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PubMed1974

The mechanism of viral replication. Structure of replication complexes of encephalomyocarditis virus.

The structure of the purified replicative intermediate of encephalomyocarditis virus was determined by electron microscopy. Approximately 80% of the replicative intermediate complexes were characterized by a filament of double-stranded RNA of widely variable length, which had a "bush" of single-stranded RNA at one end. In many examples one or more additional single-stranded bushes were appended internally to the double-stranded RNA filament. These results support the view that before deproteinization, replicative intermediate contains little if any double-stranded RNA.

Centrifugation, Density Gradient↗

PubMed2026

Structure-resolved virus-host interactomics by cross-linking mass spectrometry.

Viruses depend on host protein networks to replicate, assemble progeny, and spread between cells and organisms. Defining these virus-host protein interactions is challenging because they are highly dependent on infection stage, cell type, species, and because mechanistic interpretation requires information about structural interfaces and conformational states. Cross-linking mass spectrometry (XL-MS) addresses these challenges by adding a spatial and structural dimension to virus-host interactomics in native systems. In this review, we discuss how XL-MS has advanced from targeted analysis of viral protein complexes to structure-resolved mapping of virion architecture and infected-cell virus-host interactomes. We highlight how XL-MS complements AP-MS, cryo-EM/cryo-ET, quantitative proteomics, genetic perturbation, and structure prediction to connect physical proximity with molecular mechanisms. Finally, we discuss current limitations in sensitivity, chemical coverage, temporal resolution, and model interpretation, and outline how future quantitative and integrative XL-MS workflows may enable systems-level structural virology.

Mass Spectrometry↗

PubMed2004

Structured model of influenza virus replication in MDCK cells.

Intracellular events that take place during influenza virus replication in animal cells are well understood qualitatively. However, to better understand the complex interaction of the virus with its host cell and to quantitatively analyze the use of cellular resources for virion formation or the overall dynamic for the entire infection cycle, a mathematical model for influenza virus replication has to be formulated. Here, we present a structured model for the single-cell reproductive cycle of influenza A virus in animal cells that accounts for the individual steps of the process such as attachment, internalization, genome replication and translation, and progeny virion assembly. The model describes an average cell surrounded by a small quantity of medium and infected by a low number of virus particles. The model allows estimation of the cellular resources consumed by virus replication. Simulation results show that the number of cellular surface receptors and endosomes, as well as other resources, such as the number of free nucleotides or amino acids, is not significantly influenced by influenza virus propagation. A factor that limits the growth rate of progeny viruses and their release is the total amount of matrix proteins (M1) in the nucleus while other newly synthesized viral proteins (e.g., nucleoprotein NP) and viral RNAs accumulate. During budding, synthesis of vRNPs (viral ribonucleoprotein complexes) represents another limiting factor. Based on this model it is also possible to analyze effects of parameter changes on the dynamics of virus replication, to identify possible targets for molecular engineering, or to develop strategies for improving yields in vaccine production processes. Furthermore, a better insight into the interactions of viruses and host cells might help to improve our understanding of virus-related diseases and to develop therapies.

Animals↗

PubMed2003

Retroviral genomic RNAs are transported to the plasma membrane by endosomal vesicles.

The viral genomes of alpha- and gamma-retroviruses follow an outbound route through the cytoplasm before assembling with the budding particle at the plasma membrane. We show here that murine leukemia virus (MLV) RNAs are transported on lysosomes and transferrin-positive endosomes. Transport on transferrin-positive vesicles requires both Gag and Env polyproteins. In the presence of Env, Gag is rerouted from lysosomes to transferrin-positive endosomes, and virion production becomes highly sensitive to drugs poisoning vesicular and endosomal traffic. Vesicular transport of the RNA does not require prior endocytosis, indicating that it is recruited directly from the cytosol. Viral prebudding complexes containing Env, Gag, and retroviral RNAs are thus formed on endosomes, and subsequently routed to the plasma membrane. This may allow retroviruses to hijack the endosomal machinery as part of their biosynthetic pathway. More generally, tethering to vesicles may provide an efficient mechanism for directed RNA transport.

3T3 Cells↗

PubMed2003

Dendritic cells and measles virus infection.

Measles is a major cause of childhood mortality in developing countries which is mainly attributed to the ability of measles virus (MV) to suppress general immune responses. Paradoxically, virus-specific immunity is efficiently induced, which leads to viral clearance from the host and confers long-lasting protection against reinfection. As sensitisers of pathogen encounter and instructors of the adaptive immune response, dendritic cells (DCs) may play a decisive role in the induction and quality of the MV-specific immune activation. The ability of MV wild-type strains in particular to infect DCs in vitro is dearly established, and the receptor binding haemagglutinin protein of these viruses essentially determines this particular tropism. DC maturation as induced early after MV infection is likely to be of crucial importance for the induction of MV-specific immunity. DCs may, however, be instrumental in MV-induced immunosuppression. (1) T cell depletion could be brought about by DC-T cell fusion or TRAIL-mediated induction of apoptosis. (2) Inhibition of stimulated IL-12 production from MV-infected DCs might affect T cell responses in qualitative terms in favouring Th2 and suppressing Th1 responses. (3) The viral glycoprotein complex expressed at high levels on infected DCs late in infection is able to directly inhibit T cell proliferation by surface contact-dependent negative signalling. This most likely accounts for the failure of infected DC cultures to stimulate allogeneic and inhibit mitogen-stimulated T cell proliferation in vitro and the pronounced proliferative unresponsiveness of T cell ex vivo to polyclonal and antigen-specific stimulation which is a central finding of MV-induced immunosuppression.

Dendritic Cells↗

PubMed1992

Involvement of membrane traffic in the replication of poliovirus genomes: effects of brefeldin A.

Brefeldin A (BFA) is a macrolide antibiotic that has multiple targets in vesicular transport and blocks membrane traffic between the cis- and trans-Golgi compartments, leading to the disruption of the trans-Golgi apparatus (for a review see Pelham, 1991, Cell 67, 449-451). Consequently, BFA interferes with the maturation of viral glycoproteins and suppresses the formation of infectious viruses that contain a lipid envelope. We report that this antibiotic strongly inhibits poliovirus replication even though this virus lacks a lipid envelope and does not encode any glycoproteins. Addition of BFA from the beginning of poliovirus infection blocks the synthesis of late proteins but has no effect on p220 cleavage, indicating that the input viral RNA is translated to produce active 2Apro. The presence of BFA at later times has no effect on poliovirus protein synthesis, indicating that this step is not a direct target for the antibiotic. Indeed, the target of BFA is viral RNA synthesis, because addition of the antibiotic at any time after poliovirus infection drastically reduces the incorporation of labeled uridine into poliovirus RNA. Both plus- and minus-stranded RNA syntheses are diminished when BFA is present from the beginning of infection, but plus-stranded RNA synthesis is more affected when the inhibitor is added at later times. The replication of poliovirus RNA takes place in close association with membrane vesicles that fill the cytoplasm of the infected cells. Little is known about the origin and function of these vesicles that form part of the viral replication complexes. Our findings suggest that the replication of poliovirus genomes may require the maturation of membranous vesicles from a vesicular compartment that is affected by BFA. The effects of BFA on late protein synthesis by other animal viruses varies according to the virus species examined. Among picornaviruses, rhinoviruses are sensitive to the antibiotic, whereas encephalomyocarditis virus is resistant. A negative-stranded RNA virus such as vesicular stomatitis is blocked by BFA, whereas vaccinia virus, a cytoplasmic DNA virus, is resistant.

Antiviral Agents↗

PubMed1989

Early interactions of pseudorabies virus with host cells: functions of glycoprotein gIII.

Adsorption of mutants of pseudorabies virus (PrV) lacking glycoprotein gIII is slower and less efficient than is that of wild-type virus (C. Schreurs, T. C. Mettenleiter, F. Zuckermann, N. Snugg, and T. Ben-Porat, J. Virol. 62:2251-2257, 1988). To ascertain the functions of gIII in the early interactions of PrV with its host cells, we compared the effect on wild-type virus and gIII- mutants of antibodies specific for various PrV proteins. Although adsorption of wild-type virus was inhibited by polyvalent antisera against PrV as well as by sera against gIII and gp50 (but not sera against gII), adsorption of the gIII- mutants was not inhibited by any of these antisera. These results suggest that, in contrast to adsorption of wild-type PrV, the initial interactions of the gIII- mutants with their host cells are not mediated by specific viral proteins. Furthermore, competition experiments showed that wild-type Prv and the gIII- mutants do not compete for attachment to the same cellular components. These findings show that the initial attachment of PrV to its host cells can occur by a least two different modes--one mediated by glycoprotein gIII and the other unspecific. gIII- mutants not only did not adsorb as readily to cells as did wild-type virus but also did not penetrate cells as rapidly as did wild-type virus after having adsorbed. Antibodies against gIII did not inhibit the penetration of adsorbed virus (wild type or gIII-), whereas antibodies against gII and gp50 did. It is unlikely, therefore, that gIII functions directly in virus penetration. Our results support the premises that efficient adsorption of PrV to host cell components is mediated either directly or indirectly by gIII (or a complex of viral proteins for which the presence of gIII is functionally essential) and that this pathway of adsorption promotes the interactions of other viral membrane proteins with the appropriate cellular proteins, leading to the rapid penetration of the virus into the cells. The slower penetration of the gIII- mutants than of wild-type PrV appears to be related to the slower and less efficient alternative mode of adsorption of PrV that occurs in the absence of glycoprotein gIII.

Animals↗

PubMed1995

A molecular clasp in the human immunodeficiency virus (HIV) type 1 TM protein determines the anti-HIV activity of gp41 derivatives: implication for viral fusion.

We have previously reported that synthetic peptides representing the leucine zipper domain (DP107) and a second putative helical domain (DP178) of human immunodeficiency virus type 1 (HIV-1) gp41 exhibit potent anti-HIV activity. In this study we have used soluble recombinant forms of gp41 to provide evidence that the DP178 peptide and the DP178 region of gp41 associate with a distal site on the gp41 transmembrane protein whose interactive structure is influenced by the leucine zipper (DP107) motif. We also observed that a single coiled-coil-disrupting mutation in the leucine zipper domain transformed the recombinant gp41 protein from an inactive to an active inhibitor of HIV-1 fusion and infectivity, which may be related to that finding. We speculate that this transformation results from liberation of the potent DP178-related sequence from a molecular clasp with a leucine zipper, DP107, determinant. The results are discussed in the context of two distinct conformations for the gp41 molecule and possible involvement of these two domains in structural transitions associated with HIV-1-mediated fusion. The results are also interpreted to suggest that the anti-HIV activity of the various gp41 derivatives (peptides and recombinant proteins) may be due to their ability to form complexes with viral gp41 and interfere with its fusogenic processes.

Antiviral Agents↗

PubMed2005

Biochemical and immunogenic characterization of soluble human immunodeficiency virus type 1 envelope glycoprotein trimers expressed by semliki forest virus.

The current lack of envelope glycoprotein immunogens that elicit broadly neutralizing antibody responses remains a major challenge for human immunodeficiency virus type 1 (HIV-1) vaccine development. However, the recent design and construction of stable soluble gp140 trimers have shown that some neutralization breadth can be achieved by using immunogens that better mimic the functional viral spike complex. The use of genetic delivery systems to drive the in vivo expression of such immunogens for the stimulation of neutralizing antibodies against HIV-1 may offer advantages by maintaining the quaternary structure of the trimeric envelope glycoproteins. Here, we describe the biochemical and immunogenic properties of soluble HIV-1 envelope glycoprotein trimers expressed by recombinant Semliki Forest virus (rSFV). The results presented here demonstrate that rSFV supports the expression of stable soluble gp140 trimers that retain recognition by conformationally sensitive antibodies. Further, we show that rSFV particle immunizations efficiently primed immune responses as measured after a single boost with purified trimeric gp140 protein, resulting in a Th1-biased antibody response. This differed from the Th2-biased antibody response obtained after repeated immunizations with purified gp140 protein trimers. Despite this difference, both regimens stimulated neutralizing antibody responses of similar potency. This suggests that rSFV may be a useful component of a viral vector prime-protein boost regimen aimed at stimulating both cell-mediated immune responses and neutralizing antibodies against HIV-1.

AIDS Vaccines↗

PubMed2001

An amino-terminal amphipathic alpha-helix mediates membrane association of the hepatitis C virus nonstructural protein 5A.

Hepatitis C virus (HCV) nonstructural protein 5A (NS5A), a phosphoprotein of unknown function, is believed to be a component of a membrane-associated viral replication complex. The determinants for membrane association of NS5A, however, have not been defined. By double label immunofluorescence analyses, NS5A was found to be associated with the endoplasmic reticulum (ER) or an ER-derived modified compartment both when expressed alone or in the context of the entire HCV polyprotein. Systematic deletion and green fluorescent protein fusion analyses allowed us to map the membrane anchor to the amino-terminal 30 amino acid residues of NS5A. Membrane association occurred by a posttranslational mechanism and resulted in properties of an integral membrane protein. Circular dichroism structural studies of a synthetic peptide corresponding to the NS5A membrane anchor, designated NS5A(1-31), demonstrated the presence of an amphipathic alpha-helix that was found to be highly conserved among 280 HCV isolates of various genotypes. The detergent-binding properties of this helical peptide together with the nature and location of its amino acids suggest a mechanism of membrane insertion via the helix hydrophobic side, yielding a topology parallel to the lipid bilayer in the cytoplasmic leaflet of the ER membrane. These findings have important implications for the structural and functional organization of the HCV replication complex and may define novel targets for antiviral intervention.

Amino Acid Sequence↗

PubMed1983

Methylations of adenosine residues (m6A) in pre-mRNA are important for formation of late simian virus 40 mRNAs.

Cycloleucine, a competitive inhibitor of methionine transferase was used to generate in vivo partially methylated mRNA in SV40-infected BSC-1 cells. Cycloleucine at 0.5 mg/ml causes more than a 30% decrease in internal m6As of late SV40 mRNA with only minor effect on the dimethyladenosine of the 5' caps m7GpppmAm. After treatment with 2 and 5 mg/ml of cycloleucine, internal m6As were reduced by 10- and 100-fold, respectively. The inhibition of BSC-1 mRNA methylations paralleled that observed for late SV40 mRNAs. In cells exposed to 2 mg/ml cycloleucine production of late SV40 mRNA was inhibited by 80% whereas the amount of SV40 nuclear RNA was only slightly reduced. Size fractionation of SV40 nuclear RNA from cycloleucine-treated cells revealed a loss of SV40 19 S RNA with a corresponding increase of fragmented RNA sedimenting between 11 to 5 S, so that the total amount of SV40 RNA in the nucleus was almost unchanged. Analysis of viral transcription complexes from cells treated with cycloleucine indicated that SV40 transcription was not affected by cycloleucine. SV40-transformed cells, in contrast to BSC-1 cells, were able to process and transport undermethylated RNA. When transformed cells were treated with 2 mg/ml cycloleucine no changes in quantities or size of cytoplasmic and nuclear RNA were detected. The data argues for a role of internal m6A moieties in modulating the processing-linked transport of mRNA from the nucleus to the cytoplasm of nontransformed cells. Transformed cells may escape these controls due to structural alterations in their perinuclear regions.

Adenosine↗

PubMed1989

The carboxy terminus of the viral Jun oncoprotein is required for complex formation with the cellular Fos protein.

The products of the proto-oncogenes c-jun and c-fos are known to form a complex in vivo. Complex formation appears to stabilize protein-DNA interactions and is thought to play an important functional role in transcriptional regulation. Here we show that the viral Jun oncoprotein, which differs structurally from cellular Jun, is also capable of complex formation with Fos. Thus the oncogenic potency of viral Jun is unlikely to be due to an altered affinity for Fos. We have also defined, by deletion analysis, the domain of v-Jun responsible for complex formation to reside in the carboxy terminus encompassing the leucine zipper motif. We find that complex formation with c-Fos does not occur with v-Jun deletions affecting one or more leucine residues in the zipper domain. Our results are consistent with the hypothesis that the leucine zipper mediates Jun-Fos interaction.

DNA↗

PubMed2006

Regulated cleavages at the West Nile virus NS4A-2K-NS4B junctions play a major role in rearranging cytoplasmic membranes and Golgi trafficking of the NS4A protein.

A common feature associated with the replication of most RNA viruses is the formation of a unique membrane environment encapsulating the viral replication complex. For their part, flaviviruses are no exception, whereupon infection causes a dramatic rearrangement and induction of unique membrane structures within the cytoplasm of infected cells. These virus-induced membranes, termed paracrystalline arrays, convoluted membranes, and vesicle packets, all appear to have specific functions during replication and are derived from different organelles within the host cell. The aim of this study was to identify which protein(s) specified by the Australian strain of West Nile virus, Kunjin virus (KUNV), are responsible for the dramatic membrane alterations observed during infection. Thus, we have shown using immunolabeling of ultrathin cryosections of transfected cells that expression of the KUNV polyprotein intermediates NS4A-4B and NS2B-3-4A, as well as that of individual NS4A proteins with and without the C-terminal transmembrane domain 2K, resulted in different degrees of rearrangement of cytoplasmic membranes. The formation of the membrane structures characteristic for virus infection required coexpression of an NS4A-NS4B cassette with the viral protease NS2B-3pro which was shown to be essential for the release of the individual NS4A and NS4B proteins. Individual expression of NS4A protein retaining the C-terminal transmembrane domain 2K resulted in the induction of membrane rearrangements most resembling virus-induced structures, while removal of the 2K domain led to a less profound membrane rearrangement but resulted in the redistribution of the NS4A protein to the Golgi apparatus. The results show that cleavage of the KUNV polyprotein NS4A-4B by the viral protease is the key initiation event in the induction of membrane rearrangement and that the NS4A protein intermediate containing the uncleaved C-terminal transmembrane domain plays an essential role in these membrane rearrangements.

Animals↗

PubMed2000

The arterivirus replicase is the only viral protein required for genome replication and subgenomic mRNA transcription.

Equine arteritis virus (EAV) (ARTERIVIRIDAE:) encodes several structural proteins. Whether any of these also function in viral RNA synthesis is unknown. For the related mouse hepatitis coronavirus (MHV), it has been suggested that the nucleocapsid protein (N) is involved in viral RNA synthesis. As described for MHV, we established that the EAV N protein colocalizes with the viral replication complex, suggesting a role in RNA synthesis. Using an infectious cDNA clone, point mutations and deletions were engineered in the EAV genome to disrupt the expression of each of the structural genes. All structural proteins, including N, were found to be dispensable for genome replication and subgenomic mRNA transcription. We also constructed a mutant in which translation of the intraleader ORF was disrupted. This mutant had a wild-type phenotype, indicating that, at least in cell culture, the product of this ORF does not play a role in the EAV replication cycle.

Animals↗

PubMed1981

Differences in the subpopulations of the structural proteins of polyoma virions and capsids: biological functions of the multiple VP1 species.

The structural proteins of polyoma virions and capsids were analyzed by isoelectric focusing and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Polyoma virion VP1 was found to be composed of six distinct species which had pI's between pH 6.75 and 5.75. Polyoma capsid VP1 was found to contain four species with pI's between pH 6.60 and 5.75. The different forms of virion and capsid VP1 appeared to be generated by modifications (phosphorylation and acetylation) of the initial translation product. The most basic of the virion VP1 species (pI, pH 6.75) was absent in capsids and was found to be exclusively associated with the viral nucleoprotein complex. Three of the virion VP1 species and three of the capsid VP1 species were found in capsomere preparations enriched for hexon subunits. Two VP1 species were specifically immune precipitated from virions with hemagglutination-inhibiting antibodies. These two VP1 species were common to both virions and capsids. Polyoma virions, but not capsids, possessed a single VP1 species which was immune precipitated with neutralizing antibodies. Both virion and capsid VP2 were found to have pI's of approximately pH 5.50. Virion VP3 had a pI of approximately pH 7.00, whereas capsid VP3 had a pI of approximately pH 6.50.

Acetylation↗

PubMed1982

Identification of immunologically distinct antigens in pseudorabies virus.

Antigenic proteins of pseudorabies viruses (PrV) are poorly understood. Proteins from purified PrV and membrane proteins from these viral infected cells, therefore, have been studied by antigenic analysis, using virus neutralization and agargel immunoelectrophoresis tests and by polyacrylamide gel electrophoresis, respectively. The study of crossed immunoelectrophoresis against specific antiviral serum antibodies revealed four immunologically distinct antigens involved in PrV. According to their electromobilities, these four immunologically distinct antigens were designated as Ag 1, Ag 2, Ag 3 and Ag 4. The study of dodecyl sulfate-polyacrylamine gel electrophoresis of a membrane-bound but detergent solubilized viral antigenic complex from PrV infected cells also demonstrated the involvement of four glycoprotein antigens. By interpolations of relative mobilities between known protein markers, the molecular weights of these four glycoproteins were estimated to be 61,500, 68,000, 75,000, and 88,000. Results from two dimentional immunoelectrophoresis seemed to be concordant with those obtained by dodecyl sulfate-polyacrylamide gel electrophoresis. This report, therefore presents results, which strongly suggest antigenic similarities in the virion of PrV and cellular membrane glycoproteins of cells infected by this agent. The molecular weight of these four immunologically distinct antigens, Ag 1, Ag 2, Ag 3 and Ag 4, are presumed to have the following molecular weights of 88,000, 75,000, 68,000 and 61,500, respectively.

Antigens, Viral↗

PubMed2004

High level expression of human immunodeficiency virus type-1 Vif inhibits viral infectivity by modulating proteolytic processing of the Gag precursor at the p2/nucleocapsid processing site.

The human immunodeficiency virus type-1 Vif protein has a crucial role in regulating viral infectivity. However, we found that newly synthesized Vif is rapidly degraded by cellular proteases. We tested the dose dependence of Vif in non-permissive H9 cells and found that Vif, when expressed at low levels, increased virus infectivity in a dose-dependent manner. Surprisingly, however, the range of Vif required for optimal virus infectivity was narrow, and further increases in Vif severely reduced viral infectivity. Inhibition of viral infectivity at higher levels of Vif was cell type-independent and was associated with an accumulation of Gag-processing intermediates. Vif did not act as a general protease inhibitor but selectively inhibited Gag processing at the capsid and nucleocapsid (NC) boundary. Identification of Vif variants that were efficiently packaged but were unable to modulate Gag processing suggests that Vif packaging was necessary but insufficient for the production of 33- and 34-kDa processing intermediates. Interestingly, these processing intermediates, like Vif, associated with viral nucleoprotein complexes more rigidly than mature capsid and NC. We conclude that virus-associated Vif inhibits processing of a subset of Gag precursor molecules at the p2/NC primary cleavage site. Modulation of processing of a small subset of Gag molecules by physiological levels of Vif may be important for virus maturation. However, the accumulation of such processing intermediates at high levels of Vif is inhibitory. Thus, rapid intracellular degradation of Vif may have evolved as a mechanism to prevent such inhibitory effects of Vif.

CD4-Positive T-Lymphocytes↗

PubMed1983

Expression and cellular compartmentalization of a herpes simplex virus type 2 protein (ICP 10) in productively infected and cervical tumor cells.

Antiserum to ICP 10, a herpes simplex virus type 2 (HSV-2) protein that is expressed in cells neoplastically transformed by viral DNA sequences within the Bgl II/Hpa I CD fragment, specifically precipitates the ICP 10 protein from HSV-2 infected cells and stains cells infected with HSV-2 for 4 to 16 hrs by indirect immunofluorescence. At 4 hr post infection (p.i.), the staining is primarily perinuclear, while at 16 hr p.i., it is cytoplasmic and intranuclear. Compartmentalization studies indicate that the 35S-[L]-methionine labeled ICP 10 is detectable in both the cytoplasmic and nuclear fractions early and late in infection. However, in its phosphorylated form, ICP 10 is undetectable in the nuclear fraction late in the viral reproductive cycle. Anti-ICP 10 serum stains a high (75%-83%) proportion of cervical tissue with pathological findings of dysplasia or carcinoma, as well as atypical exfoliated cells from these patients. Cervical tumor tissue from 4 of 12 patients also stains with antiserum to another purified viral protein complex designated ICP 12/14. In the majority of atypical cells with mild or moderate changes, ICP 10 localizes in the cytoplasm, while the majority of atypical cells with severe changes also display nuclear staining with anti-ICP 10 serum. While exfoliated atypical cells from 60% of patients with dysplasia are positive for ICP 10, those from only one half of these patients stain also with anti-ICP 12/14 serum and this staining is strictly cytoplasmic. Atypical cells from three patients in these series stain with the anti-HSV-2 serum but are negative for both ICP 10 and ICP 12/14. Exfoliated atypical cells from patients with CIS or invasive cancer stain equally well with all three antisera.

Antigens, Viral, Tumor↗