Protein V is a 384-residue accessory protein of Sendai virus, produced by co-transcriptional RNA editing of the P/V/C gene: insertion of one pseudotemplated guanine at position 318 shifts the reading frame, so V shares residues 1-317 with the polymerase cofactor P and carries a unique 67-residue cysteine-rich C terminus (the Vu region) that the unedited P mRNA does not encode; the +2G product is W, and the overlapping second reading frame of the same gene encodes the unrelated C/Y proteins. V is not part of the replication machinery and is dispensable for growth in cultured cells, but it is required for virulence in mice. It is a largely intrinsically disordered, cytosolic protein-interaction hub that disables several arms of cytosolic innate immune sensing in the host cell. Its best-characterized target is the transcription factor IRF3: V binds IRF3, including a constitutively active form, retains it in the cytosol and prevents its nuclear translocation and transactivation, so that interferon-beta induction fails. V also binds the tandem CARDs of the RNA sensor RIG-I and the SPRY domain of the RIG-I regulator TRIM25, a combination that in paramyxovirus V proteins generally blocks TRIM25-mediated ubiquitination of RIG-I and the downstream RIG-I-MAVS interaction; it binds the related sensor MDA5 through the Vu region; and it binds the inflammasome sensor NLRP3, preventing NLRP3 self-oligomerization and NLRP3-dependent ASC speck formation and thereby caspase-1-dependent interleukin-1-beta maturation and secretion. The Vu region binds zinc through seven conserved cysteines; cysteine substitutions that lose zinc binding leave replication in culture intact but attenuate the virus in mice, indicating that the metal site is a structural requirement for the immune-antagonist activities rather than a catalytic centre.
Definition: A process in which a symbiont interferes with host inflammasome-mediated signal transduction specifically by binding the host sensor NLRP3 and preventing its self-oligomerization or its recruitment of the adaptor ASC, so that the inflammasome does not assemble. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Justification: GO:0141081 symbiont-mediated suppression of host inflammasome-mediated signal transduction has no children, whereas the sibling branch for cytoplasmic pattern-recognition receptor signalling names the targeted molecule (GO:0039540 via inhibition of RIG-I, GO:0039548 via inhibition of IRF3, GO:0039554 via inhibition of MDA-5). Several unrelated viral proteins converge on NLRP3 itself, and distinguishing a sensor-directed block from interference further down the inflammasome pathway is exactly the distinction those sibling terms already make. Sendai virus V is a clean case: it binds NLRP3 and blocks its self-oligomerization, while the within-organism term GO:1900226 negative regulation of NLRP3 inflammasome complex assembly, currently used for it, sits under regulation of the organism's own complex assembly rather than in the interspecies branch.
Parent term: symbiont-mediated suppression of host inflammasome-mediated signal transduction
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0030430 host cell cytoplasm | EXP PMID:22532687 Inhibition of interferon regulatory factor 3 activation by p... | ACCEPT | Summary: Immunofluorescence of V expressed in cells shows diffuse cytoplasmic signal, and UniProt curates host cytoplasm for this entry from the same paper. Reason: The cited paper images the V protein itself, not only its host partners, and finds it dispersed through the cytoplasm (PMID:22532687, Fig. 4). The location is functionally meaningful rather than incidental: V acts by retaining IRF3 in the cytosol, and the RLR sensors and NLRP3 it engages are cytosolic proteins. Host cell cytoplasm is not a root organelle term, but it is the compartment the assay resolves, and the more precise host cell cytosol is asserted on a separate row of this review from the same figure. Supporting Evidence: PMID:22532687 When only the V protein was expressed, it appeared to be dispersed in the cytosol. file:SENDZ/V__P69282/V__P69282-uniprot.txt SUBCELLULAR LOCATION: Host cytoplasm |
| GO:0030430 host cell cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic mapping of the UniProt subcellular-location term Host cytoplasm (SL-0381), which itself rests on the experimental localization in PMID:22532687. Reason: The keyword-to-GO mapping is sound and the underlying SubCell assignment is the experimentally supported one, carrying ECO:0000269|PubMed:22532687 in the record. This row reinforces the EXP row for the same term rather than competing with it. Supporting Evidence: PMID:22532687 When only the V protein was expressed, it appeared to be dispersed in the cytosol. |
| GO:0039540 symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity | IDA PMID:29321315 Paramyxovirus V Proteins Interact with the RIG-I/TRIM25 Regu... | ACCEPT | Summary: SeV V binds both the tandem CARDs of RIG-I and the SPRY domain of TRIM25; in paramyxovirus V proteins this combination blocks TRIM25-mediated RIG-I ubiquitination and the downstream RIG-I-MAVS interaction, arresting RIG-I signalling. Reason: The claim is sound, but it is worth recording precisely what this paper did with the SeV protein as opposed to its relatives. SeV V appears in the interaction experiments only: it co-precipitates with TRIM25 (Fig. 3A) and with RIG-I (Fig. 3C). The functional experiments that establish the mechanism - the IFN-beta reporter assays, the loss of RIG-IN ubiquitination (Fig. 9) and the loss of RIG-I-MAVS association (Fig. 10) - were performed with Nipah, measles and PIV5 V proteins, and the authors generalise on the strong conservation of the V C-terminal domain that mediates both interactions. SeV-specific functional support comes from the companion literature: in PMID:22532687 the SeV V protein inhibited IRF3 activation driven by a constitutively active RIG-I (Fig. 6C), and it interacts with RIG-I there too. Given curated interaction data on the SeV protein plus a conserved mechanism and a SeV-specific downstream readout, the row is accepted; the interference is with interferon induction, not with signalling downstream of the interferon receptor, and GO:0039540 correctly sits in the pattern-recognition branch. Supporting Evidence: PMID:29321315 Immunoprecipitation against the V5 tag revealed that the V proteins of MeV, NiV, and SeV all coprecipitated with TRIM25, whereas NiV W did not PMID:29321315 Immunoprecipitation revealed that both V proteins coprecipitated with RIG-I but not with the empty vector or GFP-Flag PMID:29321315 This result indicates that multiple paramyxovirus V proteins can inhibit RIG-I ubiquitination, and thus, this is a conserved mechanism. file:SENDZ/V__P69282/V__P69282-uniprot.txt Interacts with host RIGI regulatory protein (via CARDs domain) and host TRIM25 (via SPRY domain) |
| GO:0039548 symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity | IDA PMID:22532687 Inhibition of interferon regulatory factor 3 activation by p... | ACCEPT | Summary: V binds host IRF3 and its constitutively active form IRF3-5D, retains IRF3 in the cytosol so that it cannot enter the nucleus, and blocks IRF3-driven reporter activation even when the stimulus is active IRF3 itself. This is the best-supported function of the protein. Reason: CACAO row, and an exemplary one. The cited paper assays this exact claim on this exact protein by direct assay, at the right granularity. Co-immunoprecipitation shows V binds IRF3 and IRF3-5D (Fig. 3); immunofluorescence of SeV-infected, poly(I:C)-stimulated HeLa cells shows endogenous IRF3 reaching the nucleus only when V is absent (Fig. 5); and the p-55C1B reporter assay shows V suppressing IRF3 activation driven by MDA5, by constitutively active RIG-I, by constitutively active TRIF and by IRF3-5D (Fig. 6). The last of these is the decisive control: blocking a constitutively active IRF3 places the lesion at IRF3 itself rather than somewhere upstream, which is precisely what the term asserts. The cross-virus comparison in the same paper, where inhibition tracks with IRF3 binding (measles and Newcastle disease V bind and inhibit; mumps and Nipah V do neither), reinforces the mechanism. Independent earlier support in PMID:15231393. The term is neither a downstream phenotype nor a parent-level restatement, and it is in the pattern-recognition (interferon induction) branch, which is the arm the paper assays. Supporting Evidence: PMID:22532687 Here we reproduced those results showing that the SeV V protein physically interacted with RIG-I and IRF3 as well as MDA5 by IP-Western blotting PMID:22532687 In SeV WT-infected cells, nuclear staining of IRF3 was not observed PMID:22532687 When the signal was induced by IRF3-5D, the IRF3 activation was restricted in the presence of the V protein but not in the presence of the P/V and Vu proteins. PMID:15231393 C or V inhibited the double-stranded (ds) RNA- or Newcastle disease virus |
| GO:0039548 symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity | IEA GO_REF:0000043 | ACCEPT | Summary: Electronic mapping of UniProt keyword KW-1092 (Inhibition of host IRF3 by virus), which on this entry is itself assigned from the experimental work in PMID:15231393 and PMID:22532687. Reason: The keyword mapping lands on the same term as the direct-assay row above and is supported by the same experiments, so it reinforces a claim this review accepts. The keyword is not a bare prediction here: the UniProt FUNCTION statement it accompanies cites PubMed:15231393 and PubMed:22532687 with ECO:0000269. Supporting Evidence: PMID:22532687 When the signal was induced by IRF3-5D, the IRF3 activation was restricted in the presence of the V protein but not in the presence of the P/V and Vu proteins. |
| GO:0039554 symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: V binds MDA5 through its Vu region and reduces MDA5-driven IRF3 activation in reporter assays, but mouse genetics in the same study show MDA5 is not the sensor that matters for what V suppresses in vivo. Reason: The claim itself is supported for Sendai virus, not merely inferred from the keyword: PMID:22532687 shows V co-precipitating with MDA5, maps the interaction to the Vu region, and shows that MDA5 overexpression-driven IRF3 activation is reduced by V. It is kept, but as non-core rather than core, because the same paper's in vivo experiments argue that this arm is peripheral for this virus: V-deficient SeV was as attenuated in MDA5-knockout mice as in wild-type mice, whereas RIG-I knockout rescued it, and the authors conclude RIG-I is the important sensor. The term is at the correct granularity - the issue is importance, not accuracy - so KEEP_AS_NON_CORE rather than MODIFY. Part of the UniProt MDA5/LGP2 statement is propagated by similarity from P69280, which is a further reason not to treat this as a core activity of the Z-strain protein. Supporting Evidence: PMID:22532687 Overexpression of MDA5 induced IRF3 activation PMID:22532687 The activation was reduced in the presence of the V protein PMID:22532687 we infected MDA5-knockout mice with V-deficient SeV and found that MDA5 was largely unrelated to the innate immunity that the V protein suppresses in vivo PMID:22532687 However, the present work showed that RIG-I is more important for virus pathogenesis in relation to the SeV V protein. |
| GO:0044164 host cell cytosol | IDA PMID:22532687 Inhibition of interferon regulatory factor 3 activation by p... | ACCEPT | Summary: Immunofluorescence of V expressed in cells shows it dispersed in the cytosol; the truncated forms localize differently, so the signal is specific to the construct rather than a staining artefact. Reason: CACAO row, and well chosen. The paper images the viral protein itself (Fig. 4), which is the thing the cellular-component term is about, and the internal comparison - full-length V and the P/V fragment cytosolic, the Vu fragment both cytosolic and nuclear - shows the assay resolves differences in distribution rather than reporting a default. It is not a single-assay localization of the kind that has gone wrong elsewhere in this project, because the location is corroborated by UniProt's curated SUBCELLULAR LOCATION from the same work and because it is mechanistically required: V's effect on IRF3 is to hold IRF3 in the cytosol, and NLRP3, RIG-I and MDA5 are cytosolic. Supporting Evidence: PMID:22532687 When only the V protein was expressed, it appeared to be dispersed in the cytosol. PMID:22532687 These results suggest that the V protein also retained IRF3 in the cytosol in SeV-infected cells. |
| GO:0046872 metal ion binding | IEA GO_REF:0000120 | MODIFY | Summary: The Vu domain binds zinc specifically, through seven conserved cysteines, as shown experimentally for the Sendai virus protein; the generic metal ion term understates what is known. Reason: The signature behind this row (InterPro IPR024279 / Pfam PF13008 zf-Paramyx-P) is the paramyxovirus V zinc-finger-like domain, and the metal is identified: a GST-Vu fusion bound 65-Zn 7.2-fold above the GST control while the P/V common region did not, and individually substituting each of the seven conserved cysteines reduced zinc binding to 22-68 per cent of wild type (PMID:10933690). UniProt models two Zn(2+) sites over eight ligand residues on this entry. Because a specific supported descendant exists, the correct action is MODIFY to zinc ion binding rather than keeping the parent. Note the activity is structural rather than catalytic: cysteine mutant viruses replicate normally in culture but are attenuated in mice. Proposed replacements: zinc ion binding Supporting Evidence: PMID:10933690 GST-Vu bound 7.2-fold more zinc than did GST, exhibiting its potential zinc-binding capacity PMID:10933690 the zinc-binding capacities of the mutant proteins were greatly impaired file:SENDZ/V__P69282/V__P69282-uniprot.txt /ligand="Zn(2+)" file:SENDZ/V__P69282/V__P69282-uniprot.txt C->S: 50% decrease of in vitro zinc-binding. |
| GO:0052029 symbiont-mediated suppression of host signal transduction pathway | IEA GO_REF:0000117 | TOO GENERAL | Summary: True of V, but an ancestor of the specific pattern-recognition-receptor terms this review accepts, and it names no pathway. Reason: GO:0052029 is an ancestor of GO:0039548 and GO:0039540, both accepted here, so it is entailed by claims the review already makes and adds nothing: it says a host signal transduction pathway is suppressed without saying which. The claim is not in doubt - V demonstrably suppresses host RLR-to-IRF3 signalling - so this is a judgment on the term, not on the annotation. The row's source is an ARBA association rule, which is an unvetted prediction, but that is not the reason for the action. |
| GO:0052031 symbiont-mediated perturbation of host defense response | IEA GO_REF:0000043 | TOO GENERAL | Summary: The broadest of the host-interaction terms on this entry; an ancestor of both the innate-immune-suppression term and the specific receptor-pathway terms accepted here. Reason: Mapped from the Viral immunoevasion and Interferon antiviral system evasion keywords. It is true - perturbation of the host defence response is exactly what V does - but it is an ancestor of GO:0052170, GO:0039548 and GO:0039540, all retained in this review, and it does not say whether the perturbation is of innate or adaptive immunity, of sensing or of effector function. The more specific terms carry the information. |
| GO:0052170 symbiont-mediated suppression of host innate immune response | IEA GO_REF:0000043 | ACCEPT | Summary: Electronic mapping of KW-1090 (Inhibition of host innate immune response by virus). This is the apt umbrella term for a protein with several distinct innate-immune targets. Reason: Unlike the two rows above, this term is not merely a vague ancestor: it is the level at which V's function is actually stated, because the protein disables several separate arms of innate immunity (IRF3, RIG-I/TRIM25, MDA5, the NLRP3 inflammasome) and no single child covers their union. The keyword rests on experimental UniProt FUNCTION statements citing PubMed:15231393, PubMed:22532687 and PubMed:29321315, and the in vivo phenotype of V-deficient virus supports it directly. Supporting Evidence: PMID:22532687 The V protein of Sendai virus (SeV) suppresses innate immunity, resulting in enhancement of viral growth in mouse lungs and viral pathogenicity. |
| GO:0052170 symbiont-mediated suppression of host innate immune response | IMP PMID:22532687 Inhibition of interferon regulatory factor 3 activation by p... | ACCEPT | Summary: Recombinant V-deficient Sendai virus is cleared from mouse lungs, is roughly thirtyfold less virulent, and provokes markedly more interferon-beta from infected fibroblasts than wild-type virus does; the innate response V suppresses is the IRF3-dependent one. Reason: CACAO row, from a mutant-virus (IMP) perturbation. What the paper shows for this gene is the in vivo and cellular consequence of deleting V: attenuated growth in mouse lung (Fig. 1), a thirtyfold higher MLD50 (Table 1), and greater interferon-beta secretion from V-deficient-infected mouse embryonic fibroblasts and L929 cells (Fig. 2). The term matches that readout. It is worth being explicit that the readout belongs to the interferon production arm, not the interferon signalling arm: nothing in this paper or in the rest of this entry's literature assays the interferon receptor or the JAK/STAT cascade, which in Sendai virus is antagonised by the C protein rather than by V. Pleasingly, neither CACAO nor UniProt placed GO:0039502 on this entry, so the production/signalling conflation catalogued elsewhere in this project did not occur here. Because GO has no symbiont-mediated counterpart of GO:0032480, GO:0052170 is the most specific available term for a whole-organism interferon-production phenotype, and it is retained rather than called a parent-level restatement of the IRF3 row. That missing term is requested once for this project, in the Rift Valley fever virus NSs review, where this gene is named as its third case; see the suggested question below. Supporting Evidence: PMID:22532687 The V protein of Sendai virus (SeV) suppresses innate immunity, resulting in enhancement of viral growth in mouse lungs and viral pathogenicity. PMID:22532687 The V protein may suppress a point in the pathway starting from RIG-I to IRF3 activation and IFN- |
| GO:1900226 negative regulation of NLRP3 inflammasome complex assembly | IMP PMID:30021903 Sendai Virus V Protein Inhibits the Secretion of Interleukin... | MODIFY | Summary: V binds host NLRP3 and prevents its self-oligomerization and NLRP3-dependent ASC speck formation, so caspase-1 is not activated and interleukin-1-beta is not matured or secreted. The biology is right; the term chosen is the within-organism regulation term rather than the host-directed one. Reason: CACAO row, and the underlying work is strong and specific to this protein: V-deficient virus induces about sevenfold more interleukin-1-beta secretion and visible NLRP3 specks in THP1 macrophages where wild-type virus does not (Fig. 1), stable V expression suppresses ligand-driven secretion (Fig. 2), V co-immunoprecipitates with NLRP3 (Fig. 3), truncation mapping ties inhibition to the binding-competent forms (Fig. 4), and BRET and speck assays show the block is on NLRP3 self-oligomerization and NLRP3-ASC association (Figs. 5 and 6). So the student read the paper correctly. The problem is ontological. GO:1900226 sits under negative regulation of protein-containing complex assembly and regulation of NLRP3 inflammasome complex assembly: it describes an organism regulating its own inflammasome, whereas V is a viral protein acting on a host complex. GO's interspecies branch now carries GO:0141081, symbiont-mediated suppression of host inflammasome-mediated signal transduction, which was made a child of GO:0039537 in 2024 and so did not exist when this annotation was made in 2018. GO:0141081 has no child naming the mechanism, unlike the RIG-I and IRF3 cases, so a more precise child is proposed in proposed_new_terms; until it exists, GO:0141081 is the right replacement. Proposed replacements: symbiont-mediated suppression of host inflammasome-mediated signal transduction Supporting Evidence: PMID:30021903 we showed that the V protein of SeV inhibits NLRP3 self-oligomerization by interacting with NLRP3 to block the NLRP3-mediated ASC oligomerization required for full activation of the inflammasome PMID:30021903 Wild-type V and Vcys, but not Vn and Vc, inhibited NLRP3 inflammasome-dependent IL-1 PMID:30021903 indicating that NLRP3 is required for SeV V |
| GO:0140311 protein sequestering activity | IDA PMID:22532687 Inhibition of interferon regulatory factor 3 activation by p... | NEW | Summary: Proposed molecular function not present in GOA. V's mechanism against each of its host targets is to bind the target and withdraw it from the interaction it needs to make: IRF3 is held in the cytosol and cannot enter the nucleus even when constitutively active, and NLRP3 is prevented from self-oligomerizing and from recruiting ASC. This is sequestration, not catalysis, and it is the activity that underlies the process terms accepted in this review. Reason: GOA gives this entry no informative molecular function at all - only metal ion binding - while all four of its biological-process rows describe consequences of one activity. Naming that activity is what the molecular-function aspect is for, and the evidence is direct rather than inferential: V binds IRF3 and the constitutively active IRF3-5D and prevents its nuclear translocation in both transfected and infected cells (PMID:22532687, Figs. 3-6), and it binds NLRP3 and blocks NLRP3 self-oligomerization and NLRP3-ASC association by BRET and speck assays (PMID:30021903, Figs. 5 and 6). The generic alternative, protein binding, would say nothing about what the binding accomplishes. GO:0140311 is deliberately preferred over the broader molecular sequestering activity because every demonstrated target is a protein. Supporting Evidence: PMID:22532687 These results suggest that the V protein also retained IRF3 in the cytosol in SeV-infected cells. PMID:30021903 we showed that the V protein of SeV inhibits NLRP3 self-oligomerization by interacting with NLRP3 to block the NLRP3-mediated ASC oligomerization required for full activation of the inflammasome |
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Download this section (compressed HTML)Q: Sendai virus V needs a term for its interferon-production phenotype, and this review originally proposed one. The request is filed once, in the Rift Valley fever virus NSs review (symbiont-mediated suppression of host type I interferon production, parent GO:0052170), where this gene is now named as its third and mechanistically distinct case: unlike the two NSs proteins it does not shut down host transcription, and it is sensor-directed, carrying GO:0039540 and GO:0039548 by direct assay. That combination raises the scoping question the request now puts to the ontology editors - whether a production term should coexist with the sensor-specific terms on the same gene - and this entry is the case that poses it. The duplicate proposal was removed from this review so that the request is counted and justified once.
Q: Does Sendai virus V itself block TRIM25-mediated ubiquitination of RIG-I, as its Nipah, measles and PIV5 counterparts do? PMID:29321315 establishes the interactions for the Sendai protein but runs the ubiquitination and MAVS-association assays on the other three.
Suggested experts: Megan L. Shaw, Adolfo Garcia-Sastre, Maria Teresa Sanchez-Aparicio
Q: V has at least four cytosolic targets (IRF3, RIG-I, TRIM25, MDA5, NLRP3) and is largely disordered outside the 67-residue Vu domain. Are these engaged simultaneously by distinct surfaces, or competitively by one promiscuous interface whose apparent breadth is partly an artefact of overexpression, as the authors of PMID:22532687 themselves raise?
Suggested experts: Takashi Irie, Takemasa Sakaguchi
Q: The zinc-coordinating point mutant Vcys still binds NLRP3 and still inhibits the inflammasome, yet cysteine mutant viruses are attenuated in mice. Which of V's activities actually requires an intact zinc site, and is attenuation attributable to loss of the IRF3 or the RIG-I arm rather than the inflammasome arm?
Suggested experts: Takashi Komatsu, Bin Gotoh
Q: Is there any Sendai virus V activity downstream of the type I interferon receptor, or is interferon antagonism by this virus cleanly divided between V (induction) and C (JAK/STAT signalling)? The answer determines whether any symbiont-mediated interferon-signalling term should ever apply to V.
Suggested experts: Bin Gotoh, Takemasa Sakaguchi
Experiment: Repeat the GST-RIG-IN pulldown ubiquitination assay and the RIG-IN-MAVS co-precipitation assay of PMID:29321315 with the Sendai virus V construct included alongside the Nipah control, and in parallel in cells infected with wild-type and V-deficient Sendai virus so that the readout is obtained at native expression levels rather than by transfection. Include the Vu-deletion and cysteine point mutants to test whether the C-terminal domain that mediates the interactions is also required for the ubiquitination block.
Hypothesis: Sendai virus V blocks TRIM25-dependent ubiquitination of RIG-I by the same mechanism demonstrated for Nipah, measles and PIV5 V proteins.
Experiment: Determine the interaction interfaces by crosslinking mass spectrometry or hydrogen-deuterium exchange on V complexed separately with IRF3, the RIG-I CARDs, and NLRP3, then design separation-of-function point mutants and test each for loss of one interaction with retention of the others. Validate the informative mutants in recombinant virus and measure interferon-beta and interleukin-1-beta output and virulence in mice, which would say which arm drives the attenuation of V-deficient virus.
Hypothesis: V's several innate-immune targets are engaged through distinct surfaces rather than one promiscuous interface.
Experiment: In cells expressing V alone, and in cells infected with wild-type or V-deficient virus, measure in parallel the induction of interferon-beta after RIG-I ligand stimulation and the induction of a panel of interferon-stimulated genes after addition of exogenous recombinant interferon-beta, with STAT1 phosphorylation as the proximal readout. Running the two arms side by side in one experiment would settle which GO branch applies, and would separate V's contribution from that of the C protein, which is the known STAT1 antagonist of this virus.
Hypothesis: V suppresses host type I interferon production but has no effect on signalling downstream of the interferon receptor.
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