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Sugarcane disease surveys were conducted from 2010 to 2014 at major sugarcane growing areas in 5 provinces (Nakhon Pathom, Kanchanaburi, Udon Thani, Khon Kaen, Nakhon Ratchasima) and germplasm collection fields. Random samples of the virus-like sugarcane leaves obtained from the surveyed areas suggested yellow streak mosaic symptoms. Direct antigen coating ELISA using locally produced SCSMV antiserum, revealed widespread incidence of SCSMV in the major sugarcane growing areas and the germplasm collection fields, ranging from 43.48-90.91% and 54.17-100% respectively. The virus isolate from sugarcane in Kamphaeng Saen, Nakhon Pathom, designated as THA-NP3, was characterized by genomic sequencing. Complete genome of THA-NP3 (JN163911) contained 9,781 nucleotides, excluding 3¢ Poly (A) tail which encoded a polyprotein of 3,130 amino acid residues comprising 10 functional proteins, namely P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, NIa-Pro, NIb and CP. Sequence comparisons revealed that THA-NP3 showed 97.84% nucleotide identity to JP2 (JF488065) from China and 81.39-97.78% nucleotide identities to other recorded SCSMV sequences. Detection for the presence of CP gene by RT-PCR indicated 1094 bp containing 846 bp of the CP coding region. Analysis of the CP gene revealed genetic variation of 58 Thai SCSMV isolates, 86.17-100% nucleotide identities among them and 85.70-99.29% nucleotide identities to SCSMV isolates from other countries. Recombination events existed in the CP coding regions between two distinct sub-populations, the germplasm isolates and the farmers’ field isolates. These results suggested the incidence of SCSMV variants between the farmers’ fields and the germplasm collection fields.

Characterization and Genetic Variation of Sugarcane Streak Mosaic Virus, a Poacevirus Infecting Sugarcane in Thailand