5'-terminal sequences influence the segregation of ground squirrel hepatitis virus RNAs into polyribosomes and viral core particles.

To determine which of the major ground squirrel hepatitis virus RNAs serve as mRNAs and which serve as templates for reverse transcription of the genome, we analyzed the subcellular distribution of these RNAs in livers of infected ground squirrels. Both major classes of viral RNA, the 2.3- and 3.5-kilobase (kb) classes, are unspliced, are polyadenylated at a common position, and display heterogeneous 5' ends that can encode proteins with different amino termini (G.H. Enders, D. Ganem, and H. Varmus, Cell 42:297-308, 1985). Both of the 2.3-kb RNAs, which encode surface antigens, appear to be predominantly associated with polyribosomes. Of the three 3.5-kb RNAs, the two longer, which can encode a protein initiated from the first methionine codon in the core antigen gene, appear to be predominantly associated with polyribosomes, and a minority of the shortest 3.5-kb RNAs, which can encode a protein initiated from the second methionine in the core antigen gene, appears to be associated with polyribosomes. This last RNA is instead found predominantly within viral core particles, consistent with evidence that indirectly implicates it in two steps of viral DNA synthesis (C. Seeger, D. Ganem, and H.E. Varmus, Science 232:477-484, 1986). None of the other viral RNAs is detectably packaged into cores. These findings provide independent evidence that the shortest 3.5-kb RNA is the template for synthesis of the viral genome and reveal a novel selectivity in viral RNA packaging.