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Rotaviruses of species A (RVA) are a common cause of diarrhea in children and the young of various other mammals worldwide. Interspecies transmission of RVA may lead to the emergency of novel RVA strains which may potentially affect rotavirus vaccine efficacy. The aim of this study was to investigate for possible interspecies transmission of RVAs in Uganda. Whole-genome sequencing of eighteen human (under-fives with diarrhea) and six animal (one bovine, one caprine, and four porcine) RVA strains identified in Uganda in the same geographical region, between 2012 and 2014 was undertaken using the Illumina HiSeq platform. RotaC version 2, a classification tool for RVAs was used to assign genotypes to all eleven genome segments of each isolate. Phylogenetic analysis was carried out using the maximum likelihood method in MEGA 6.06. Human RVA strains had either a Waor a DS-1-like genetic constellation. One human strain was a Wa-like mono-reassortant containing a DS-1-like VP2 gene of possible animal origin. In addition, three human RVA strains had one or two genes with possible zoonotic origin. All eleven genes of the bovine RVA strain were closely related to those of human RVAs. The caprine strain had a mixed genotype backbone, suggesting that it emerged from multiple re-assortment events involving different host species. Porcine RVA strains had mixed genotype backbones with possible multiple reassortant events with strains of human and bovine origin. Interspecies transmission of RVA strains occurred in this setting. RVA strains causing diarrhea in children are primarily transmitted from person to person. Rotavirus vaccination in children in Uganda will control rotavirus transmission. It is recommended to continue molecular surveillance of RVAs in humans and animals living in the same geographical region to understand the molecular epidemiology and evolution of RVAs in Uganda and other countries.

A49 Phylogenetic evaluation of the Zika virus emergence in the Americas: 2015–2016