Arch Virol (2005) 150: 2407–2420 DOI 10.1007/s00705-005-0610-1 The diversity of Banana streak virus isolates in Uganda G. Harper 1 , D. Hart 1 , S. Moult 1 , R. Hull 1 , A. Geering 2 , and J. Thomas 2 1 John Innes Centre, Colney Lane, Norwich, U.K. 2 Department of Primary Industries and Fisheries, Indooroopilly, Queensland, Australia Received January 1, 2005; accepted June 24, 2005 Published online August 12, 2005 c  Springer-Verlag 2005 Summary. In a study of the variation among isolates of Banana streak virus (BSV) in Uganda, 140 sequences were obtained from 49 samples by PCR across the conserved reverse transcriptase/RNaseH region of the genome. Pairwise com- parison of these sequences suggested that they represented 15 different species and phylogenetic analyses showed that all species fell into three major clades based on 28% sequence difference. In addition to the Ugandan sequences, clade I also contained BSV species that are known as both integrated sequences and episomal viruses; clade II also contained integrated BSV sequences but which have not previously been identified as episomal viruses. Clade III comprised of Sugarcane bacilliform virus isolates and Ugandan BSV sequences and for which there is no evidence of integration.The possible reasons for the extraordinary levels of virus sequence variation and the potential origins and epidemiology of these viruses causing banana streak disease are discussed. Introduction Musa, as dessert banana and plantain, is a major subsistence crop in many developing countries. The modern varieties are mainly hybrids of various ploidies of two parental species, Musa acuminata (A genome) and Musa balbisiana (B genome). Banana streak virus (BSV; genus Badnavirus), the causal agent of banana streak disease (BSD) [31] is a major constraint to Musa breeding programmes and germplasm dissemination. BSV is a pararetrovirus with a circular dsDNA genome of 7.4 kbp [18] and like retroviruses, replicates via a ssRNA intermediate, which is converted back to dsDNA through the action of a virus-encoded reverse transcriptase (RT). Seven conserved domains have been The EMBL accession numbers of the sequences reported in this paper are AJ968419– AJ968559.