The nucleic acid of a serologically distinct potyvirus, originally isolated out of sugar cane from Pakistan, was reverse transcribed and the 3Π terminal 2000 bp was PCR amplified, cloned, and sequenced. Phylogenetic comparisons of viruses representing each genus of the Potyviridae show that the Pakistani isolate is most closely related to the rymoviruses wheat streak mosaic virus (WSMV) and brome streak mosaic virus. We therefore propose that this new virus species be named sugar cane streak mosaic virus to reflect its similarity to WSMV. The phylogenetic data also show that the genus Rymovirus contains at least two unique evolutionary lineages. Thus the current taxonomy, based on transmission vector, is paraphyletic. We present an analysis of the taxonomic relationships among members of the family and propose a classification that both resolves the paraphyly and more accurately represents the evolutionary history of the Potyviridae. 1998 Academic Press Current classification places the Potyviridae in the picornavirus-like supergroup of plus-stranded, RNA viruses, with the families Picornaviridae, Nepoviridae, and Comoviridae. The family is composed of four genera Potyvirus, Rymovirus, Bymovirus, and Ipomovirus (Shukla et al., 1994;Colinet et al., 1996) that are defined by the type of vectors that transmit the viruses, namely aphids, eriophyid mites, fungi, and whiteflies, respectively.
Recent evidence suggests that the aphid-transmitted macluraviruses comprise another genus (Badge et al., 1997) and that the genus Rymovirus is actually two distinct groups of viruses (Salm et al., 1996b). The increasing availability of potyvirus sequence data presents new opportunities for comparisons that may reveal insights about the phylogeny and evolution of this important family of viruses. An accurate phylogenetic framework is an essential component of accurate nomenclature and the comparative understanding of the etiology, epidemiology, and evolution and speciation of these viruses.