Nucleotide sequence analysis of virus isolates indicates the presence of three potyvirus species in Allium plants.

cDNAs of potyviruses from Allium plants cultivated in different parts of the world were cloned by RT-PCR with a common primer for amplifying the 3' terminal genomic RNAs of onion yellow dwarf virus (OYDV), leek yellow stripe virus (LYSV) and, probably, of closely related potyviruses. Their nucleotide sequences bearing the viral coat protein (CP) gene and the 3' non-coding sequence were determined and compared. The degree of their sequence similarities clearly differentiated the respective viruses into 3 groups, namely OYDV "garlic-type", "wakegi-type" and LYSV group. The "garlic-type" included all the garlic isolates and two Indonesian shallot isolates. The "wakegi-type" group consisted of the isolates from Indonesian shallot and previously reported ones from Japanese Allium plants excluding garlic. The LYSV group was represented by LYSV isolates from garlic and leek. The CP sequences of LYSV group viruses differed from those of OYDV "garlic-type" and "wakegi-type" viruses (less than 60% similarities). In contrast, the sequence similarities between the OYDV "wakegi-type" and "garlic-type" isolates were 73.5 to 76.7%, suggesting they were closely related but should be discriminated as distinct species. These findings indicate that at least three distinct potyviruses, clearly distinguishable by the viral CP sequence, are present in Allium species. Finally, we concluded that the "garlic-type" viruses correspond to the typical OYDV and the "wakegi-type" viruses represent the viruses previously identified as Welsh onion yellow stripe virus (WoYSV) and shallot yellow stripe virus (SYSV). We propose the name wakegi yellow dwarf virus (WYDV) for the "wakegi-type" viruses.