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Eleven complete BKV genomes (GenBank accession numbers: JN192431\u2010JN192441) were sequenced from urine samples of allogenic hematopoietic stem cell transplant recipients and compared to complete BKV genomes in the published literature. Of the 11 isolates, seven (64%) were subgroup Ib\u20101, three (27%) isolates belonged to subgroup Ib\u20102 and a single isolate belonged to subtype III. The analysis of single\u2010nucleotide polymorphisms in this study showed that isolates could be subclassified into subtypes I\u2013IV and subgroups Ib\u20101 and Ib\u20102 on the basis of VP1 of the first part of the Large T\u2010antigen (LTag). The non\u2010coding control region (NCCR) of the 11 isolates was also sequenced. These sequences showed that there was consistent sequence homology within subgroups Ib\u20101 and Ib\u20102. Two new mutations were described in the isolates, G\u2192C at O<jats:sub>84<\/jats:sub> in isolate SJH\u2010LG\u2010310, and a deletion at R<jats:sub>2\u20107<\/jats:sub> in isolate SJH\u2010LG\u2010309. No known transcription factor is thought to be present at the site of either of these mutations. There were no rearrangements seen in isolates and this may be because the patients were not followed up over time. There were five nucleotide positions at which subgroup Ib\u20101 isolated differed from subgroup Ib\u20102 isolates in the NCCR sequence, O<jats:sub>41<\/jats:sub>, P<jats:sub>18<\/jats:sub>, P<jats:sub>31<\/jats:sub>, R<jats:sub>4<\/jats:sub>, and S<jats:sub>18<\/jats:sub>. The mutation O<jats:sub>41<\/jats:sub> is present in the promoter granulocyte\/macrophage stimulating factor) gene and the P<jats:sub>31<\/jats:sub> mutation is present in the NF\u20101 gene. J. Med. 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