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Cited by 8Viral gastroenteritis research and epidemiologyEnzyme Structure and FunctionAdvanced Electron Microscopy Techniques and Applications

Vesivirus 2117 capsids more closely resemble sapovirus and lagovirus particles than other known vesivirus structures

Open access
Conley, Michaela, Emmott, Edward, Orton, Richard, Taylor, David, Carneiro, Daniel G., Murata, Kazuyoshi, Goodfellow, Ian G., Hansman, Grant S. +1 more·2017·Journal of General Virology
DOI 10.1099/jgv.0.000658PMC PMC5370393
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Abstract

Vesivirus 2117 is an adventitious agent that, in 2009, was identified as a contaminant of Chinese hamster ovary cells propagated in bioreactors at a pharmaceutical manufacturing plant belonging to Genzyme. The consequent interruption in supply of Fabrazyme and Cerezyme (drugs used to treat Fabry and Gaucher diseases, respectively) caused significant economic losses. Vesivirus 2117 is a member of the Caliciviridae, a family of small icosahedral viruses encoding a positive-sense RNA genome. We have used cryo-electron microscopy and three-dimensional image reconstruction to calculate a structure of vesivirus 2117 virus-like particles as well as feline calicivirus and a chimeric sapovirus. We present a structural comparison of several members of the Caliciviridae, showing that the distal P domain of vesivirus 2117 is morphologically distinct from that seen in other known vesivirus structures. Furthermore, at intermediate resolutions, we found a high level of structural similarity between vesivirus 2117 and Caliciviridae from other genera: sapovirus and rabbit hemorrhagic disease virus. Phylogenetic analysis confirms vesivirus 2117 as a vesivirus closely related to canine vesiviruses. We postulate that morphological differences in virion structure seen between vesivirus clades may reflect differences in receptor usage.

AI snapshot

Written from the paper’s full text.

TL;DR

Cryo-EM structures show vesivirus 2117 virus-like particles have a P2 domain morphology distinct from other known vesiviruses and more closely resemble sapovirus and rabbit hemorrhagic disease virus capsids. Phylogenetics still places vesivirus 2117 within the genus Vesivirus, closely related to canine vesiviruses.

Key findings

  • Vesivirus 2117 VLPs were reconstructed at 10 Å resolution from 960 particles from 242 micrographs; the P2 domain has pronounced horn-like structures unlike previously solved vesivirus capsids.
  • A chimeric sapovirus VLP was reconstructed at 10 Å from 2943 particles from 222 micrographs, and FCV strain F9 was reconstructed at 7 Å from 6965 particles from 241 micrographs.
  • Cross-correlation with vesivirus 2117 was highest for chimeric sapovirus (0.9214), followed by RHDV (0.9007), FCV F9 (0.8478), norovirus GII.10 (0.8498), and NoV (0.8117).
  • Phylogenetic analysis placed vesivirus 2117 firmly in Vesivirus, closely related to canine vesiviruses and in a clade distinct from FCV and VESV.

Methods

  • Vesivirus 2117 VLPs were produced by baculovirus expression of VP1 in Hi5 cells; FCV F9 was propagated in Crandell Rees feline kidney cells; chimeric sapovirus VLPs were made in Tn5 cells.
  • Cryo-EM images were processed for 3D icosahedral reconstruction; resolution was estimated by Fourier shell correlation with a 0.5 cutoff.
  • Structural comparisons used density maps from PDB/EMDB filtered to 10 Å, with correlation values calculated in UCSF Chimera; phylogenetic analysis used 57 selected protein sequences, ClustalW/MEGA, neighbor-joining with 1000 bootstrap replicates, and 402 final alignment positions.

Limitations

  • The paper states that at 10 Å resolution, gross morphological similarities or differences may not indicate common tertiary structures, so such comparisons should be interpreted with care.
  • The paper notes a paucity of data on pathology caused by vesiviruses in the CCV and 2117 clades, and that the natural host and pathology of 2117 remain unknown.
  • Evident from the text: the 2117 and sapovirus structures are from VLPs rather than native virions, and the study reports structural correlations without direct receptor-binding or entry experiments.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1099/jgv.0.000658

Cites

52 of 52 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

16 of 30 cited sources checked · 10 supported · 0 flagged · accuracy not yet measured

  • Findingcitation

    The 2117 structure closely resembled a published low-resolution structure of Parkville virus (a sapovirus).

    “We observed that our 2117 structure closely resembled a published low-resolution structure of Parkville virus (a sapovirus) [31].”
    Quote in the paperSubstantial claim1 of 1 sources checked
  • Findingown data

    The distal P domain of vesivirus 2117 is morphologically distinct from that seen in other known vesivirus structures.

    “showing that the distal P domain of vesivirus 2117 is morphologically distinct from that seen in other known vesivirus structures.”
    • Also stated in: § Vesivirus 2117 VLPs are structurally distinct from known vesivirus capsid structures · plain
      “This is quite distinct from the morphology seen in previously solved vesivirus capsid structures [13, 14, 32].”
    Quote in the paperSubstantial claim2 of 3 sources checked
    • cites [13] source

      The Results describe feline calicivirus (FCV) and say its structure is strongly reminiscent of another vesivirus, SMSV; they do not compare vesivirus 2117 with other structures. Searches for “2117” and for a distinct distal P-domain morphology found no passage addressing the claim. (LLM, conf=0.75)

      Experimental — accuracy not yet measured
    • cites [14] source

      The P-domain section compares the distal P2 subdomain of San Miguel sea lion virus (SMSV) with that of Norwalk virus, and the Discussion describes differences between those viruses. A search for “vesivirus 2117” found no passage about its structure, so our copy does not establish the claimed distinction from other vesivirus structures. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
    • cites [32] source
  • Premisecitation

    MuNV exhibits prominent horn-like protrusions on the outer surface of the P2 domain of VP1.

    “MuNV also exhibits prominent horn-like protrusions on the outer surface of the P2 domain of VP1 [34].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
  • Findingown data

    Vesivirus 2117 VLPs exhibit the characteristic calicivirus morphology: a T=3 icosahedral capsid composed of VP1 dimers, giving rise to arch-like capsomeres.

    “Vesivirus 2117 VLPs were seen to exhibit the characteristic calicivirus morphology: a T=3 icosahedral capsid composed of VP1 dimers, giving rise to arch-like capsomeres.”
    Quote in the paperSubstantial claim
  • Findingown data

    At intermediate resolutions, there is a high level of structural similarity between vesivirus 2117 and Caliciviridae from other genera: sapovirus and rabbit hemorrhagic disease virus.

    “Furthermore, at intermediate resolutions, we found a high level of structural similarity between vesivirus 2117 and Caliciviridae from other genera: sapovirus and rabbit hemorrhagic disease virus.”
    • Also stated in: § Structural comparison of members of the Caliciviridae · hedged
      “The P domains of vesivirus 2117, sapovirus and RHDV (Fig. 5a–c, respectively) appear rather similar, showing a compact morphology.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The chimeric sapovirus VLP structure is representative of native sapovirus capsid structure.
  • Classified as probably not a substantial claim. 16
  • May combine two claims. 20

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Expression of a recombinant form of the major capsid protein is sufficient for the assembly of virus-like particles (VLPs), which exhibit the same morphology as virions.

    “As is the case for many members of the Caliciviridae, expression of a recombinant form of the major capsid protein is sufficient for the assembly of virus-like particles (VLPs), which exhibit the same morphology as virions [26–29].”
    Quote in the paperNot a substantial claim2 of 4 sources checked
    • cites [26] source
    • cites [27] source
    • cites [28] source

      The Abstract (page unavailable) says that recombinant chimeric VP1 self-assembled into VLPs. It describes those VLPs as morphologically similar to parental VLPs, not as having the same morphology as virions. The Results and Discussion report structural similarities to a vesivirus virion, but do not establish the broader morphology claim. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [29] source

  • May combine two claims.

    Findingcitation

    The VP1 dimers of vesivirus 2117 form intradimeric interactions between P2 domains and interdimeric interactions between P1 domains, similar to those seen in FCV and as previously described for SMSV.

    “The VP1 dimers also appear to form intradimeric interactions between P2 domains and interdimeric interactions between P1 domains, similar to those seen in FCV and as previously described for SMSV [31].”
    Quote in the paperNot a substantial claim1 of 1 sources checked

  • May combine two claims.

    Findingcitation

    The P domains of vesivirus 2117, sapovirus and FCV appear to be raised off the S domain, as previously observed for RHDV and MuNV-1, in contrast to the P domains of NoV, which form a more collapsed conformation.

    “The P domains of vesivirus 2117, sapovirus and FCV appear to be raised off the S domain, as previously observed for RHDV and MuNV-1, in contrast to the P domains of NoV, which form a more collapsed conformation in relation to the S domain [33, 34].”
    Quote in the paperSubstantial claim2 of 2 sources checked

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Two molecules of feline junctional adhesion molecule-A bind to the flat surface of the FCV capsomere in a head-to-tail arrangement.

    “Two molecules of feline junctional adhesion molecule-A bind to the flat surface in a head-to-tail arrangement [13, 32].”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [13] source
    • cites [32] source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The outer face of the FCV capsomere incorporates the receptor-binding site.

    “The outer face of the FCV capsomere incorporates the receptor-binding site.”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [13] source
    • cites [32] source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The P2 domains of FCV form a rhombus-shaped structure with a flatter outer surface, similar to that of SMSV and Tulane virus.

    “Conversely, the P2 domains of FCV form a rhombus-shaped structure with a flatter outer surface (similar to that of SMSV and Tulane virus [36, 37]).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [36] source
    • cites [37] source

      The Results section (“The Fold of the Major Capsid Protein (VP1) of TV”; page unavailable) compares Tulane virus’s P2 subdomain with SMSV but does not describe a rhombus shape or a flatter outer surface. The Results section on flexible P domains also compares Tulane virus and FCV without making that shape claim. Searches for “rhombus” and for FCV, SMSV, and P2 surface shape found no passage that verifies the attributed comparison. (LLM, conf=0.73)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    RHDV and human noroviruses bind histo-blood group antigens - complex carbohydrates linked to glycoproteins or glycolipids on the surface of erythrocytes and mucosal epithelial cells.

    “while RHDV and human noroviruses bind histo-blood group antigens – complex carbohydrates linked to glycoproteins or glycolipids on the surface of erythrocytes and mucosal epithelial cells [40–42].”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [40] source

      The Abstract describes RHDV binding an H-type histo-blood group antigen and identifies these antigens as carbohydrates on glycoproteins or glycolipids. The Discussion reports that Norwalk virus particles bind H-type antigens on cells, but explicitly says whether other human norovirus strains do so remains unknown. The claim therefore extends the finding beyond the strain tested; our copy provides no page numbers for these passages. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [41] source
    • cites [42] source

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    The P2 domain plays a critical role in the viral infection cycle as it contains both the major immunodominant epitopes and the receptor-binding site.

    “However, the P2 domain plays a critical role in the viral infection cycle as it contains both the major immunodominant epitopes and the receptor-binding site [32, 35].”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [32] source
    • cites [35] Radford, 1999, The capsid gene of feline calicivirus contains linear B-cell epitopes in both variable and conserved regions, J Virol source

      The Discussion identifies the 5′ hypervariable region of capsid region E as an important immunodominant region containing B-cell epitopes. It does not identify that region as the P2 domain or locate a receptor-binding site there; indeed, it says regions that interact with host proteins are largely unknown for caliciviruses. Thus, the epitope portion is supported, but the P2 and receptor-binding portions are not established by this paper. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    The outermost surface of the P2 domain of vesivirus 2117 shows horn-like protrusions at either end, whereas the P2 domains of the sapovirus VLPs appear to have a more curved structure without such large protuberances.

    “The outermost surface of the P2 domain of vesivirus 2117 shows horn-like protrusions at either end, whereas the P2 domains of the sapovirus VLPs appear to have a more curved structure without such large protuberances (Fig. 2d).”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: The chimeric sapovirus VLP structure is representative of native sapovirus capsid structure.

  • May combine two claims.

    Findingown data

    Phylogenetic analysis of capsid protein sequences supports the classification of vesivirus 2117 as a member of the genus Vesivirus, although it resides in a clade distinct from FCV and the VESV and SMSV groups.

    “Phylogenetic analysis of capsid protein sequences supports the classification of vesivirus 2117 as a member of the genus Vesivirus, although it resides in a clade distinct from FCV and the vesicular exanthema of swine virus (VESV) and San Miguel sea lion virus (SMSV) groups.”
    • Also stated in: § Phylogenetic analysis of vesivirus 2117 · boosted
      “As expected, this analysis placed vesivirus 2117 firmly within the Vesivirus genus and showed that the sapoviruses are more closely related to the vesiviruses than the Lagovirus genus.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Vesivirus 2117 capsid structure more closely resembles that of sapoviruses, and surprisingly a lagovirus, than it does other known vesivirus structures.

    “These data reveal that the vesivirus 2117 capsid structure more closely resembles that of sapoviruses, and surprisingly a lagovirus, than it does other known vesivirus structures.”
    • Also stated in: § Structural comparison of members of the Caliciviridae · plain
      “The structure that produced the highest correlation value when aligned to the vesivirus 2117 structure was the chimeric sapovirus described here, giving a correlation value of 0.9214.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The chimeric sapovirus VLP structure is representative of native sapovirus capsid structure.

  • May combine two claims.

    Findingown data

    The chimeric sapovirus structure exhibits typical calicivirus morphology, with notable similarities to that of vesivirus 2117.

    “The sapovirus structure also exhibits typical calicivirus morphology, with notable similarities to that of vesivirus 2117.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The chimeric sapovirus VLP structure is representative of native sapovirus capsid structure.

  • May combine two claims.

    Findingown data

    There are substantial differences in virion morphology between clades of the genus Vesivirus and similarities between vesivirus 2117 and structures for both sapoviruses and lagoviruses at comparatively low resolution.

    “Here we see substantial differences in virion morphology between clades of the genus Vesivirus and, albeit at comparatively low resolution, similarities between vesivirus 2117 and structures for both sapoviruses and lagoviruses.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The chimeric sapovirus VLP structure is representative of native sapovirus capsid structure.

  • May combine two claims.

    Findingown data

    The capsomeres of FCV, norovirus GII.10 and NoV appear quite distinct in conformation; there are notable differences between the two norovirus structures GII.10 and Norwalk.

    “The capsomeres of FCV, norovirus GII.10 and NoV (Fig. 5d–f, respectively), however, appear to be quite distinct in conformation; indeed, there are notable differences between the two norovirus structures GII.10 and Norwalk.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The FCV structure exhibits striking differences from the vesivirus 2117 and sapovirus structures; the FCV P2 region forms a flattened, rhombus-shaped outer face.

    “This structure exhibits striking differences from the vesivirus 2117 and sapovirus structures set out above; the FCV P2 region forms a flattened, rhombus-shaped outer face (Fig. 3c, d).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Vesivirus 2117, canine vesivirus, canine caliciviruses, SMSV8 and mink calicivirus are distinct from the FCV and VESV clades.

    “These viruses along with the canine caliciviruses, SMSV8 and mink calicivirus are distinct from the FCV and VESV clades.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Phylogenetic analysis placed vesivirus 2117 firmly within the Vesivirus genus and showed that sapoviruses are more closely related to vesiviruses than the Lagovirus genus.

    “As expected, this analysis placed vesivirus 2117 firmly within the Vesivirus genus and showed that the sapoviruses are more closely related to the vesiviruses than the Lagovirus genus.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The P2 domains of norovirus GII.10 seem similar to those of vesivirus 2117, whereas the S domains and P1 domains of FCV seem to resemble those of vesivirus 2117.

    “When observing the structures in Fig. 4, the P2 domains of norovirus GII.10 seem similar to those of vesivirus 2117, whereas the S domains and P1 domains of FCV seem to resemble those of vesivirus 2117.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Vesivirus 2117 isolates and canine vesivirus are clearly closely related and occupy their own clade.

    “Vesivirus 2117 isolates and canine vesivirus are clearly closely related and occupy their own clade.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The top blastp hit to the 2117 capsid amino acid sequence was an existing 2117 sequence (AAQ24846; 99% identity).

    “The top hit was to an existing 2117 sequence (AAQ24846; 99 % identity)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Cross-correlation data indicated a high degree of similarity between vesivirus 2117 and both sapovirus and RHDV but a lesser degree when compared with FCV.

    “Cross-correlation data indicated a high degree of similarity between vesivirus 2117 and both sapovirus and RHDV but a lesser degree when compared with FCV.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The chimeric sapovirus VLP structure is representative of native sapovirus capsid structure.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The next hits were three other suspected 2117 sequences sampled in Geel, Belgium (ACV95479; 85% identity) and Allston, USA (ACV95474, ACV95477; 84% identity).

    “followed by three hits to other suspected 2117 sequences sampled in Geel, Belgium (ACV95479; 85 % identity) and Allston, USA (ACV95474, ACV95477; 84 % identity).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    Morphological differences in virion structure seen between vesivirus clades may reflect differences in receptor usage.

    “We postulate that morphological differences in virion structure seen between vesivirus clades may reflect differences in receptor usage.”
    • Also stated in: § Introduction · hedged
      “The striking differences in P domain morphology within vesiviruses may indicate functional differences, perhaps related to receptor usage and entry mechanisms.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    The striking differences in P domain morphology within vesiviruses may indicate functional differences, perhaps related to receptor usage and entry mechanisms.

    “The striking differences in P domain morphology within vesiviruses may indicate functional differences, perhaps related to receptor usage and entry mechanisms.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Structural analysis has been proposed to provide insights into the common ancestry of distantly related viruses following the discovery of fold conservation between viruses that infect highly divergent branches on the tree of life.

    “Structural analysis has been proposed to provide insights into the common ancestry of distantly related viruses following the discovery of fold conservation between viruses that infect highly divergent branches on the tree of life [30].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [30] source

  • May combine two claims.

    Interpretationreasoning

    Morphological differences/similarities in the P domain may be uncoupled from genetic relatedness but may provide important clues concerning critical aspects of virus biology, such as entry pathway.

    “Thus, morphological differences/similarities in the P domain may be uncoupled from genetic relatedness but may provide important clues concerning critical aspects of virus biology, such as entry pathway.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Typically, receptor-binding sites of viruses are embedded in hyper-variable regions of capsid proteins.

  • Classified as probably not a substantial claim.

    Study design and conductown data

    The evolutionary history of the 2117 capsid sequence was inferred using the neighbour-joining method with 1000 bootstrap replicates.

    “The evolutionary history of the 2117 capsid sequence was inferred using the neighbour-joining method (1000 bootstrap replicates) to generate a phylogenetic tree”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing). May combine two claims.

    Interpretationnone given

    At 10 Å resolution, gross morphological similarities or differences may not indicate common tertiary structures; therefore, such comparisons should be interpreted with care.

    “At 10 Å resolution, gross morphological similarities or differences may not indicate common tertiary structures; therefore, such comparisons should be interpreted with care.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationreasoning

    The substantial impact of vesivirus 2117 contamination highlights the need for effective adventitious agent testing.

    “The substantial impact of this contamination highlights the need for effective adventitious agent testing.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    A FSC cut-off value of 0.5 was taken.

    “A FSC cut-off value of 0.5 was taken (Fig. S1, available in the online Supplementary Material).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Resolution estimates for each map were determined by dividing the data set into two and calculating 3D reconstructions from each half.

    “Resolution estimates for each map were determined by dividing the data set into two and calculating 3D reconstructions from each half.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Vesivirus 2117 contamination of CHO-cell bioreactors at Genzyme caused significant financial losses and delayed drug delivery to patients with Gaucher or Fabry disease.

    “Vesivirus 2117 has caused significant financial losses owing to the contamination of bioreactors at Genzyme (Allston Landing and Geel facilities) where CHO cells were used for the production of biopharmaceuticals.”
    • Also stated in: § Discussion · plain
      “The contamination necessitated the shutdown and decontamination of bioreactors, causing a significant delay in the delivery of drugs to patients with Gaucher or Fabry disease (17).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [17] source

  • May combine two claims.

    Interpretationreasoning

    Differences in capsid morphology between the vesivirus clades and similarities between vesivirus 2117 and viruses in different genera within the Caliciviridae may allude to important functional differences and similarities.

    “Thus, differences in capsid morphology between the vesivirus clades and similarities between vesivirus 2117 and viruses in different genera within the Caliciviridae may allude to important functional differences and similarities, respectively.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The chimeric sapovirus VLP structure is representative of native sapovirus capsid structure.
33 of 33

  • The paper relies on this without support.

    The chimeric sapovirus VLP structure is representative of native sapovirus capsid structure.

    “To draw a comparison between vesivirus 2117 capsids and those of the genus Sapovirus at higher resolution, we calculated a 3D structure from images of VLPs produced by a chimeric VP1 construct that has been shown to yield high levels of expression [28].”
    “The chimera consisted of the N-terminal arm, S domain and P1.1 domain of the Yokote strain and the P2 domain, P1.2 domain and VP2 of the Mc114 strain [28].”

  • The paper relies on this without support.

    There is a paucity of data concerning pathology caused by vesiviruses in the CCV and 2117 clades.

    “There is a paucity of data concerning pathology caused by vesiviruses in the CCV and 2117 clades.”

  • The paper relies on this without support.

    For vesivirus 2117, the natural host and pathology remain unknown.

    “whereas for 2117, the natural host and pathology remain unknown.”

  • The paper relies on this without support.

    Within the Caliciviridae, VP1 proteins share a common topology.

    “Within the Caliciviridae, VP1 proteins share a common topology.”

  • The paper relies on this without support.

    Typically, receptor-binding sites of viruses are embedded in hyper-variable regions of capsid proteins.

    “Typically, receptor-binding sites of viruses are embedded in hyper-variable regions of capsid proteins.”

  • The paper relies on this without support.

    The outer face of the P domain presents the receptor-binding site and major immunodominant epitopes.

    “The fact that the outer face of the P domain presents the receptor-binding site and major immunodominant epitopes”

  • The paper relies on this without support.

    The separation of the first and second ORFs by a stop codon is typical of noroviruses and vesiviruses.

    “which is typical of the noroviruses and vesiviruses.”

  • The paper relies on this without support.

    FCV is the only calicivirus that has been shown to enter via attachment to a protein receptor.

    “FCV is the only calicivirus that has been shown to enter via attachment to a protein receptor.”
8 of 8

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Conflicting descriptions of the genera in the phylogenetic analysis

    Minor

    The Results describe the tree as based on sequences from three genera, while the Fig. 6 caption identifies five genera in that tree.

1 of 1

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Works this paper cites that were later retracted, from the retraction notices publishers deposit. Major when the notice came out before this paper was published.

  • Cites a retracted work: 10.1128/jvi.01208-12

    Info

    The cited work was retracted on 2017-11-29 (notice 10.1128/jvi.01708-17), not before this paper was published (2017-01-01).

    Cited work 10.1128/jvi.01208-12 · retracted 2017-11-29 · notice 10.1128/jvi.01708-17 · this paper published 2017-01-01

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Authors
Conley, M., Emmott, E., Orton, R., Taylor, D., Carneiro, D. G., Murata, K., Goodfellow, I. G., Hansman, G. S., & Bhella, D.
Affiliations
  • MRC University of Glasgow Centre for Virus Research (GB)
  • University of Cambridge (GB)
  • Howard Hughes Medical Institute (US)
  • Present address: School of Immunity and Infection, Institute of Biomedical Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
  • National Institute for Physiological Sciences (JP)
  • University Hospital Heidelberg (DE)
Corresponding author
Bhella, David
ORCID
Venue
Journal of General Virology
Publisher
Microbiology Society
Published
2017-01-01
Volume
98
Issue
1
Pages
68-76
ISSN
  • 0022-1317 (ISSN-L)
  • 1465-2099
DOI
10.1099/jgv.0.000658
PMC
PMC5370393
OpenAlex
W2563728193
Semantic Scholar
0b8c36762eb0e698a0d0258617c0aa713d5df652
Cited by
8
References
53
Citations by year
2024: 1 · 2021: 1 · 2020: 1 · 2019: 2 · 2018: 2 · 2017: 1
FWCI
1.54
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of General Virology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion)
  • Griffith Research Online (submittedVersion, cc-by)
Funders
  • Wellcome Trust
  • Medical Research Council (MC_UU_12014/7, MC_UU_12014/3)
  • Biotechnology and Biological Sciences Research Council (BB/J013854/1, 1371508)
  • Japan Society for the Promotion of Science
Topics
  • Health Sciences › Medicine › Infectious Diseases › Viral gastroenteritis research and epidemiology
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
Keywords
Caliciviridae, viral capsid structure, virus-like particles, sapovirus, Lagovirus, feline calicivirus, rabbit hemorrhagic disease virus, P domain, Fabry disease, Gaucher disease, receptor usage, viral phylogeny
MeSH terms
Animals, Capsid, Cricetulus, Phylogeny, RNA, Viral, Sequence Analysis, DNA, Cryoelectron Microscopy, Imaging, Three-Dimensional, Lagovirus, Sapovirus, Vesivirus

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-28.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-28.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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