Two independent, long-term infections were analyzed to determine whether changes in viral replication could contribute to the establishment and/or maintenance of persistent Seoul virus infections. Infected cell cultures initially contained high levels of infectious virus and intracellular viral RNA that peaked between approximately 7 to 16 days postinfection and then gradually declined until day 26. After day 26, the viral titers and the levels of the small (S), medium (M), and large (L) viral RNAs varied cyclically until the end of the studies. The changes in the concentrations of the RNAs and titer were similar in pattern and appeared to result from changes in the regulation of replication. Neither internal deletions nor an accumulation of nucleotide changes were found in the RNAs. However, fine mapping and sequence analysis revealed short deletions in some of the RNAs in the conserved complementary terminal sequences believed to contain the signals for initiation of replication and transcription. Deletions at the 3 termini of S, M, and L virus-sense RNAs (vRNAs) accumulated during the acute phase of infection just before the time that the viral titer and the concentration of vRNAs and virus complementary-sense RNAs (cRNAs) began to decline. The absence of deletions at the 5 termini of the S, M, and L cRNAs suggests that the 3-deleted vRNAs may not be replication competent. Thus, as the percentage of 3-deleted vRNAs increase in the population, they could potentially compete with standard virus and downregulate viral replication. Deletions at the 3 L cRNA and 5 L vRNA termini were also observed, and the proportion of these deleted RNAs varied cyclically during the infections. We propose a model in which terminal nucleotide deletions arise by nuclease activity of the viral polymerase. In addition, we speculate that cleaved terminal fragments might be used as primers during replication, resulting in the repair of some of the deleted RNAs.The Hantavirus genus, in the family Bunyaviridae, is composed of a large group of enveloped negative-strand RNA viruses with a tripartite segmented genome (32). The three segments, small (S), medium (M), and large (L), encode the viral nucleocapsid (N), envelope glycoproteins (G1 and G2), and polymerase (L), respectively (33,35,36). Hantaviruses replicate in the cell cytoplasm, and replication is likely to proceed by mechanisms similar to those used by other negative-strand RNA viruses. That is, synthesis of mRNA and antigenome or virus complementary-sense RNA (cRNA) is initiated from the 3Ј terminus of viral RNA templates, and the synthesis of virus-sense RNA (vRNA) is initiated from the 3Ј terminus of cRNA templates. The signals for initiation of replication and transcription have not yet been defined but are believed to reside in the imperfect inverted repeat present at the termini of each genomic segment. This sequence is approximately 20 nucleotides long and is conserved among all members of the genus. Because bunyavirus ribonucleocapsids are circular (24, 26) and the termin...