Yellow Leaf Virus Strain Diversity within the South African Sugarcane Industry

Yellow Leaf Syndrome is a relatively new disease of sugarcane caused by Sugarcane Yellow Leaf Virus (SCYLV) and/or Sugarcane Yellows Phytoplasma (SCYP). Common symptoms include yellowing of the leaf midrib, sucrose accumulation in the leaves and leaf necrosis. Tissue-blot immunoassay and Titan One Tube RT-PCR are routinely used to determine the presence of SCYLV. Leaf samples taken from six imported varieties, held in the SASRI variety collection, and four quarantined imported varieties, all tested positive for the virus. The genotypic diversity of SCYLV in varieties from five countries, including South Africa, was determined through cloning and sequencing part of the viral genome. Using Clustal X sequence alignment and Neighbor-Joining phylogenetic methods, four different strains of virus were detected. Sequences were compared with known sequences from GenBank. Closely related viral sequences from varieties CP72/1210, CP79/1348, 94Z/0155, 94Z/0144, N30 and N32 represent one strain that was found to be similar to a Guatemalan strain G2. Sequences from CP78/2114 and the quarantined import CC87/505 from Colombia represent a second strain, similar to Colombian strains C1 and C3, and the three quarantined SP varieties were similar to the Brazilian strain B1. One putative strain has been found in SP71/3146. It has been observed that genetic variability exists in SCYLV.