Variable repeats and poly (A)-stretches in the leader sequence of alfalfa mosaic virus RNA 3.

The complete nucleotide sequence of RNA 3 of the L strain of alfalfa mosaic virus (AlMV) was deduced and the 5'-terminal sequence of RNA 3 of the S-strain was revised. A comparison of the RNA sequences of AlMV strains L, S, and M showed that a sequence of 27 to 30 nucleotides is repeated two times in the 5' noncoding regions of all strains. In addition, sequences of 56 and 75 nucleotides are duplicated in the leaders of strain S and L, respectively. An A-rich sequence of 10 nucleotides, present in strain S and M, was found to be extended to 40 nucleotides in strain L. The data provide further information on the fidelity of RNA-dependent RNA polymerases.