Genetic variation during lytic reovirus infection: high-passage stocks of wild-type reovirus contain temperature-sensitive mutants

Viral Coinfections

In nature, viral coinfection is as widespread as viral infection alone. Viral coinfections often cause altered viral pathogenicity, disrupted host defense, and mixed-up clinical symptoms, all of which result in more difficult diagnosis and treatment of a disease. There are three major virus-virus interactions in coinfection cases: viral interference, viral synergy, and viral noninterference. We analyzed virus-virus interactions in both aspects of viruses and hosts and elucidated their possible mechanisms. Finally, we summarized the protocol of viral coinfection studies and key points in the process of virus separation and purification.

Virological and Immunological Outcomes of Coinfections

Coinfections involving viruses are being recognized to influence the disease pattern that occurs relative to that with single infection. Classically, we usually think of a clinical syndrome as the consequence of infection by a single virus that is isolated from clinical specimens. However, this biased laboratory approach omits detection of additional agents that could be contributing to the clinical outcome, including novel agents not usually considered pathogens. The presence of an additional agent may also interfere with the targeted isolation of a known virus. Viral interference, a phenomenon where one virus competitively suppresses replication of other coinfecting viruses, is the most common outcome of viral coinfections. In addition, coinfections can modulate virus virulence and cell death, thereby altering disease severity and epidemiology. Immunity to primary virus infection can also modulate immune responses to subsequent secondary infections. In this review, various virological mechanisms that determine viral persistence/exclusion during coinfections are discussed, and insights into the isolation/detection of multiple viruses are provided. We also discuss features of heterologous infections that impact the pattern of immune responsiveness that develops.

Reovirus sigmaNS protein is required for nucleation of viral assembly complexes and formation of viral inclusions

Progeny virions of mammalian reoviruses are assembled in the cytoplasm of infected cells at discrete sites termed viral inclusions. Studies of temperature-sensitive (ts) mutant viruses indicate that nonstructural protein sigmaNS and core protein mu2 are required for synthesis of double-stranded (ds) RNA, a process that occurs at sites of viral assembly. We used confocal immunofluorescence microscopy and ts mutant reoviruses to define the roles of sigmaNS and mu2 in viral inclusion formation. In cells infected with wild-type (wt) reovirus, sigmaNS and mu2 colocalize to large, perinuclear structures that correspond to viral inclusions. In cells infected at a nonpermissive temperature with sigmaNS-mutant virus tsE320, sigmaNS is distributed diffusely in the cytoplasm and mu2 is contained in small, punctate foci that do not resemble viral inclusions. In cells infected at a nonpermissive temperature with mu2-mutant virus tsH11.2, mu2 is distributed diffusely in the cytoplasm and the nucleus. However, sigmaNS localizes to discrete structures in the cytoplasm that contain other viral proteins and are morphologically indistinguishable from viral inclusions seen in cells infected with wt reovirus. Examination of cells infected with wt reovirus over a time course demonstrates that sigmaNS precedes mu2 in localization to viral inclusions. These findings suggest that viral RNA-protein complexes containing sigmaNS nucleate sites of viral replication to which other viral proteins, including mu2, are recruited to commence dsRNA synthesis.

Serial passage of human immunodeficiency virus type 1 generates misalignment deletions in non-essential accessory genes

Human immunodeficiency virus type 1 (HIV-1) derived from an infectious molecular clone pNL432 was extensively passaged in tissue culture by repeated rounds of acute infection. We previously showed the natural occurrence of a nonsense mutation in the vpr gene during continued passage of this virus. In this report, we show that two forms of large deletions (561 and 518 base pairs containing short direct repeats at the deletion junctions) occur after passage 50 in the region that spans the vif and vpr open reading frames. One model to explain the occurrence of these deletion regions is that such mutations result from misalignment of the growing point at a limited number of nucleotide positions. Infection of CD4+ T-cells with a recombinant HIV-1 construct containing the same vif to vpr deletion showed virtually no cytopathogenic phenotype. Thus, misalignment deletions at non-essential accessory genes of HIV-1 might be induced during replication, which result in the generation of virus with a low cytopathogenic potential.

Generation and role of defective proviruses in cytopathic feline leukemia virus (FeLV-FAIDS) infections

Cytopathic feline leukemia virus (FeLV) infections of feline T-cell line (FeT-cell) cultures led to the accumulation and maintenance of threefold more proviruses with deletions within the polymerase gene (pol) than minimally cytopathic FeLV infections. Over 60% of the viral DNA from cytopathic infections bore deletions in pol. Characterization of DNA sequences adjoining the deletions revealed that the junctions were most often flanked by RNA splice donor and acceptor consensus motifs. A thymidine-to-cytidine mutation introduced at the +2 position of one RNA splice donor-like motif inhibited formation of the two most prevalent viral DNA species with deletions, confirming the origin of many proviruses with deletions from reverse transcription of aberrantly spliced viral RNA species. An example of deletion by misalignment was also characterized. Viral inocula obtained from cells recovered after cytopathic infections were attenuated in their ability to cause cytopathic effects (CPE) and were able to confer superinfection resistance to naïve FeT-cells, despite maintaining envelope gene (env) sequences with full cytopathic potential. This suggested that viral genomes with deletions, rather than being required for cytopathicity, play a role in protecting cells from CPE. Indeed, expression of a molecularly cloned provirus bearing one of the characterized deletions attenuated CPE in FeT-cells caused by superinfecting cytopathic virus.

Establishment of persistent reovirus infection in SC1 cells: absence of protein synthesis inhibition and increased level of double-stranded RNA-activated protein kinase

In the present study we report the establishment and characterization of an SC1 cell line persistently infected by reovirus. We observed that a significant percentage of SC1 cells was resistant to cell lysis upon infection with non-defective reovirus stocks. The apparent resistance of SC1 cells to the virus-induced inhibition of protein synthesis is probably an important factor favoring the establishment of such a persistence. The remaining cells, obtained following reovirus infection at a high multiplicity of infection, were kept as a continuous cell line and shown to have normal growth rate. They also released a high titer of virus that did not appear to differ from the original stock in neither infectivity nor genomic pattern. Electron microscopic examination further confirmed the presence of well-developed viral inclusions in the persistently infected cells. These cells were resistant to viral superinfection and exhibited a high constitutive level of the double-stranded RNA-activated protein kinase that might be involved in this resistance. We suggest that this cell line might be an interesting, and possibly more natural system than most previously used cell lines, for the continuing study of virus-host cell interactions during establishment of viral persistence using the much-studied model of reovirus infection.

Identification of sequence elements containing signals for replication and encapsidation of the reovirus M1 genome segment

In reovirus the genetic signals that control genome replication and encapsidation are unknown. Serial passage of reovirus results in the accumulation of deletion mutants that contain fragments of genome segments. The smallest fragments found in deletion mutants will consist of the minimum essential sequences for genome replication and assembly. T1 x T3 reassortants containing the L2 segment from T3 and the M3 segment derived from T1 generate deletions in segment M1 on serial passage. Fragments of M1 segments were produced by serial passage, characterized by PAGE and Northern blotting before amplification by PCR, cloning, and sequencing. Thirteen of the smallest deletion fragments were sequenced. All of the smallest fragments contained sequences from both termini of segment M1. The smallest fragment was 344 nucleotides long. The consensus sequences consisted of 132-135 nucleotides from the 5' end of the plus strand and 183-185 nucleotides from the 3' end of the plus strand. It is concluded that these regions contain all the signals necessary for the replication and assembly of the M1 genome segment.

Evolution of sex in RNA viruses

The distribution of deleterious mutations in a population of organisms is determined by the opposing effects of two forces, mutation pressure and selection. If mutation rates are high, the resulting mutation-selection balance can generate a substantial mutational load in the population. Sex can be advantageous to organisms experiencing high mutation rates because it can either buffer the mutation-selection balance from genetic drift, thus preventing any increases in the mutational load (Muller, 1964: Mut. Res. 1, 2), or decrease the mutational load by increasing the efficiency of selection (Crow, 1970: Biomathematics 1, 128). Muller's hypothesis assumes that deleterious mutations act independently, whereas Crow's hypothesis assumes that deleterious mutations interact synergistically, i.e., the acquisition of a deleterious mutation is proportionately more harmful to a genome with many mutations than it is to a genome with a few mutations. RNA viruses provide a test for these two hypotheses because they have extremely high mutation rates and appear to have evolved specific adaptations to reproduce sexually. Population genetic models for RNA viruses show that Muller's and Crow's hypotheses are also possible explanations for why sex is advantageous to these viruses. A re-analysis of published data on RNA viruses that are cultured by undiluted passage suggests that deleterious mutations in such viruses interact synergistically and that sex evolved there as a mechanism to reduce the mutational load.

The viral protein sigma 3 participates in translation of late viral mRNA in reovirus-infected L cells

Reovirus late (uncapped) mRNA was previously shown to be efficiently translated in vitro extracts prepared from infected cells but not from uninfected cells. We demonstrated that different fractions from infected cells can stimulate translation of late viral mRNA when added to uninfected extracts. The activity of the different fractions correlated with their relative content of the sigma 3 capsid protein; the fraction prepared by high-salt wash of the ribosomes had the highest specific activity. The activity present in this fraction was abolished by preincubation with an anti-sigma 3 serum. Purified sigma 3 protein also stimulated the translation of late viral mRNA, confirming that it was the factor involved. Altogether, these results suggest that this protein plays the role of a late-viral-mRNA-specific initiation factor. The absence of an inhibitory effect of sigma 3 on the translation of other mRNAs indicates that this protein is not directly involved in the inhibition of host and early viral mRNA translation that occurs in infected cells but that a second mechanism is probably operative.

Association of reovirus proteins with the structural matrix of infected cells

The interaction of reovirus with the cytoskeleton was investigated. The soluble components of infected cells were extracted with the nonionic detergent NP-40 in a physiological buffer, and a cytoskeletal extract was prepared from the detergent-insoluble fraction. We observed a selective association of viral-specified products with the cytoskeleton that was temporally controlled. Viral dsRNA appeared first on the framework but after several hours was found also in the soluble phase, encapsidated in mature virions. The initial viral translation products were associated exclusively with the soluble fraction, but concomitant with the appearance of dsRNA, viral proteins microNS and sigma 3 were detected on the cytoskeleton. Several hours later, all viral proteins were detected on the framework. Viral polypeptide microNS exhibited unique spatial distribution patterns that correlated with viral assembly: Before dsRNA replication, it appeared as diffusely distributed protein; a few hours later, it was detected in punctate foci interconnected by tiny filaments; several hours later, it appeared as an extensive fiber network that traversed the foci. The other viral proteins were detected only within viral foci. MicroNS remained bound to the matrix fraction after treatment with DNase, Mg2+, and high salt, treatments that released other viral proteins. This distribution pattern was virus-directed because passage of virus at high multiplicity of infection induced mutations that prevented assembly of the microNS-coated filament organization. A small fraction of the viral-specified products that included polypeptide microNS, but not viral dsRNA, was coprecipitated from cytoskeletal extracts with proteins of mol wt approximately 55K by monoclonal antibodies that recognized tubulin and vimentin. Disruption of this interaction by long exposure to colchicine did not prevent association of viral proteins or RNA with the matrix, indicating that viral products were not transported through these interactions. The results indicate that reovirus morphogenesis includes temporal and spatial controls not described previously.

Evolutionary variants of Rous sarcoma virus: large deletion mutants do not result from homologous recombination

Large deletion (LD) mutants of Prague strain Rous sarcoma virus, subgroup B (PrB), derived by serial undiluted passage through chicken (C/E) cells, were isolated and characterized. Individual LD viruses were initially isolated by cloning in soft agar of infected, chemically transformed quail (QT6) cells. Two regions of the PrB genome were deleted in the formation of the LD virus. This resulted in the junction of gag sequences in p12 to env sequences in gp37, and in the loss of the src gene. DNA restriction analysis of biologically active lambda Charon 27-LD recombinant clones indicated that individual LD viruses contained similar but not identical deletion endpoints. Two LD isolates, LD25 and LD85, were further subcloned into pBR322, and the deletion junctions were examined by DNA sequencing. Although the gag-env deletion endpoints were identical in the two subclones, heterogeneity was observed across the src deletion in that both mutants analyzed had the same 5' endpoint but slightly different 3' endpoints. In all cases, only a single homologous base (always an A residue) was found at the deletion endpoint. S1 nuclease analysis of the RNA from a number of QT6-LD clones gave similar results, indicating that the LD population was composed of viruses with similar but not identical deletion endpoints. Such viruses may have been generated from errors during reverse transcription of the virion RNA with subsequent selection assuring their dominance in the population.

Differential effects of defective interfering Semliki Forest virus on cellular and virus polypeptide synthesis

Defective interfering Semliki Forest virus (DI SFV) inhibited virus RNA and virus polypeptide synthesis in cells coinfected with standard virus but did not delay or alter kinetics of RNA synthesis. Inhibition of polypeptide synthesis was 20-fold greater than that of RNA synthesis which presumably reflected the amplification resulting from cumulative translation of mRNAs. At high concentration, DI virus p12e inhibited the shutoff of host protein synthesis and allowed no synthesis of structural or nonstructural polypeptides. Dilution of DI virus restored the inhibition of host protein synthesis but further dilution was necessary before virus-specified polypeptide synthesis could be demonstrated. Another DI virus (p20a) with the same interference titre as p12e also inhibited shutoff of host protein synthesis but synthesis of virus-induced polypeptides was inhibited differentially: significant amounts of polypeptides comigrating with the structural precursor polypeptide p62 and the nonstructural polypeptide nsp63 were present and the synthesis of nsp90 was little affected at any concentration of DI virus p20a tested. None of the DI viruses tested induced the synthesis of any viral or novel polypeptide. It was concluded that DI SFV preparations have qualitatively different interfering activities in relation to their effects on virus and host cell polypeptide synthesis.

Selection of genetic variants of lymphocytic choriomeningitis virus in spleens of persistently infected mice. Role in suppression of cytotoxic T lymphocyte response and viral persistence

We studied the mechanism of lymphocytic choriomeningitis virus (LCMV) persistence and the suppression of cytotoxic T lymphocyte (CTL) responses in BALB/c WEHI mice infected at birth with LCMV Armstrong strain. Using adoptive transfer experiments we found that spleen cells from persistently infected (carrier) mice actively suppressed the expected LCMV-specific CTL response of spleen cells from normal adult mice. The suppression was specific for the CTL response and LCMV -specific antibody responses were not affected. Associated with the specific CTL suppression was the establishment of persistent LCMV infection. The transfer of spleen or lymph node cells containing LCMV -specific CTL resulted in virus clearance and prevented establishment of the carrier state. The suppression of LCMV -specific CTL responses by carrier spleen cells is not mediated by a suppressor cell, but is due to the presence of genetic variants of LCMV in spleens of carrier mice. Such virus variants selectively suppress LCMV-specific CTL responses and cause persistent infections in immunocompetent mice. In striking contrast, wild-type LCMV Armstrong, from which these variants were generated, induces a potent CTL response in immunocompetent mice and the LCMV infection is rapidly cleared. Our results show that LCMV variants that emerge during infection in vivo play a crucial role in the suppression of virus-specific CTL responses and in the maintenance of virus persistence.

Extragenic suppression of temperature-sensitive phenotype in reovirus: mapping suppressor mutations

Independently isolated, spontaneous pseudorevertants of temperature-sensitive (ts) mutants of reovirus type 3 have previously been genetically characterized (R. F. Ramig and B. N. Fields, 1979, Virology 92, 155-167). Eighteen of these pseudorevertants were backcrossed to wild-type reovirus type 1 and reassortant progeny expressing the parental ts phenotype were selected. Analysis of segregation of genome segments in the reassortant, parental ts, progeny clones allowed the determination of the genome segment bearing the suppressor mutation of four pseudorevertants. The suppressor of tsA(201) phenotype mapped to segment S4 in the pseudorevertants RtsA(201)101 and RtsA(201)121 and to segment L3 in pseudorevertant RtsA(201)122. The suppressor of tsB(352) phenotype mapped to segment S1 in the pseudorevertant RtsB(352)b. In two other pseudorevertants the suppressor could not be mapped to a single genome segment due to the small number of progeny clones examined. These genetic results indirectly support the "compensating protein interactions" hypothesis for the mechanism of suppression.

Selection of a mutant S1 gene during reovirus persistent infection of L cells: role in maintenance of the persistent state

LR-7 cells, variant L cells derived from a type 3 reovirus persistently infected (p.i.) carrier culture (R. Ahmed, W. M. Canning, R. S. Kauffman, A. H. Sharpe, J. V. Hallum, and B. N. Fields, Cell 25, 325-332, 1983) were used to define the viral genes critical for maintenance of the persistent state. A cloned viral isolate (L/C virus) derived from the p.i. culture replicated normally in LR-7 cells, while wild-type (wt) viruses of the three reovirus serotypes replicated less efficiently. To identify the viral gene(s) permitting enhanced replication of L/C virus in LR-7 cells, viral reassortants were prepared by mixed infection of L cells with L/C virus and type 1 wt. Study of the one-step growth curves and final yields of large numbers of reassortants in both L cells and LR-7 cells revealed that the presence of the S1 gene from L/C virus was critical for normal viral replication in LR-7 cells. However, this phenotype was suppressed by the simultaneous presence in reassortants of both the M2 and S4 genes from the type 1 wt parent. The critical change in the S1 gene occurred by passage 13 (63 days) after initiation of the carrier culture. Although multiple mutations are present in the viral population from p.i. cultures, certain specific mutations can be identified as critical for maintenance of the persistent state.

Genetic variation during persistent reovirus infection: isolation of cold-sensitive and temperature-sensitive mutants from persistently infected L cells

We have examined the evolution of reovirus in two independently established persistently infected (p.i.) cell lines. We found that reovirus undergoes extensive mutation during persistent infection in L cells. However, there was no consistent pattern of virus evolution; in one p.i. cell line temperature-sensitive (ts) mutants were selected, whereas cold-sensitive (cs) mutants were isolated from the second p.i. culture. Neither the cs nor the ts mutants isolated from the carrier cultures expressed their defect at 37 degrees, the temperature at which the p.i. cells were maintained, indicating that the cs and ts phenotypes were nonselected markers. These results emphasize the point that emergence of the ts or cs mutants during persistent infection only signifies that the virus has changed; it does not necessarily imply that the particular mutant is essential for the maintenance of the persistent infection. Given the high mutation rate of viruses, and the wide spectrum of viral mutants present in carrier cultures, it is essential to distinguish the relevant changes from those which may simply represent an epiphenomenon. In the accompanying paper (R. S. Kauffman, R. Ahmed, and B. N. Fields Virology, 130, 79-87, 1983), we show that by using a genetic approach, it is possible to identify the viral gene(s) which are critical for the maintenance of persistent reovirus infection.

Genetic and molecular mechanisms of viral pathogenesis: implications for prevention and treatment

The pathogenesis of infection of mice by the mammalian reoviruses involves several discrete steps. Each of the three viral outer capsid proteins has a highly distinct and specialized role: one protein (sigma 1) binds to cell surface receptors; a second protein (mu 1C) determines the capacity for viral growth at mucosal surfaces; and the third protein (sigma 3) is responsible for inhibiting cell macromolecular synthesis. A detailed picture of the molecular basis of reovirus virulence and attention is now emerging.

Rapid evolution of RNA genomes

RNA viruses show high mutation frequencies partly because of a lack of the proofreading enzymes that assure fidelity of DNA replication. This high mutation frequency is coupled with high rates of replication reflected in rates of RNA genome evolution which can be more than a millionfold greater than the rates of the DNA chromosome evolution of their hosts. There are some disease implications for the DNA-based biosphere of this rapidly evolving RNA biosphere.

Role of the host cell in persistent viral infection: coevolution of L cells and reovoirus during persistent infection

Mutant L cells, designated LR cells, were isolated after "curing" a persistently infected cell line (L/C) with antireovirus serum. The LR cells were shown to be virus-free; no reovirus was detectable by infectious center assays, plaque assays, presence of viral proteins, presence of viral dsRNA and immunofluorescence studies. Persistent infections were readily established n LR cells following infection with either cloned, low passage wild-type reovirus or cloned, low passage reovirus isolated from carrier cultures. Reovirus isolated from carrier cultures, however, grew much better than wild-type reovirus in LR cells and showed complete dominance over wild-type reovirus in coinfection experiments. Infection of LR cells with wild-type reovirus resulted in a low-level persistent infection with inefficient viral replication; these mutant L cells were partially resistant to infection with wild-type reovirus. In contrast, infection of the mutant L cells with virus isolated from the persistently infected cells resulted in a persistent infection accompanied with efficient viral replication. Infection of the original L cells with either wild-type reovirus or reovirus isolated from the persistently infected cells resulted in a lytic infection with no surviving cells. Thus the host cell plays a crucial role in the maintenance of persistent reovirus infection. Our results show that there is a coevolution of both mutant L cells and mutant reovirus during persistent infection.

Tryptic peptide analysis of outer capsid polypeptides of mammalian reovirus serotypes 1, 2, and 3

We studied the structural relationships among the outer capsid polypeptides of prototype strains of mammalian reovirus serotypes 1, 2, and 3 by tryptic peptide mapping. The micron1C polypeptide showed an extraordinary degree of conservation of its methionine-containing tryptic peptides. In contrast, the most abundant viral polypeptide, sigma 3, contained both conserved and unique methionine-containing tryptic peptides. The viral type-specific antigen, the sigma 1 polypeptide, contained both conserved and unique methionine- and tyrosine-containing tryptic peptides. These results suggested that the mammalian reovirus genome segments encoding each of the viral outer capsid polypeptides were derived from common ancestral segments which have diverged to different degrees.

Genetic variation during persistent reovirus infection: presence of extragenically suppressed temperature-sensitive lesions in wild-type virus isolated from persistently infected L cells

Persistent reovirus infection of L cells was established with a serially passaged stock of temperature-sensitive (ts) mutant C(447) containing greater than 90% defective interfering particles. Within a month after establishment of the carrier culture, the ts mutant was replaced by virus that expressed the wild-type (ts(+)) temperature phenotype (R. Ahmed and A. F. Graham, J. Virol. 23:250-262, 1977). To determine whether the ts(+) phenotype of the virus was due to intragenic reversion or to the presence of an extragenic mutation suppressing the original ts defect, several clones were backcrossed to wild-type reovirus, and the progeny of each cross were screened for temperature sensitivity. The results indicated that the original tsC lesion had reverted. However, in two of the seven clones examined, new ts lesions were found. These new ts lesions appeared phenotypically as ts(+) due to the presence of extragenic suppressor mutations. Temperature-sensitive mutants representing three different groups were rescued from one suppressed clone, indicating that this ts(+) clone contained multiple ts lesions. Among the ts mutants rescued were the initial isolates of a new recombination group which we have designated H. Some of the ts mutants rescued from the suppressed clones are capable of interfering with the growth of wild-type reovirus and may play a role in maintaining the carrier state. The results of this study show that persistently infected L cells contain a genetically heterogeneous population of reovirus even though all virus clones express the ts(+) phenotype. It is thus critical to distinguish between genotype and phenotype when analyzing viruses that emerge during persistent infection.