Accumulation of Terminally Deleted RNAs May Play a Role in Seoul Virus Persistence

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 3′ terminus of viral RNA templates, and the synthesis of virus-sense RNA (vRNA) is initiated from the 3′ 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 terminal nucleotides of the vRNAs and cRNAs appear to be base paired, the RNAs are thought to exist as panhandle structures in cells (Fig. ​(Fig.1)1) (28). Thus, both the terminal nucleotide sequence and the structure of the panhandle may be important in proper initiation at the 3′ termini of the vRNAs and cRNAs. FIG. 1 The 5′- and 3′-terminal 20 nucleotides of SR-11 virus L, M, and S vRNAs shown base paired in one version of a proposed panhandle structure. Hantaviruses cause persistent infections in rodents in nature, and each strain is normally associated with a specific host species. While much is known about the geographic distribution and antigenic and genetic differences among the hantaviruses, information about persistence is limited because thus far only a few studies have described long-term infections. This is partially due to the difficulty in detecting virus, vRNA, and viral protein in infected animals (39; R. Yanagihara et al., Letter, Lancet i:1013, 1984). Despite these limitations, a few basic features of hantavirus persistence have emerged from experimental animal infections. As for other persistent viruses, hantavirus infections appear to consist of a short acute phase followed by a prolonged persistent phase. Acute infection seems to last about 3 to 4 weeks, and during this time animals are transiently viremic. Viremia peaks around 7 to 14 days postinfection (p.i.) (4, 12, 16, 17, 19, 40). During persistence, the levels of infectious virus or antigen-positive cells are generally lower, and in some tissues or secretions may vary or disappear and reappear several times during the course of the study in a wave-like pattern (4, 12, 16, 17, 18, 38, 40). Thus, while virus and/or antigen can be detected in many tissues and bodily fluids during the acute stage, they are often only detected sporadically from the same sites during persistence. Taken together, the reduction in virus and antigen after the acute phase of infection and the cyclic variations in infectious virus and antigen during persistence suggest that some stage of the virus life cycle is downregulated when persistence is established and at cyclic intervals during the time that persistence is maintained. To understand the mechanism by which hantaviruses persist in cells, we investigated whether changes occur in Seoul virus (SEOV) replication during a long-term infection and, if so, how those changes could account for the apparent downregulation in viral gene expression that is associated with the establishment and maintenance of persistence in animals.