The nucleotide sequence of citrus leaf rugose ilarvirus (CiLRV) RNA-2 consists of 2990 nucleotides and contains one open reading frame (ORF) which encodes a deduced translation product of 832 amino acids with a calculated of 95 501 (95K). The 5′ terminus of the RNA has a mGppp cap. Both the nucleotide sequence of CiLRV RNA-2 and its translated polypeptide share homologies with the nucleotide sequence and translated polypeptide, respectively, of RNA-2 of alfalfa mosaic virus (AIMV). The homology occurs in the central region of both the nucleic acid sequence and the polypeptide. Homologies between either CiLRV or AlMV and other (cucumber mosaic virus - CMV, brome mosaic virus - BMV and cowpea chlorotic mottle virus - CCMV) were far less. Alignment of the 104 amino acid region (polymerase signature) of the 95K protein against 10 other ‘alpha-like’ plant viral polymerase signatures showed that CiLRV and A1MV are more closely related to each other than to CMV, BMV or CCMV. This is the first report of the full-length sequence of RNA-2 of an ilarvirus.


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