A broad spectrum, one-step RT-PCR to detect Satsuma dwarf virus variants using universal primers targeting both segmented RNAs 1 and 2

Universal primers to detect Satsuma dwarf virus (SDV), including distantly related strains Citrus mosaic virus (CiMV), Navel orange infectious mottling virus (NIMV), and Hyuganatsu virus (HV), were tested in a convenient one-step RT-PCR assay. SDV was the most broadly detected using uSDVup/uSDVdo primers that specifically targeted a nucleotide sequence in the 3′-noncoding region that is conserved in both segmented RNAs 1 and 2 of SDV among the tested primers. Nucleotide sequence analysis confirmed that the amplified RT-PCR products could be derived from RNAs 1 or 2 of SDV variants, some of which had interesting genetic diversity.