable new data on NoV genotypes circulating in environmental water sources and the surrounding communities in Kenya.