BK viruses (BKV) comprise four subtypes that are distinguishable by serological and molecular methods with the latter indicating up to four subgroups within subtype I. In this study, the phylogeny of all BKV subtypes was analyzed. Phylogenetic analyses of the viral structural protein VP1, concatenated sequences including the T-Ag, t-Ag, VP1 and VP2 genes and the entire coding region of BKV, each employing several tree inference methods, consistently revealed seven strongly supported clades that correlate with BKV subtypes and subgroups. In general, subtype II and III viruses were found to be sister groups, the genetic distances between which were significantly lower than those between either and the other BKV subtypes. Two benchmarks of human evolution (emergence of modern humans, 200,000 years ago; out-of-Africa migration, 100,000 years ago) were assumed for the internal calibration of BKV evolution. Utilization of either calibration point resulted in the diversification of most BKV subgroups coinciding with human radiation less than 50,000 years ago. Another approach, external calibration by linking BKV divergence to the evolution of mammals, was rejected as it advances BKV divergence prior to the emergence of modern humans.
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