The complete nucleotide sequence of the rice grassy stunt virus genome and genomic comparisons with viruses of the genus Tenuivirus.

Rice grassy stunt virus (RGSV, IRRI isolate) has six genomic RNA segments. The nucleotide (nt) sequences of RNAs 1-4 were determined. The cumulative length of the RGSV genome, including RNAs 5 and 6, was 25142 nt. All six RNA segments had an ambisense coding strategy and almost identical terminal sequences over 17 nt. The virus complementary (vc) sequence of the largest segment, RNA1, had an open reading frame encoding a protein of Mr 339133 (the 339.1K protein), while the virus sense (v) sequence encoded a protein of Mr 18910 in the 5'-proximal region. The predicted 339.1K protein contained the highly conserved motifs of the RNA-dependent RNA polymerase and a short but distinct Arg/Gly-rich stretch at the C terminus. The putative RNA polymerase showed strong similarity with that of rice stripe tenuivirus (RSV); they shared 37.9% amino acid identity over 2140 residues. The predicted proteins of Mr 23280 on vRNA2 and 93 879 on vcRNA2 were only slightly similar in sequence to the proteins encoded by vRNA2 and vcRNA2 of other tenuiviruses. The predicted proteins encoded by RNA3 and RNA4 did not show significant similarity to any database proteins. Only the putative RNA polymerase encoded on RNA1 was well-conserved between RGSV and RSV. The low sequence similarities in proteins encoded by RNAs 2, 5 and 6, together with the unique RNA segments 3 and 4, indicate that RGSV may be distinct from other tenuiviruses.