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Cited by 160RNA and protein synthesis mechanismsEvolution and Genetic DynamicsFractal and DNA sequence analysis

Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias

Open access
Kunec, Dusan, Osterrieder, Nikolaus·2016·Cell Reports
DOI 10.1016/j.celrep.2015.12.011
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Abstract

Codon pair bias is a remarkably stable characteristic of a species. Although functionally uncharacterized, robust virus attenuation was achieved by recoding of viral proteins using underrepresented codon pairs. Because viruses replicate exclusively inside living cells, we posited that their codon pair preferences reflect those of their host(s). Analysis of many human viruses showed, however, that the encoding of viruses is influenced only marginally by host codon pair preferences. Furthermore, examination of codon pair preferences of vertebrate, insect, and arthropod-borne viruses revealed that the latter do not utilize codon pairs overrepresented in arthropods more frequently than other viruses. We found, however, that codon pair bias is a direct consequence of dinucleotide bias. We conclude that codon pair bias does not play a major role in the encoding of viral proteins and that virus attenuation by codon pair deoptimization has the same molecular underpinnings as attenuation based on an increase in CpG/TpA dinucleotides.

AI snapshot

Written from the paper’s full text.

TL;DR

Codon pair bias in viruses is largely a byproduct of dinucleotide bias, especially CpG and TpA suppression, rather than selection for host-preferred codon pairs. The authors conclude that attenuation by codon pair deoptimization/SAVE likely reflects increased CpG/TpA dinucleotides rather than impaired use of specific codon pairs.

Key findings

  • Human viruses are only marginally influenced by host codon pair preferences: 50%–60% of codon pairs in viral genes have positive CPSs versus 65% in human genes, and many viral ORFeomes have negative CPB scores; only Influenza C virus and BK polyomavirus matched the human ORFeome CPB of 0.075.
  • CpG dinucleotide relative abundance negatively correlates with CPB in both DNA and RNA viruses (R² ≥ 0.75), and 94% of codon pairs with TpA at position P3-A1 and 98% with CpG at P3-A1 are underrepresented in the human ORFeome.
  • Arboviruses do not preferentially use codon pairs overrepresented in their arthropod hosts: among 159 viruses from Reoviridae (53), Flaviviridae (62), Togaviridae (30), and Bunyaviridae (14), CPB scores calculated with arthropod CPSs were not significantly higher in arthropod-borne or arthropod-specific viruses than in non-vectored sister viruses.
  • Recoding in prior SAVE studies increased CpG dinucleotides dramatically (140%–360% in DENV-2 and 480%–630% in HRSV) and TpA only moderately (30%–60%), while TpG and CpA decreased 20%–60%, supporting dinucleotide increase as the likely attenuation basis.

Methods

  • Protein coding sequences were retrieved from NCBI CCDS, NCBI Genome, and VectorBase via Biomart. Analyses included 92 human viruses (41 DNA, 51 RNA) across all Baltimore classes, plus 159 viruses from Reoviridae, Flaviviridae, Togaviridae, and Bunyaviridae; species CPSs were calculated for five vertebrates (human, pig, mouse, chicken, zebrafish) and four arthropods (Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis).
  • Codon pair scores (CPSs) were calculated for all 3,721 codon pairs as the natural logarithm of observed over expected occurrences, following Coleman et al. (2008); CPB was the mean CPS per ORF or ORFeome. Synonymous codons were randomly reshuffled to generate 30 randomized ORFs per ORF, and DCPB was defined as CPB(WT) − CPB(random).
  • Dinucleotide relative abundance was assessed by odds ratio rXY = fXY/fXfY, with rXY < 0.78 considered low and > 1.25 high relative abundance. The contribution of adjacent and nonadjacent nucleotide pairs to CPSs was analyzed by sorting codon pairs by CPS and examining dinucleotide distributions.

Limitations

  • The paper states that the exact molecular mechanisms responsible for attenuation by SAVE or by increased CpG/TpA dinucleotides remain unknown, and that experimental confirmation of the authors’ predictions is beyond the scope of the work.
  • The paper states that genetic stability, safety, and efficacy of codon pair-deoptimized viruses must be studied exhaustively, including in outbred populations, before vaccine use.
  • Evident from the text: the study is computational and correlational, relying on annotated ORFeomes and existing databases, and it does not itself perform viral fitness or attenuation experiments; some interpretations depend on prior SAVE and echovirus studies.

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

Integrity signals

Registry

Crossref · 10.1016/j.celrep.2015.12.011

Cites

32 of 32 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

26 of 37 cited sources checked · 17 supported · 1 flagged · accuracy not yet measured

  • Premisecitation

    DENV-2 and RVFV are biased for codon pairs that are overrepresented in the vertebrate host but not in the respective mosquito vector.

    “Similar to our results, the data presented for DENV-2 and RVFV show that these viruses are biased for codon pairs that are overrepresented in the vertebrate host but not in the respective mosquito vector (Shen et al., 2015).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Shen et al., 2015 source

      The passage labeled Significance says RVFV favors codon pairs with high scores in both sheep and mosquitoes, and DENV favors pairs with high scores in both humans and mosquitoes (Fig. S1 A–B; Fig. 1 A–C). The Discussion likewise describes arboviruses as having a balanced codon-pair bias between hosts, contrary to the claim that the pairs are overrepresented in vertebrates but not mosquito vectors. (LLM, conf=0.91)

      Checked by a reasoning model — may be wrong.

      Experimental — accuracy not yet measured
  • Findingcitation

    Closely related species have similar codon pair bias.

    “A comparison of CPSs derived from different organisms (Figure 1; Figure S1) confirmed that closely related species have a similar codon pair bias (CPB) (Moura et al., 2007;Shen et al., 2015).”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites Moura et al., 2007 source
    • cites Shen et al., 2015 source
  • Premisecitation

    During adaptation viruses often change their genome structure according to the genome features of their new hosts.

    “During adaptation viruses often change their genome structure according to the genome features of their new hosts (Greenbaum et al., 2009).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Greenbaum et al., 2009 source
  • Premisecitation

    When SAVE is done using vertebrate CPSs, it inadvertently increases the number of CpG and, to a lesser degree, TpA dinucleotides in recoded sequences.

    “when done using vertebrate CPSs, inadvertently increases the number of CpG and, to lesser degree, also TpA dinucleotides in recoded sequences”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Atkinson et al., 2014 source

      The Discussion (Relationship between virus replication and CpG and UpA frequencies; page unavailable) reports that earlier codon de-optimization increased CpG and UpA frequencies. It does not establish that SAVE using vertebrate codon-pair scores causes those increases, or that the increase in UpA (TpA in DNA notation) is smaller than the increase in CpG. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
  • Premisecitation

    The bias in analyzed arboviruses for overrepresented codon pairs of the corresponding vertebrates was identified only in a small set of codon pairs that are used with higher frequency.

    “The bias in analyzed arboviruses for overrepresented codon pairs of the corresponding vertebrates was identified only in a small set of codon pairs that are used with higher frequency.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Shen et al., 2015 source
  • Classified as probably not a substantial claim. 13
  • May combine two claims. 29

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

    Premisecitation

    Codon pair preference has been found in every species studied and can be radically dissimilar between phylogenetically distant species.

    “Codon pair preference has been found in every species studied and can be radically dissimilar between phylogenetically distant species (Moura et al., 2005;Mueller et al., 2010).”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites Moura et al., 2005 source
    • cites Mueller et al., 2010 source

  • Classified as probably not a substantial claim.

    Premisecitation

    Dinucleotide bias appears to be linked with codon pair bias.

    “Dinucleotide bias also appears to be linked with codon pair bias (Moura et al., 2007;Shen et al., 2015), but this relationship has not been thoroughly explored.”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Moura et al., 2007 source
    • cites Shen et al., 2015 source

  • May combine two claims.

    Interpretationcitation

    The two groups of viruses are exposed to different selection pressures and the pressure is imposed by the respective hosts.

    “suggesting that the two groups of viruses are exposed to different selection pressures and that the pressure is imposed by the respective hosts (Lobo et al., 2009).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Lobo et al., 2009 source

  • May combine two claims.

    Premisecitation

    A study of echovirus mutants demonstrated that the increase of CpG and TpA frequencies impaired virus fitness but that alteration of CPB without changing the CpG and TpA frequency did not.

    “A study that analyzed a library of echovirus mutants -in which either CpG and TpA frequency or the overall CPB was kept constant while the other feature was altered -demonstrated that the increase of CpG and TpA frequencies impaired virus fitness but that alternation of CPB without changing the CpG and TpA frequency did not (Tulloch et al., 2014).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Tulloch et al., 2014 source

  • Probably not a substantial claim: may not pass S1 (asserted).

    Premisecitation

    The trade-off hypothesis predicts that constraining evolution in one host species diminishes fitness in the other.

    “The trade-off hypothesis predicts that constraining evolution in one host species diminishes fitness in the other (Vasilakis et al., 2009).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Vasilakis et al., 2009 source

      The Introduction says the trade-off hypothesis predicts that a fitness increase in one host usually diminishes fitness in the other. The Discussion likewise predicts that adaptation to one host or cell line reduces fitness in others. The claim substitutes ‘constraining evolution in one host species’ for adaptation or a fitness increase in that host, which is not the prediction the paper states. (LLM, conf=0.85)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Viruses that are exclusively hosted by mammals are evolutionarily related to either tick- or mosquito-borne viruses.

    “The viruses that are exclusively hosted by mammals (rodents and bats) are evolutionarily related to either tick-or mosquito-borne viruses (Moureau et al., 2015).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Moureau et al., 2015 source

      The Results (NKVs; A timed evolutionary perspective) place bat-associated no-known-vector viruses within a mosquito-borne clade and describe a rodent-associated lineage that gave rise to both no-known-vector and arthropod-borne lineages. The Introduction describes these viruses as primarily associated with rodents or bats, but does not establish that they are exclusively hosted by mammals. (LLM, conf=0.82)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Mammals share essentially the same codon pair bias, which can be different among phylogenetically distant species.

    “Mammals share essentially the same codon pair bias, which can be different among phylogenetically distant species (Mueller et al., 2010).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Mueller et al., 2010 source

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

    Premisecitation

    SAVE increases the number of codon pairs that are underrepresented in coding sequences of the target host.

    “Previous studies have shown that SAVE not only increases the number of codon pairs that are underrepresented in coding sequences of the target host”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Atkinson et al., 2014 source

      The Discussion (page unavailable) reports that earlier mutants increased bias toward unfavourable codon pairs, supporting the core point about increasing disfavoured pairs. It does not identify those pairs as underrepresented in the target host’s coding sequences or name the approach SAVE. (LLM, conf=0.78)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Insect-specific-like flaviviruses likely evolved from mosquito-borne viruses.

    “insect-specific-like flaviviruses, which likely evolved from mosquito-borne viruses (Blitvich and Firth, 2015;Moureau et al., 2015).”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites Blitvich and Firth, 2015 source
    • cites Moureau et al., 2015 source

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

    Premisecitation

    Many extant RNA vertebrate and plant viruses evolved from insect viruses.

    “It is becoming clear that many extant RNA vertebrate and plant viruses evolved from insect viruses (Li et al., 2015;Marklewitz et al., 2015).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Li et al., 2015

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Marklewitz et al., 2015 source

      The Discussion says arbo-bunyaviruses likely evolved from arthropod-specific ancestors, and the Significance passage says this includes vertebrate-infecting bunyaviruses. The paper notes that bunyaviruses include plant pathogens, but it does not establish that many plant viruses evolved from insect viruses. Its findings also concern a particular RNA virus family, rather than RNA vertebrate and plant viruses broadly. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

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

    Interpretationcitation

    Restriction of TpA use might reduce the improper binding of regulatory factors.

    “Therefore, restriction of TpA use might reduce the improper binding of regulatory factors (Karlin and Burge, 1995;Karlin and Ladunga, 1994).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Karlin and Burge, 1995 source
    • cites Karlin and Ladunga, 1994 source

  • May combine two claims.

    Interpretationcitation

    The suppression of TpA in DNA destined for expression from mRNA in the cytosol may be accounted for by the fact that TpA dinucleotide is present in two canonical stop codons (TAA and TAG) and that UpA dinucleotides in RNA are preferential targets for ribonucleases.

    “This suppression may be accounted for by the fact that TpA dinucleotide is present in two canonical stop codons (TAA and TAG) and that UpA dinculeotides in RNA are preferential targets for ribonucleases (Beutler et al., 1989).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Beutler et al., 1989 source

      Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable, 1 not checked. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured

  • May combine two claims.

    Interpretationcitation

    The results of the echovirus study, although questioned, are in line with our observations, which also suggest that the basis of attenuation by SAVE is the increase of CpG dinucleotides in coding sequences.

    “Therefore, the results of this study, although questioned (Shen et al., 2015), are in line with our observations, which also suggest that the basis of attenuation by SAVE is the increase of CpG dinucleotides in coding sequences.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Shen et al., 2015 source

  • May combine two claims.

    Interpretationreasoning

    Viruses that were engineered by SAVE might not be weakened per se but are attenuated because they induce stronger immune responses.

    “This means that viruses that were engineered by SAVE might not be weakened per se but that they are attenuated because they induce stronger immune responses (Tulloch et al., 2014).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Tulloch et al., 2014 source

  • May combine two claims.

    Findingown data

    Some analyzed arboviruses show a bias for codon pairs that are overrepresented in vertebrate hosts, but these viruses also display a marked suppression of CpG dinucleotides.

    “Although some of the analyzed arboviruses show a bias for codon pairs that are overrepresented in the vertebrate hosts, these viruses also display a marked suppression of CpG dinucleotides.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Most human viruses predominantly use codon pairs with positive CPSs, but the percentage of such codon pairs in viral genes is lower (50%-60%) than in human genes (65%).

    “Most of the human viruses predominantly use codon pairs that have positive CPSs and are potentially preferred in the human, but the percentage of codon pairs with positive CPSs in viral genes is lower (50%-60%) than in human genes (65%) (Figure 2D).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The CPB scores of many human viruses are less than 0, and only Influenza C virus and BK polyomavirus match the human ORFeome CPB of 0.075.

    “the CPB scores of many viruses were less than 0, and only in two cases (Influenza C virus and BK polyomavirus) did they match the CPB of the human ORFeome (0.075).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Mosquitoes do not display underrepresentation of CpG and overrepresentation of TpG and CpA dinucleotides in their genomes.

    “Mosquitoes, unlike vertebrates, do not display underrepresentation of CpG and overrepresentation of TpG and CpA dinucleotides in their genomes (Figure S2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Chikungunya virus and O'nyong'nyong virus display moderate suppression of CpG dinucleotides (relative abundance 0.81 and 0.76), contain few codon pairs overrepresented in the vertebrate host (52%), and have low CPB scores (-0.05 and -0.04).

    “protein coding sequences of viruses such as Chikungunya virus or O'nyong'nyong virus, which display only moderate suppression of CpG dinucleotides in their genomes (relative abundance 0.81 and 0.76, respectively), contain only very few codon pairs that are overrepresented in the vertebrate host (52%), which results in very low CPB scores (À0.05 and À0.04, respectively) (Figure 2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    The only association between viral host and CPB is within the insect-specific and insect-specific-like groups of flaviviruses, which have lower CPB scores relative to human than most other flaviviruses.

    “The only association between the viral host and CPB can be observed within the insect-specific and the insect-specific-like groups of flaviviruses, which appear to have lower CPB scores relative to the human than most other flaviviruses (Figure 6).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    DNA viruses with the smallest genomes (≤5 kb) have the highest CPB scores (0-0.08), papillomaviruses and intermediate-sized adenoviruses have lower CPB scores (-0.03-0.03), and herpesviruses and poxviruses have the lowest CPB scores (-0.07-0.03).

    “Viruses with the smallest genomes ($5 kb, polyomaviruses and parvoviruses) had clearly the highest CPB scores (0-0.08),papillomaviruses ($7.5 kb) and intermediate-sized adenoviruses ($35 kb) had lower CPB scores (À0.03-0.03),and herpesviruses and poxviruses (genomes >150 kb) had the lowest CPB scores (À0.07-0.03).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Insect-specific flaviviruses on average use more CpG dinucleotides than insect-specific-like viruses, and these more than the dual-host flaviviruses from which they evolved.

    “insect-specific flaviviruses, on average, use more CpG dinucleotides than insect-specific-like viruses, and these more than the dual-host flaviviruses from which they evolved (Figure S5).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    CpA and TpG dinucleotides are overrepresented in small DNA viruses and in the majority of RNA viruses.

    “Unexpectedly, CpA and TpG dinucleotides are not only overrepresented in small DNA viruses, which might be explained by the cytosine methylation-deamination-mutation hypothesis (Bird, 1980), but also in the majority of RNA viruses.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Bird, 1980 source

  • May combine two claims.

    Findingown data

    In general, human ORFs have higher CPB scores than those of the viruses, and ORFs of RNA viruses have higher CPB scores than those of the DNA viruses.

    “In general, human ORFs have higher CPB scores than those of the viruses, and ORFs of RNA viruses have higher CPB scores than those of the DNA viruses.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The majority of human ORFs have a positive CPB value (the CPB average of the entire human ORFeome = 0.075).

    “The majority of human ORFs have a positive CPB value (the CPB average of the entire human ORFeome = 0.075).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The average CPB scores of RNA and DNA viruses were correlated with the genome size, ORFeome size, C+G content, and relative abundance of CpG dinucleotides in the viral ORFeome.

    “The average CPB scores of RNA (A) and DNA (B) viruses were correlated with the genome size, ORFeome size, C+G content, and relative abundance of CpG dinucleotides in the viral ORFeome.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    Arboviruses comprise a large and polyphyletic group of viruses that are transmitted between vertebrate hosts by hematophagous arthropod vectors.

    “Arboviruses comprise a large and polyphyletic group of viruses that are transmitted between vertebrate hosts by hematophagous arthropod vectors (Hanley and Weaver, 2008).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Hanley and Weaver, 2008 source

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

    Premisecitation

    CpG and TpA dinucleotides are significantly suppressed in the genomes of most RNA and small DNA vertebrate viruses.

    “For unknown reasons, CpG and TpA dinucleotides are also significantly suppressed in the genomes of most RNA and small DNA vertebrate viruses (Karlin et al., 1994).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Karlin et al., 1994

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationreasoning

    The slight underrepresentation of codon pairs that have high human CPSs in insect-specific flaviviruses is not a result of selection for codon pairs preferred in mosquitoes but a consequence of nonexistent selection against CpG dinucleotides in viral sequences.

    “Therefore, the slight underrepresentation of codon pairs that have high human CPSs in the insect-specific flaviviruses is not a result of selection for codon pairs that are preferred in the mosquitoes but, rather, a consequence of nonexistent selection against CpG dinucleotides in viral sequences.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The similarity in codon pair preferences of arboviruses can simply be explained by suppression of CpG dinucleotides, which concomitantly increases the number of codon pairs that are overrepresented in vertebrates.

    “Therefore, as in the human viruses, the similarity in codon pair preferences of arboviruses can simply be explained by suppression of CpG dinucleotides, which concomitantly increases the number of codon pairs that are overrepresented in vertebrates.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S4 (based). May combine two claims.

    Study design and conductnone given

    Dinucleotides XY with rXY < 0.78 (> 1.25) are considered of low (high) relative abundance because each rXY occurs with the probability of less than 0.001 for sufficiently long ($20 kb) random sequences.

    “As a conservative criterion, we considered dinucleotides XY with rXY < 0.78 (> 1.25) of low (high) relative abundance because each rXY occurs with the probability of less than 0.001 for sufficiently long ($20 kb) random sequences.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Avoidance of TpA reduces the risk of nonsense mutations and increases the stability of RNA.

    “Avoidance of TpA reduces the risk of nonsense mutations and increases the stability of RNA.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    CpG dinucleotides are underrepresented only in the nuclear DNA of plants and vertebrates as well as in the mitochondrial genomes of all metazoan species, be they invertebrates or vertebrates.

    “Although TpA dinucleotides are underrepresented in the genomes of almost all species, CpG dinucleotides are underrepresented only in the nuclear DNA of plants and vertebrates as well as in the mitochondrial genomes of all metazoan species, be they invertebrates or vertebrates (Cardon et al., 1994).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Cardon et al., 1994 source

  • May combine two claims.

    Interpretationreasoning

    Attenuation by SAVE is not caused by impaired gene decoding or protein production but, rather, by a different mechanism.

    “The logical implication of this conclusion is that that attenuation by SAVE is not caused by impaired gene decoding or protein production but, rather, by a different mechanism.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Attenuation of vertebrate viruses by SAVE is not caused by increasing non-preferred codon pairs but, rather, by increasing underrepresented dinucleotides.

    “This analysis seems to lend further support to our interpretation that attenuation of vertebrate viruses by SAVE is not caused by increasing non-preferred codon pairs but, rather, by increasing underrepresented dinucleotides.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S1 (asserted).

    Interpretationown data

    Codon pairs that contain CpG or TpA dinucleotides at the codon pair boundary might not be underrepresented in protein coding sequences because they are less fit for encoding proteins but, simply, because CpG and TpA dinucleotides show the highest level of suppression (relative abundance 0.48 and 0.56, respectively).

    “Based on our findings, we put forward the hypothesis that codon pairs that contain CpG or TpA dinucleotides at the codon pair boundary might not be underrepresented in protein coding sequences because they are less fit for encoding proteins but, simply, because CpG and TpA dinucleotides show the highest level of suppression (relative abundance 0.48 and 0.56, respectively).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductown data

    Random reshuffling removed codon pair preferences but preserved codon bias; i.e., all ORFs contained exactly the same codons.

    “Random reshuffling removed codon pair preferences but preserved codon bias; i.e., all ORFs contained exactly the same codons.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    All four RNA families contain species that do not require an arthropod for transmission, implicating that the arthropod-borne lifestyle evolved several times independently in different groups of viruses.

    “all four RNA families contain species that do not require an arthropod for transmission, implicating that the arthropod-borne lifestyle evolved several times independently in different groups of viruses (Hanley and Weaver, 2008).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Hanley and Weaver, 2008 source
38 of 38

  • The paper relies on this without support.

    Viruses replicate exclusively inside living cells and depend on the protein synthesis and chaperone machineries of the host.

    “Because viruses replicate exclusively inside of living cells and depend on the protein synthesis and chaperone machineries of the host, we speculated that the primary structure of viral genes might be shaped by the same forces that are responsible for the codon pair preferences in genes of their hosts and posited that viral preferences reflect those of their host(s).”

  • The paper relies on this without support.

    Random reshuffling normalizes the relative abundance of dinucleotides at the codon pair boundary.

    “Conversely, we expected that viruses with considerable sup-pression of CpG dinucleotides will also have a high DCPB (difference between the CPB of the wild-type and reshuffled ORFeome) because reshuffling normalizes the relative abundance of dinucleotides at the codon pair boundary, and the level of normalization depends on the length and codon bias of the ORF.”

  • The paper relies on this without support.

    The level of normalization of dinucleotide abundance at the codon pair boundary depends on the length and codon bias of the ORF.

    “Conversely, we expected that viruses with considerable sup-pression of CpG dinucleotides will also have a high DCPB (difference between the CPB of the wild-type and reshuffled ORFeome) because reshuffling normalizes the relative abundance of dinucleotides at the codon pair boundary, and the level of normalization depends on the length and codon bias of the ORF.”
3 of 3

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Codon pair preferences and dinucleotide frequencies are tightly linked.

    “As codon pair preferences and dinucleotide frequencies are tightly linked, disentangling the effects of two phenomena is exquisitely difficult (Kunec and Osterrieder, 2016;Tulloch et al., 2014).”

    From Mechanism of Virus Attenuation by Codon Pair Deoptimization (2020) · cites this paper as Kunec and Osterrieder, 2016

  • CPD of vertebrate viruses also increases the frequency of TpA/UpA dinucleotides in recoded sequences, albeit to a lesser degree than CpG.

    “In addition to CpG dinucleotides, CPD of vertebrate viruses also increases the frequency of TpA/UpA dinucleotides in recoded sequences, albeit to a lesser degree (Kunec and Osterrieder, 2016).”

    From Mechanism of Virus Attenuation by Codon Pair Deoptimization (2020) · cites this paper as Kunec and Osterrieder, 2016

Self-check

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

  • Flaviviridae subgroup counts exceed the stated family total

    Minor

    The stated Flaviviridae subgroups contain 55 and eight viruses, totaling 63, but the paper reports 62 Flaviviridae viruses in its total of 159.

    Reported 62 · recomputed 63

1 of 1

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Authors
Kunec, D., & Osterrieder, N.
Affiliations
Freie Universität Berlin (DE)
Corresponding author
Osterrieder, Nikolaus
ORCID
Osterrieder, Nikolaus
Venue
Cell Reports
Publisher
Elsevier BV
Published
2016-01
Volume
14
Issue
1
Pages
55-67
ISSN
2211-1247 (ISSN-L)
DOI
10.1016/j.celrep.2015.12.011
OpenAlex
W2282841281
Semantic Scholar
47bbe0e84c5595364614e5adf03581cdb002ff90
Cited by
159
References
32
Citations by year
2026: 8 · 2025: 18 · 2024: 15 · 2023: 16 · 2022: 11 · 2021: 38 · 2020: 15 · 2019: 14 · 2018: 12 · 2017: 8 · 2016: 4
FWCI
3.09
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Reports (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Refubium (Universitätsbibliothek der Freien Universität Berlin) (submittedVersion, cc-by-nc-nd)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Keywords
codon pair bias, viral attenuation, arboviruses
MeSH terms
Animals, Arboviruses, Codon, Humans, Insecta, Models, Genetic, Species Specificity

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 2026-10-12.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-12.

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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