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Varroa mite (Varroa destructor Anderson and Trueman) is a major global threat to the western honey bee (Apis mellifera L.). The ectoparasite has been implicated in the spread of honeybee viruses. Beekeeping plays a major role in transmission of the mite. The study aimed at assessing levels of Varroa infestation, bee viruses and bacteria incidences in domesticated honeybee colonies. Samples of adult honey bees, bee brood and Varroa mites were collected from Baringo, Narok, Kwale, Magarini, Voi, Ijara, Busia and Siaya in Kenya. Ten hives in each site were inspected for the presence of Varroa mites on adult bees using the icing sugar technique and forceps in sealed brood cells. The number of mites observed were recorded per site. Ribonucleic acid was extracted from the mites, brood and adult bees and a polymerase chain reaction was performed to detect the black queen cell virus. Pooled RNA samples of brood and adult bees were used in next generation sequencing on a 454 GS FLX platform to detect bee viruses and bacteria. Varroa mites were reported in all the study sites at varying levels. The black queen cell virus and three iflaviruses, European foul brood and its secondary causative agent Enterococcus faecalis were reported. The Kenyan honeybee population is threatened by bee pests and pathogens. There is a need for constant monitoring of bee pests and diseases in honeybee colonies in the country for early detection and to provide data on the status of bee health. All stakeholders in the beekeeping value chain should be enlightened on their role in pest and disease transmission.  相似文献   
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