Mechanisms of persistent infections by cytopathic viruses in tissue culture. Brief review

Beyond cells - The virome in the human holobiont

Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as the most effective geo-transforming genetic engineers and resource recyclers, acting on all life strata in any habitat. Yet, most of this uncanny viral world remains vastly unexplored to date, greatly hindered by the bewildering complexity inherent to such studies and the methodological and conceptual limitations. Viromic studies are just starting to address some of these issues but they still lag behind microbial metagenomics. In recent years, however, higher-throughput analysis and resequencing have rekindled interest in a field that is just starting to show its true potential. In this review, we take a look at the scientific and technological developments that led to the advent of viral and bacterial metagenomics with a particular, but not exclusive, focus on human viromics from an ecological perspective. We also address some of the most relevant challenges that current viral studies face and ponder on the future directions of the field.

Molecular genetic analysis of the Influenza A(H1N1)pdm09 virus from lethal and recovered cases in Russia from 2009 to 2014: Deletions in the nucleoprotein

Influenza A(H1N1)pdm09 virus caused about 2000 laboratory confirmed lethal cases in Russia during 2009-2010 and 1302, 135 and 29 cases in the 2010-2011, 2012-2013 and 2013-2014 seasons respectively. The on average short duration (7.8±5 days) of lethal cases of Influenza A(H1N1)pdm09 infections in Russia suggests primary viral rather than secondary bacterial pneumonia. Hemorrhagic syndrome was recorded in 36.6% of patients. An examination of 221 lung samples from lethal influenza cases for the presence of bacterial DNA that could cause pneumonia did not reveal bacterial superinfections in 86% of cases. Molecular-genetic analyses of Influenza A(H1N1)pdm09 viruses from lethal and recovered cases were performed. Amino acids G and N at position 222 of the influenza virus hemagglutinin, which increase the affinity for the lower respiratory tract receptors, were detected more often in the lungs of patients who died than in respiratory swabs collected from recovered patients (p<0.0001 and p=0.007). Viruses harboring various mutations (222D/G/N/S) was significantly associated with lung samples compared with respiratory swabs from recovered patients (p<0.0001). Amino acid 222E, which increases the affinity for upper respiratory tract receptors, was found more frequently in recovered patients than in patients with lethal disease (27% versus 3%, p=0.005). Phylogenetic analysis identified an isolated cluster of viruses in the 2009-2010 season that harbored amino acid 222E, which could explain the high transmissibility of the virus at the beginning of the pandemic. Bayesian skyline plot implied a decline in the effective population size of Influenza A(H1N1)pdm09 viruses in Russia from 2010-2011 to 2011-2012, followed by an increase in 2012-2013; this trend was accompanied by the increased genetic diversity of the hemagglutinin antigenic sites. Mutations of viral RNA leading to oseltamivir resistance were found in 2.8% of tested patients during only 2010-2011 season. Deletions in the nucleoprotein cDNA were found in influenza viruses from two patients.

Identification and characterization of a ross river virus variant that grows persistently in macrophages, shows altered disease kinetics in a mouse model, and exhibits resistance to type I interferon

Alphaviruses, such as chikungunya virus, o'nyong-nyong virus, and Ross River virus (RRV), cause outbreaks of human rheumatic disease worldwide. RRV is a positive-sense single-stranded RNA virus endemic to Australia and Papua New Guinea. In this study, we sought to establish an in vitro model of RRV evolution in response to cellular antiviral defense mechanisms. RRV was able to establish persistent infection in activated macrophages, and a small-plaque variant (RRV(PERS)) was isolated after several weeks of culture. Nucleotide sequence analysis of RRV(PERS) found several nucleotide differences in the nonstructural protein (nsP) region of the RRV(PERS) genome. A point mutation was also detected in the E2 gene. Compared to the parent virus (RRV-T48), RRV(PERS) showed significantly enhanced resistance to beta interferon (IFN-β)-stimulated antiviral activity. RRV(PERS) infection of RAW 264.7 macrophages induced lower levels of IFN-β expression and production than infection with RRV-T48. RRV(PERS) was also able to inhibit type I IFN signaling. Mice infected with RRV(PERS) exhibited significantly enhanced disease severity and mortality compared to mice infected with RRV-T48. These results provide strong evidence that the cellular antiviral response can direct selective pressure for viral sequence evolution that impacts on virus fitness and sensitivity to alpha/beta IFN (IFN-α/β).

The serine proteinase inhibitor (serpin) plasminogen activation inhibitor type 2 protects against viral cytopathic effects by constitutive interferon alpha/beta priming

The serine proteinase inhibitor (serpin) plasminogen activator inhibitor type 2 (PAI-2) is well characterized as an inhibitor of extracellular urokinase-type plasminogen activator. Here we show that intracellular, but not extracellular, PAI-2 protected cells from the rapid cytopathic effects of alphavirus infection. This protection did not appear to be related to an effect on apoptosis but was associated with a PAI-2-mediated induction of constitutive low-level interferon (IFN)-alpha/beta production and IFN-stimulated gene factor 3 (ISGF3) activation, which primed the cells for rapid induction of antiviral genes. This primed phenotype was associated with a rapid development of resistance to infection by the PAI-2 transfected cells and the establishment of a persistent productive infection. PAI-2 was also induced in macrophages in response to viral RNA suggesting that PAI-2 is a virus response gene. These observations, together with the recently demonstrated PAI-2-mediated inhibition of tumor necrosis factor-alpha induced apoptosis, (a) illustrate that PAI-2 has an additional and distinct function as an intracellular regulator of signal transduction pathway(s) and (b) demonstrate a novel activity for a eukaryotic serpin.

Alphavirus-specific cytotoxic T lymphocytes recognize a cross-reactive epitope from the capsid protein and can eliminate virus from persistently infected macrophages

Persistent alphavirus infections in synovial and neural tissues are believed to be associated with chronic arthritis and encephalitis, respectively, and represent likely targets for CD8+ alphabeta cytotoxic T lymphocytes (CTL). Here we show that the capsid protein is a dominant target for alphavirus-specific CTL in BALB/c mice and that capsid-specific CTL from these mice recognize an H-2Kd restricted epitope, QYSGGRFTI. This epitope lies in the highly conserved region of the capsid protein, and QYSGGRFTI-specific CTL were cross reactive across a range of Old World alphaviruses. In vivo the acute primary viraemia of these highly cytopathic viruses was unaffected by QYSGGRFTI-specific CTL. However, in vitro these CTL were able to completely clear virus from macrophages persistently and productively infected with the arthrogenic alphavirus Ross River virus.

A review of the possible mechanisms for the persistence of foot-and-mouth disease virus

Foot-and-mouth disease (FMD) was the first animal disease to be attributed to a virus, and the second virus to be discovered [1]. It is a positive-sense, singlestranded RNA picornavirus and the sole member of the genus Aphthovirus. Each infectious virus particle contains a single strand of RNA approximately 8-5 kb long. This is translated into a single polypeptide which is then cleaved into the structural and non-structural virus proteins.

Evolution of in vitro persistence of two strains of canine parainfluenza virus. Brief report

Lytic stock virus (CPI+) exhibited prominent CPE in Vero cell monolayers. The non-syncytial giant cell forming strain (CPI-) was isolated from brain tissues of a dog after experimental infection with syncytial giant cell-forming (CPI+) virus. In mixed infection experiments, CPI(-) virus interfered with the replication of CPI(+) virus in that simultaneously infected cells showed strand-forming CPE typical of CPI(-) and reduction of CPI(+) yield. The CPI(-) virus established immediate in vitro persistence, followed by a severe crisis at passage (p) 8 and several similar crises until p 31; no further crises occurred throughout the remaining observation period (p 80). The CPI(+) did not establish immediate in vitro viral persistence and experienced several lytic crises until p 29. No further crises were observed throughout the observation period (p 100).

Vero cells persistently infected with Tacaribe virus: role of interfering particles in the establishment of the infection

Eight Vero cell sublines (Vero T) persistently infected with wild type Tacaribe virus replicated in different hosts were established. In order to unravel the mechanism involved in the initiation and maintenance of persistence, the properties of virus shed by the sublines and the presence of interfering particles (IP) were analyzed. During the course of infection, persistent virus (Tac-pi) underwent mutations although no consistent pattern of virus evolution was observed. ts mutants were isolated from two Vero T sublines, whereas a slow growth variant was shed by another. The remaining sublines released virus resembling wt parental virus. Except for Vero T1 sublines, Vero T cultures shed no detectable IP. These results emphasize the point that neither the emergence of virus mutants nor the synthesis of IP is essential for the maintenance of the persistent state. To define the role of IP in the initiation of persistence, coinfection experiments with a characterized inoculum were performed. For that purpose, attempts were made to obtain IP stocks free from pfu by serial transfers of undiluted virus. Neither enrichment nor amplification of IP occurred, and virus stocks were freed of infectious virus by UV irradiation. If normal Vero cells were infected with Tac-pi virus released by Vero T2, Vero T3, Vero T4, Vero T5, Vero T6, Vero T7 and Vero T10 sublines, a complete destruction of the monolayer without cell recovery was observed. In contrast, parental and Vero T1 viruses always originated persistently infected sublines. Similarly, the addition of IP to virus inocula constituted by Tac-pi viruses released by Vero T2, Vero T3, Vero T4, Vero T5, Vero T6, Vero T7 and Vero T10 sublines gave rise to persistently infected cultures. These results suggest that although IP are not important by themselves in the maintenance of persistence, they play a major role in initiation.

Persistent viral infection. The carrier state

A persistent viral infection is one in which the virus in a replicating or non-replicating form persists in the host beyond the normal recovery and elimination period for that particular viral infection. The clinical significance and mechanisms of persistence, when known, are discussed for the important viral infections of dogs and cats. Particular emphasis is given to feline viral rhinotracheitis, feline calicivirus, canine distemper, and feline leukemia.

Group B coxsackieviruses readily establish persistent infections in human lymphoid cell lines

Exposing human lymphoid cell lines to uncloned or recently cloned group B coxsackieviruses results in the frequent establishment of chronically infected cultures. Persistence is maintained by a carrier culture mechanism involving virus spread through the medium and replication among a minority of cells at any given time. These studies provide a model for persistence by highly cytocidal viruses.

Lifelong persistence of paramyxovirus Sendai-6/94 in C129 mice: detection of a latent viral RNA by hybridization with a cloned genomic cDNA probe

C129 mice infected intracerebrally with Sendai-6/94 virus were examined periodically for the presence of viral proteins and viral RNA over a span of 423 days. On postinfection Day 15 (PID 15) an acute infection was demonstrated by increased anti-6/94 antibody titers and expression of viral proteins. More than a year later, on PIDs 373 and 423, no viral antigens were detected. Rescue of infectious virus from the mouse brains was only observable for 74 days following cocultivation of the cells on PID 15. Later, no signs of viral persistence were found at the protein level. In a further experiment, the murine tissues and cell cultures were examined for the presence of viral RNA. Virus-specific cDNA was cloned in the bacteriophage lambda system and used as a highly specific hybridization probe. Surprisingly, 6/94 viral RNA was detectable lifelong in the brain tissue of infected mice although no proteins were expressed. Murine brain cells cocultivated on PID 15 still contained viral RNA after 245 days in culture, although the expression of viral proteins was measureable for only 80 days. The results indicate a stable latency of the 6/94 virus in cell cultures and in animals at the RNA level without detectable protein expression.

Defective interfering particles of mouse hepatitis virus

After six to eight serial undiluted passages of mouse hepatitis virus (JHM strain) in DBT cell culture, a decrease in the yield of infectious virus occurred, and with further passages fluctuating yields of infectious virus were observed. The serially passaged virus interfered with the multiplication of the standard JHM virus, but not with vesicular stomatitis virus. After sucrose equilibrium centrifugation of high passage virus, a single peak contained both infectious virus and interfering activity. This virus population resembled the original JHM virus in its structural proteins, but it contained an increased proportion of a protein with a molecular weight of 65 X 10(3). Genomic RNA from standard JHM virus contained a single species of RNA with a molecular weight of 5.4 X 10(6). After five undiluted passages, however, the virion population contained two RNA species with molecular weights of 5.4 X 10(6) and 5.2 X 10(6). RNase T1 resistant oligonucleotide finger-printing of these RNAs showed that the lower molecular weight RNA had lost several oligonucleotide spots that were present in the genomic RNA of the standard JHM virus. After several serial diluted passages of passage 10 virus, a single virus population was obtained which again had only standard virus RNA with a molecular weight of 5.4 X 10(6) and lacked interfering activity. These results indicated that defective interfering particles were generated by serial undiluted passages of JHM virus.

Scanning electron microscope examination of epithelial cells infected with enveloped viruses

The apical surface structure of virus infected epithelial cells (MDBK and MDCK) was examined in the SEM. Cells were infected with related enveloped viruses (influenza, Sendai, and vesicular stomatitis) under conditions of productive, nonproductive, and persistent infections. Fewer microvilli were seen in persistent infections with Sendai virus and the standard virus infected cells appeared to be normal. Extensive morphological changes, stunting of microvilli or budding effects, were noted in productive infections with influenza virus (WSN) and a reduction in the relative number of microvilli in a nonproductive infection with the PR8 strain. Although budding occurs on the basal lateral surface of VSV infected cells, morphological alterations were evident on the apical surface unlike that seen in influenza and Sendai virus infections.

Biological and macromolecular properties of murine cells persistently infected with MHV-JHM

A persistently-infected neuroblastoma culture [Neuro-2A( JHMV )] was established with the murine hepatitis virus JHM [MHV-JHM]. After 100 days of passage, the endogenous virus [Neuro-2A( JHMV ) end] released by this culture was unable to induce the syncytia typical of MHV-JHM and the endogenous virus was not temperature-sensitive. The Neuro-2A( JHMV ) culture was cured of virus production by passage under neutralizing antibody [Neuro-2A( JHMV )Ab]. The Neuro-2A( JHMV ) and the Neuro-2A ( JHMV ) Ab cultures were as susceptible to heterologous infection with mengovirus and vesicular stomatitis virus as the uninfected Neuro-2A culture. However, the Neuro-2A ( JHMV ) and Neuro-2A( JHMV ) Ab cultures were partially resistant to homologous superinfection by MHV-JHM and the closely related MHV-A59. Virus related to MHV-JHM was rescued from the antibody-cured cells by cell fusion. The synthesis of MHV-JHM specific antigens by Neuro-2A( JHMV ) cells, Neuro-2A( JHMV ) Ab cells and 17 Cl-1 cells infected by Neuro-2A( JHMV ) end was studied by SDS-PAGE. The genomic RNAs of MHV-JHM and Neuro-2A( JHMV ) end were compared by oligonucleotide mapping. The results of the protein and RNA studies indicated that the genome of Neuro-2A( JHMV ) end was substantially modified from the genome of MHV-JHM, but the modifications did not significantly alter the molecular size of the viral-specific proteins.

Propagation of Aleutian disease parvovirus in cell line CCC clone 81

Aleutian disease parvovirus (ADV), mutant Gorham of the Utah-1 strain, was grown and comparatively assayed in feline cell lines CRFK and CCC clone 81 at 31.8 degrees C. The maximum virus titres as determined by a fluorescent focus assay were found to be about 10(5) FFU/ml in CRFK at day 6 p. i. and 10(6) FFU/ml at day 4 p. i. in CCC clone 81 cells. Shifting of the incubation temperature from 31.8 to 37 degrees C led to a reduced virus production after three passages. The synchronization of the CCC clone 81 cells by 1 X 10(-3) M hydroxyurea followed by infection with low (less than or equal to 0.8) multiplicities of infection (MOI) did not significantly influence the virus titres. Several mammalian cell lines such as MiCl 1 (S+L-), Mv1-Lu, 64F3 clone 7 and FEF or fish cell lines such as BB and CHSE 114 developed abortive infections after inoculation with the temperature-sensitive mutant Gorham of the ADV strain Utah-1 (ADV-G). Three new isolates designated ADV-Sl1--ADV-Sl3 were isolated from spleen and blood lymphocytes and bone marrow cells of ADV-infected mink and were adapted to grow in CCC clone 81 cells at 31.8 degrees C with virus titres between 10(4) and 10(4.7) FFU/ml. ADV particle populations varying in their bouyant density between 1.32, 1.36 and 1.43 g/ml were isolated from infected cells and culture supernatants. By protein blotting and immunodetection two major protein components with apparent M. W. of 85 and 75 KD and three minor polypeptides of 33, 28.9 and 27.5 KD were detected.

Characterization of small plaque mutants of mouse hepatitis virus, JHM strain

Two small plaque mutants designated as 1a and 2c were isolated from DBT cells persistently infected with the JHM strain of mouse hepatitis virus. Unlike the wild type JHM, these two mutant viruses grew more slowly with no prominent cell fusion. The buoyant densities of the mutants were slightly lower and 2c was revealed to have fewer peplomers than JHM by electron microscopy. The purified JHM contained five polypeptides with molecular weights (M.W.) of 260,000, 105,000 (GP105), 65,000, 60,000 (P60), and 23,000 (GP23). In addition to two polypeptides, P60 and GP23, which were common to JHM and the mutants, 1a was found to contain three other specific polypeptides with M.W. of 180,000 (GP180), 110,000, and 95,000 (GP95), while 2c had GP180, GP105, GP95, and one with a M.W. of 175,000. All of these polypeptides were shown to be glycosylated except for P60. After bromelain treatment, all these viruses lost the peplomers and contained P60 and another new 18,000 dalton polypeptide.

Defective interfering particles of Sindbis virus do not interfere with the homologous virus obtained from persistently infected BHK cells but do interfere with Semliki Forest virus

Defective interfering particles derived from wild-type Sindbis virus no longer interfere with the infectious virus cloned from BHK cells persistently infected with Sindbis virus for 16 months. These particles do interfere with the replication of Semliki Forest virus.

Establishment and maintenance of a persistent infection of L132 cells by human coronavirus strain 229E

A persistent infection by human coronavirus 229E (HCV/229E) was established in a human continuous cell line (L132). Following the initial infection with stock HCV/229E, several cultures were established of which two (HV1 and HV4) have been maintained by continuous passage for two years. These cultures have shed high titres of infectious virus continuously into the supernatant fluid since their initiation. The persistently infected cells were resistant to homologous super-infection but supported polio virus replication to normal titres. Preliminary tests indicated that 50-100 percent of the cells contain virus. Neither interferon nor reverse transcriptase could be detected in these cultures and the presence of defective interfering particles could not be demonstrated. VH1 and VH4 coronaviruses, isolated from these persistently infected cultures (HV) and identified by 229E antiserum neutralization, were more cytocidal than the parent virus as judged by plaque characteristics and CPE, however they were indistinguishable on the basis of density, EM morphology, and genome size. Present evidence indicated that temperature plays an important but as yet undetermined role in the establishment and maintenance of stable 229E persistently infected cell cultures.

Persistent viral infections as models for research in virus chemotherapy

The acute systemic virus infection is commonly used as an experimental model in chemotherapy research despite the fact that the chance for an effective chemotherapy of acute virus infections is small. In most acute infections, virus multiplication is well advanced before the disease is expressed and treatment will, in many cases, come too late. However, control by chemotherapy might be promising for persistent virus infections, where, owing to the slow progression of the disease, sufficient time for treatment is available. Although there are various ways in which viruses can persist in their hosts, comparative studies in vitro and in vivo reveal common features that shall be briefly reviewed. Animal models with persistent virus infections are usually difficult to experiment with because of the varying length of the incubation period brought about by the complex relationship among virus replication, immune reactions, and disease.

Defective interfering influenza viruses and host cells: establishment and maintenance of persistent influenza virus infection in MDBK and HeLa cells

WSN (H0N1) influenza virus upon undiluted passages in different species of cells, namely, bovine kidney (MDBK), chicken embryo (CEF), and HeLa cells, produced a varying amount of defective interfering (DI) virus which correlated well with the ability of the species of cell to produce infectious virus. However, the nature of the influenza DI viral RNA produced from a single clonal stock was essentially identical in all three cells types, suggesting that these cells do not exert a great selective pressure in the amplification of specific DI viral RNAs either at early or late passages. DI viruses produced from one subtype (H0N1) could interfere with the replication of infectious viruses belonging to other subtypes (H1N1, H3N2). DI viral RNAs could also replicate with the helper function of other subtype viruses. The persistent infection of MDBK and HeLa cells could be initiated by coinfecting cells with both temperature-sensitive mutants (ts-) and DI influenza viruses. Persistently infected cultures cultures at early passages (up to passage 7) showed a cyclical pattern of cell lysis and virus production (crisis), whereas, at later passages (after passage 20), they produced little or no virus and were resistant to infection by homologous virus but not by heterologous virus. The majority of persistently infected cells, however, contained the complete viral genome since they expressed viral antigens and produced infectious centers. Selection of a slow-growing temperature-sensitive variant rather than the presence of DI virus or interferon appears to be critical in maintaining persistent influenza infection in these cells.