Esteban Domingo’s research while affiliated with Biomedical Research Network Center for Liver and Digestive Diseases and other places

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Publications (531)


A general and biomedical perspective of viral quasispecies
  • Article
  • Full-text available

December 2024

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15 Reads

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1 Citation

RNA

Esteban Domingo

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Brenda Martinez-Gonzalez

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Pilar Somovilla

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[...]

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Viral quasispecies refers to the complex and dynamic mutant distributions (also termed mutant spectra, clouds or swarms) that arise as a result of high error rates during RNA genome replication. The mutant spectrum of individual RNA virus populations is modified by continuous generation of variant genomes, competition and interactions among them, environmental influences, bottleneck events, and bloc transmission of viral particles. Quasispecies dynamics provides a new perspective on how viruses adapt, evolve and cause disease, and sheds light on strategies to combat them. Molecular flexibility, together with ample opportunity of mutant cloud traffic in our global world, are key ingredients of viral disease emergences, as exemplified by the recent COVID-19 pandemic. In the present article we present a brief overview of the molecular basis of mutant swarm formation and dynamics, and how the latter relates to viral disease and epidemic spread. We outline future challenges derived of the highly diverse cellular world in which viruses are necessarily installed.

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Fig. 3 | Virus genotypic complexity: from the hypercube to the ultracube. a Classical view of quasispecies evolution in a hypercube for 4-bit sequences. Each node of the network connects two genotypes via a single-point mutation. Sequences evolve to first neighbors by single-bit (nucleotide) substitutions during replication. Homologous recombination may allow genotypes to jump to further neighbors (blue arrow). b Example of a sequence space for binary genomes of length five considering deletions (blue dashed arrows) and insertions (green solid arrows)
Quasispecies theory and emerging viruses: challenges and applications

November 2024

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73 Reads

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2 Citations

npj Viruses


Figure 1. Milestones in quasispecies theory in Virology. Time arrow showing some key achievements in the development of quasispecies theory for viruses since its birth in 1971. The colors indicate whether the results have been achieved from theoretical/computational research (blue), from experimental data (violet), and/or from data from infected patients (green). CChMVd: Chrysanthemum chlorotic mottle viroid; CSVd: Chrysanthemum stunt viroid; FMDV: foot-andmouth disease virus; HCV: hepatitis C virus; HIV-1: human immunodeficiency virus type-1; LCMV: lymphocytic choriomeningitis virus; VSV: vesicular stomatitis virus; PV: poliovirus.
Figure 2. Simulating the evolutionary dynamics of digital quasispecies in silico. (a) Single-peak fitness landscape (illustrated with a 3-bits hypercube).The size of the balls is proportional to the genotypes' fitness. The quasispecies population plots show the error threshold for the single-peak fitness landscape for geometric (b) and stamping machine (c) replication. (d) Fitness landscape with antagonistic epistasis also for 3-bit genomes where the effects of mutations are less severe in combination than individually. Here we also display the error threshold for e for geometric (e) and stamping machine (f) replication modes. All the diagrams show the stationary populations of the master sequence (000, thick lines) and the pool of mutants (with 1, 2 or 3 mutations, thin lines) averaged over 200 replicas at increasing the per-bit mutation probability. See Sardanyés et al. (2009) for further details.
Figure 3. Virus genotypic complexity: from the hypercube to the ultracube. (a) Classical view of quasispecies evolution in a hypercube for 4-bit sequences. Each node of the network connects two genotypes via a single-point mutation. Sequences evolve to first neighbors by single-bit (nucleotide) substitutions during replication. Homologous recombination may allow genotypes to jump to further neighbors (blue arrow). (b) Example of a sequence space for binary genomes of length five considering deletions (blue dashed arrows) and insertions (green solid arrows) during replication. These processes produce mutants and connect hypercubes of different dimensions, giving rise to a more complex sequence space that we label ultracube and which can be conceived as a multiplex network. For clarity, we do not display all the nodes but exemplify some processes of deletion and insertion, which give rise to a set of connected hypercubes of dimensions 5 (gray), 4 (black), 3 (blue), 2 (red),
Quasispecies Theory and Emerging Viruses: Challenges and Applications

September 2024

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74 Reads

The dawn of quasispecies theory revolutionized our understanding of viral evolution and pathogenesis. This theory conceptualises viruses as dynamic populations of closely related but genetically diverse variants that constantly mutate and adapt to environmental pressures. Quasispecies dynamics govern key aspects of virus-host interactions, such as adaptive evolution, immune evasion, drug resistance, and host tropism. In this article, we discuss the fundamental role of quasispecies theory in elucidating viral fitness landscapes, shaping antiviral strategies, and predicting viral emergence and evolution. We provide a concise overview of the original quasispecies model and its latest advancements, which enable the study of the connection between viral dynamics and the significant genetic diversity exhibited by viruses. We then point out some key features of virus dynamics that need to be incorporated into quasispecies theory. We continue with examples of convergence between theory and real viruses by discussing theoretical results supported by RNA virus data and vice versa. Next, we discuss the need to extend the concept of sequence space beyond the classical hypercube towards more complex, multidimensional connected sequence spaces that we have called ultracubes. Finally, we highlight the necessity of developing multi-scale models to understand how viral evolutionary dynamics within a host can affect epidemiological patterns. We also examine the limitations of quasispecies theory in predicting virus evolution and emergence.


Scheme of viral quasispecies. Each line represents a viral genome, and the symbols on the lines show point mutations. The set corresponds to the population of a RNA virus isolated from a single patient or cell culture.
Artistic recreation of the rhizomatic quasispecies chimera. The illustration depicts the sequence space occupied by a viral quasispecies, where sequences are not organized like a branching tree but rather as numerous rhizomatic extensions akin to that of ginger or potato terrestrial plant parts.
Construction of a sequence space using two digits, X and Y. Each sequence is positioned at a point in space, at a distance from other sequences given by the difference between the digits (i.e., number of point mutations separating both sequences). For example, a difference of 1 mutation results in a separation of 1 cm, while 2 mutations lead to a 2 cm separation, and so on. As the sequence length increases, a shape known as a hypercube is formed. ⁴⁶
Modified from
Artistic rhizomatic evolutionary map. Representation illustrating the multiple potential evolutionary trajectories between different positions in a complex sequence space for an evolving viral quasispecies depicted by faint gray lines. Three potential pathways between specific points A and B are marked with thick white lines.
Adapting the rhizome concept to an extended definition of viral quasispecies and the implications for molecular evolution

August 2024

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93 Reads

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3 Citations

The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from “symbiotic” relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain.


Fig. 1. Location and functional implication of the selected amino acid substitutions in the nsp12 protein of SARS-CoV-2. (A) The Left panel shows the location of the amino acid substitutions studied here (P323L, V330S, V341S, L372F, L372P, V373A, D499G, L527H, V560A, and M668V) in the three-dimensional structure of nsp12. The structure used as reference is that of the nsp12-nsp8-nsp7-RNA complex (PDB: 6YYT), depicted as a cartoon representation with nsp12 colored by domains (NiRAN in gray, interface in white, and the RdRp domain in dark green, green, and dark yellow for the fingers, palm, and thumb subdomains, respectively). The cofactors nsp8 and nsp7 are colored in orange and cyan, respectively, and the RNA is depicted in dark blue. Substituted amino acids are shown as red spheres and explicitly labeled. The Right panel shows a close-up view, highlighting the positions of the amino acid substitutions in the nsp12-nsp8 F contact interface (side chains in red sticks). (B) Detailed views of the interactions around the mutated positions. Side chains of substituted amino acids and neighboring residues are shown as sticks in different colors (white for residues in the nsp12 interface domain, green for residues in the nsp12 fingers, and orange for nsp8), and explicitly labeled. Both wild type and mutated side chains are seen in the different panels. The Upper Left panel shows the P323L substitution placed in the nsp12 interface (depicted in white for proline and in red for the mutated leucine). The Upper Right panel shows substitutions V330S and V341S, within the nsp12 interface (white for the valine side chains and red for the mutated serine residues). The Bottom Left panel shows L372F and L372P side chain substitutions, within de nsp12 fingers (side chain depicted in green for leucine, red for phenylalanine, and yellow for proline). The Bottom Right panel shows V373A and L527H substitutions, also within the nsp12 fingers (green for valine and leucine side chains and red for alanine and histidine).
Fig. 2. Location and functional implication of the SARS-CoV-2 nsp12-nsp8-nsp7 complex, harboring amino acid substitutions in nsp8, specially designed to weaken the nsp12-nsp8 interaction interface. (A) Mapping of the nsp8-R111A/D112A double mutant. The central image shows a cartoon representation of the nsp12-nsp7-nsp8-RNA complex colored as in Fig. 1. In this representation the first 76 amino acids of nsp8 have been removed to show a model of the nsp8(Δ1-76) construct. The position of the double mutation R111A/D112A is shown as red spheres in the two nsp8 molecules of the complex. The two Insets at the Left and Right sides of the central image show close-up views of the environment and interactions of the replaced residues in nsp8 F (Left side Insets) and nsp8 T (Right side Insets). Side chains of the original (Upper Insets), mutated residues (Lower Insets), and interacting amino acids (within a 5 Å radius) are shown as sticks in different colors, and explicitly labeled. (B-D) Comparative in vitro RNA synthesis activities of the SARS-CoV-2 nsp12-nsp7-nsp8 WT and mutants nsp8(R111A/D112A) and nsp8(Δ1-76). Reactions were performed at 33 °C, and activities were measured in gel-based nonradioactive primer extension assays. (B) P/T duplexes used in the assays, with the arrow indicating the location and direction of primer extension. (C) SDS-PAGE analysis of the purified SARS-CoV-2 RdRp WT and mutant complexes, employed in the primer-extension assays. (D) Primer-extension activities of the different RdRp complexes on a representative PAGE, 18% polyacrylamide, 7M urea/Tris-Borate-EDTA (TBE). The Bottom panels show the relative efficiencies of full-length RNA synthesis by the different RdRp mutants compared to the WT. SDs from three independent experiments are shown. Statistical significance of the differences was calculated by one-way ANOVA followed by Dunnett's multiple comparison test (SI Appendix, Table S1 in https://saco.csic.es/index.php/s/Xp33GCyPMp8Lif7).
Fig. 3. Comparative in vitro RNA synthesis activities of the SARS-CoV-2 nsp12-nsp7-nsp8 complex, WT and nsp12 mutants harboring amino acid substitutions in the nsp12-nsp8 F interface. Activities were measured in gel-based nonradioactive primer extension assays. (A) The Top panel shows the P/T 20/28 nt RNA used in the assays. The Middle panel shows the primer-extension activities of the different RdRp complexes on a representative PAGE, 18% polyacrylamide, and 7M urea/TBE. Reactions were performed at 33 °C, and samples were collected at 10 min intervals. The Bottom panel shows the relative efficiencies of fulllength RNA synthesis by the different RdRp mutants compared to the WT. SDs from three independent experiments are shown. Statistical significance of the differences was calculated by one-way ANOVA followed by Dunnett's multiple comparison test (see also SI Appendix, Table S1 in https://saco.csic.es/index.php/s/ Xp33GCyPMp8Lif7). (B) SDS-PAGE analysis of the purified SARS-CoV-2 RdRp WT and mutant complexes, employed in the primer-extension assays. (C) The Top panel shows the P/T 10/40 RNA used in the assays, with the arrow indicating the location and direction of primer extension. The Right panel shows the primerextension activities of the different RdRp complexes on a representative PAGE, performed as in A. The Left panel shows the relative efficiencies of full-length RNA synthesis by the different RdRp mutants compared to the WT. SDs from three independent experiments are shown. Statistical significances are calculated as in A (SI Appendix, Table S1 in https://saco.csic.es/index.php/s/Xp33GCyPMp8Lif7).
Point mutations at specific sites of the nsp12-nsp8 interface dramatically affect the RNA polymerization activity of SARS-CoV-2

July 2024

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34 Reads

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1 Citation

Proceedings of the National Academy of Sciences

In a recent characterization of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variability present in 30 diagnostic samples from patients of the first COVID-19 pandemic wave, 41 amino acid substitutions were documented in the RNA-dependent RNA polymerase (RdRp) nsp12. Eight substitutions were selected in this work to determine whether they had an impact on the RdRp activity of the SARS-CoV-2 nsp12–nsp8–nsp7 replication complex. Three of these substitutions were found around the polymerase central cavity, in the template entry channel (D499G and M668V), and within the motif B (V560A), and they showed polymerization rates similar to the wild type RdRp. The remaining five mutations (P323L, L372F, L372P, V373A, and L527H) were placed near the nsp12–nsp8 F contact surface; residues L372, V373, and L527 participated in a large hydrophobic cluster involving contacts between two helices in the nsp12 fingers and the long α-helix of nsp8 F . The presence of any of these five amino acid substitutions resulted in important alterations in the RNA polymerization activity. Comparative primer elongation assays showed different behavior depending on the hydrophobicity of their side chains. The substitution of L by the bulkier F side chain at position 372 slightly promoted RdRp activity. However, this activity was dramatically reduced with the L372P, and L527H mutations, and to a lesser extent with V373A, all of which weaken the hydrophobic interactions within the cluster. Additional mutations, specifically designed to disrupt the nsp12–nsp8 F interactions (nsp12-V330S, nsp12-V341S, and nsp8-R111A/D112A), also resulted in an impaired RdRp activity, further illustrating the importance of this contact interface in the regulation of RNA synthesis.


Figure 2. Simulating the evolutionary dynamics of digital quasispecies in silico. (a) Error threshold (orange lines) in the single-peak fitness landscape (illustrated with a 3-bits hypercube) for geometric and stamping machine replication modes. The size of the balls is proportional to the genotype's fitness. (b) Fitness landscape with antagonistic epistasis where the effects of mutations are less severe in combination than individually. Here we also display the error threshold for this landscape for geometric and stamping machine replication. All the diagrams show the stationary distributions of the master sequence (000, thick lines) and the pool of mutants (thin lines) averaged over 200 replicas. See Sardanyés et al. (2009) for further details.
Figure 3. Virus genotypic complexity: from the hypercube to the ultracube. (a) Classical view of quasispecies evolution in a hypercube schematized with 3-bits sequences. Each node of the network connects two genotypes via a single-point mutation. Sequences evolve to first neighbours by single bit (nucleotide) substitutions during replication. Homologous recombination may allow genotypes to jump to further neighbors (blue arrow). (b) Example of a sequence space for binary genomes of length five considering deletions (blue dashed arrows) and insertions (green solid arrows) during replication. These processes produce mutants and connect hypercubes of different dimensions, giving rise to a more complex sequence space that we label ultracube and which can be conceived as a multiplex network. For clarity, we do not display all the nodes but exemplify some processes of deletion and insertion, which give rise to a set of connected hypercubes of dimension 5 (gray), 4 (black), 3 (blue), 2 (red), and 1 (orange). (c) Schematic diagram of connected hypercubes of different dimensions illustrated schematically as multilayered networks.
Quasispecies Theory and Emerging Viruses: Challenges and Applications

July 2024

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112 Reads

The dawn of quasispecies theory revolutionized our understanding of viral evolution and pathogenesis. This theory conceptualises viruses as dynamic populations of closely related but genetically diverse variants that constantly mutate and adapt to environmental pressures. Quasispecies dynamics govern key aspects of virus-host interactions, such as adaptive evolution, immune evasion, drug resistance, and host tropism. In this article, we discuss the fundamental role of quasispecies theory in elucidating viral fitness landscapes, shaping antiviral strategies, and predicting viral emergence and evolution. We provide a concise overview of the original quasispecies model and its latest advancements, which enable the study of the connection between viral dynamics and the significant genetic diversity exhibited by viruses. We then point out some key features of virus dynamics that need to be incorporated into quasispecies theory. We continue with examples of convergence between theory and real viruses by discussing theoretical results supported by RNA virus data and vice versa. Next, we discuss the need to extend the concept of sequence space beyond the classical hypercube towards more complex, multidimensional connected sequence spaces that we have called ultracubes. Finally, we highlight the necessity of developing multi-scale models to understand how viral evolutionary dynamics within a host can affect epidemiological patterns. We also examine the limitations of quasispecies theory in predicting virus evolution and emergence.



Synergism between remdesivir and ribavirin leads to SARS‐CoV‐2 extinction in cell culture

April 2024

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64 Reads

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7 Citations

Background and Purpose There is a need for effective anti‐COVID‐19 treatments, mainly for individuals at risk of severe disease such as the elderly and the immunosuppressed. Drug repositioning has proved effective in identifying drugs that can find a new application for the control of coronavirus disease, in particular COVID‐19. The purpose of the present study was to find synergistic antiviral combinations for COVID‐19 based on lethal mutagenesis. Experimental Approach The effect of combinations of remdesivir and ribavirin on the infectivity of SARS‐CoV‐2 in cell culture has been tested. Viral populations were monitored by ultra‐deep sequencing, and the decrease of infectivity as a result of the treatment was measured. Key Results Remdesivir and ribavirin exerted a synergistic inhibitory activity against SARS‐CoV‐2, quantified both by CompuSyn (Chou‐Talalay method) and Synergy Finder (ZIP‐score model). In serial passage experiments, virus extinction was readily achieved with remdesivir‐ribavirin combinations at concentrations well below their cytotoxic 50 value, but not with the drugs used individually. Deep sequencing of treated viral populations showed that remdesivir, ribavirin, and their combinations evoked significant increases of the number of viral mutations and haplotypes, as well as modification of diversity indices that characterize viral quasi‐species. Conclusion and Implications SARS‐CoV‐2 extinction can be achieved by synergistic combination treatments based on lethal mutagenesis. In addition, the results offer prospects of triple drug treatments for effective SARS‐CoV‐2 suppression.


SARS-CoV-2 genomic sequences, clade identification, and epidemiological context. (A) Representation of the SARS-CoV-2 genome, with encoded proteins (top), followed by the consensus genomic sequence of the isolates from the 11 patients analyzed in the present work. Sequences were obtained by COVIDSeq. The patient code is given on the left, and the clade assigned to each isolate is written on the right. Mutations relative to the sequence of the Wuhan-Hu-1 genome (NCBI sequence NC_045512.2) are indicated as short vertical lines; mutations that served for clade identification are in red color, and their location in the genome is depicted in the boxes below the alignment. Other mutations are depicted in blue. Several mutations used for clade identification are also present in virus that belong to a different clade; these mutations are drawn as blue lines. All mutations (and corresponding amino acid substitutions) and deletions are listed in Supplementary Table S3. (B) Schematic representation of the consensus genomic sequence of the laboratory populations derived from SARS-CoV-2 USA-WA1/2020 analyzed in the present study. The absence or presence of drug (Rdv, remdesivir; Rib, ribavirin) and its concentration is indicated on the left. Mutations relative to the Wuhan-Hu-1 genome (NCBI sequence NC_045512.2) are indicated as short vertical blue lines; their position in the genome is given in the box below the alignment. Mutations A22206G and C23525T have been used to define VOCs (https://clades.nextstrain.org). Mutations relative to the Wuhan-Hu-1 isolate that were present in the parental USA-WA1/2020 are not included. (C) Temporal position of the SARS-CoV-2 analyzed in the present study, and of the clade-discordant lineages identified in their mutant spectrum, that compiled with the inclusion criteria. Symbol code is given in the upper box, and epidemiological time is depicted at the bottom. Each asterisk identifies a discordant clade and lineage, that may be represent several times in our analysis (see text).
Heat map of all clade-discordant amino acid substitutions and deletions found in the S-coding region of virus from the 11 patients analyzed in the present study. The top box gives the color code for the frequency of each substitution or deletion (Δ) (indicated between the two grid panels); INS:214EPE means an insertion of amino acids EPE in position 214. Patient code is given on the left of the top panel. The bottom grid panel depicts as filled squares the substitutions used to define lineages and sub-lineages (according to https://clades.nextstrain.org) (region covered by A1–A6 amplicons of S-coding region). The subset of clade discordant amino acids that meet the inclusion criteria detailed in the text are listed in Table 2.
Heat map of all clade-discordant amino acid substitutions found in the S-coding region of virus from SARS-CoV-2 USA-WA1/2020 in absence or presence of drug (Rdv, remdesivir; Rib, ribavirin). The top box gives the color code for the frequency of each substitution (indicated between the two grid panels); no deletions were identified in the mutant spectrum of these populations. Drug concentration is given on the left. The bottom grid panel depicts as filled squares the substitutions used to define lineages and sub-lineages (according to https://clades.nextstrain.org) (region covered by A5 and A6 amplicons of S-coding region). The subset of clade discordant amino acids that meet the inclusion criteria detailed in the text are listed in Table 3. All passage series in the absence and presence of drugs, and all titrations for virus quantifications were carried out in triplicate (n = 3) (García-Crespo et al., 2024). Differences in infectious progeny production between absence and presence of drugs were statistically significant for Rdv 10 μM, Rib 150 μM, and for the combination of Rdv 5 μM + Rib 100 μM; Kruskal-Wallis with Dunn’s multiple comparison test.
Demographic data of patients and classification of the consensus sequence of the samples analyzed.
Amino acids in the spike SARS-CoV-2 mutant spectra that are typical of a different viral clade a .
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation?

March 2024

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21 Reads

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3 Citations

Introduction SARS-CoV-2 isolates of a given clade may contain low frequency genomes that encode amino acids or deletions which are typical of a different clade. Methods Here we use high resolution ultra-deep sequencing to analyze SARS-CoV-2 mutant spectra. Results In 6 out of 11 SARS-CoV-2 isolates from COVID-19 patients, the mutant spectrum of the spike (S)-coding region included two or more amino acids or deletions, that correspond to discordant viral clades. A similar observation is reported for laboratory populations of SARS-CoV-2 USA-WA1/2020, following a cell culture infection in the presence of remdesivir, ribavirin or their combinations. Moreover, some of the clade-discordant genome residues are found in the same haplotype within an amplicon. Discussion We evaluate possible interpretations of these findings, and reviewed precedents for rapid selection of genomes with multiple mutations in RNA viruses. These considerations suggest that intra-host evolution may be sufficient to generate minority sequences which are closely related to sequences typical of other clades. The results provide a model for the origin of variants of concern during epidemic spread─in particular Omicron lineages─that does not require prolonged infection, involvement of immunocompromised individuals, or participation of intermediate, non-human hosts.



Citations (53)


... In particular, substitutions F396L, S384P, L372P, V405A, and D545G are located close to the contact interface nsp12-nsp8 F (Fig. 3A). We have previously shown that amino acid changes in this region, and in particular those that disrupted direct nsp12-nsp8 F interactions or that weakened the hydrophobic contacts near the nsp12-nsp8 F interface, including L372P, significantly reduced the RdRp activity of nsp12 (40). Additional nsp12 substitutions, whose position in the replication complex suggested that they could lead to alterations in RdRp activity, include T409A, V410A, D445G, and F441L located at the fingers close to the thumb subdomain, near the nsp12-nsp7 interface (Fig. 3A), and K430R, S433G, F419L, D421G, F422L, V424A, and S425P, also within the fingers, close to the thumb subdomain and near the nsp12-nsp8 T interface (Fig. 3A). ...

Reference:

Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps
Point mutations at specific sites of the nsp12-nsp8 interface dramatically affect the RNA polymerization activity of SARS-CoV-2

Proceedings of the National Academy of Sciences

... Therapies based on the error catastrophe concept have been brought forward 81,115 . Maintenance of inheritable genetic information conditioned to a limitation in error introduction has also been documented with catalytic ribozymes 116 . ...

Synergism between remdesivir and ribavirin leads to SARS‐CoV‐2 extinction in cell culture

... Bernadeta Dadonaite et al. [14] employed pseudovirus deep mutational scanning to assess how various mutations in the spike protein affect its binding affinity with ACE2, providing insights into potential future viral evolution. Soledad Delgado et al. [15] used self-organized maps to examine the diversification of haplotypes in infected patients, seeking potential strains that may emerge in the future. ...

Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps

Proceedings of the National Academy of Sciences

... The presence of a mutant spectrum was initially demonstrated through clonal analyses of RNA bacteriophage Qβ populations in an infection initated with a single viral particle [21]. Since this finding, viral quasispecies have been identified and quantified in multitude of viruses such as foot-and-mouth disease virus [17,51], vesicular stomatitis virus [26,27], hepatitis viruses [14,33,34,39], or SARS-CoV-2 [19], to cite some examples. ...

Puzzles, challenges, and information reservoir of SARS-CoV-2 quasispecies

... With every infection event the cellular organism is affected by RNA networks, that are sometimes exapted and co-opted for cellular needs (Koonin and Dolja 2013). RNA stem-loop groups represent an unmanageable quantity of sophisticated regulatory networks (Clark et al. 2013;Mattick and Amaral 2023;Ariza-Mateos et al. 2023). These groups are crucial in the following functions: ...

Natural languages and RNA virus evolution

... The agent for hepatitis delta only infects the human liver if co-infected with the hepatitis B virus 12 , and the Sputnik virophage behaves as a parasite of the mimivirus, a protist giant virus 7 . Also, after a virus infection, the reactivation of ancient molecular activities or configurations of the cell that are typically not expressed in uninfected cells may represent another type of relation within the cell 13 . ...

Viruses as archaeological tools for uncovering ancient molecular relationships

... One driving force for such coevolution can be the affinity between the involved interaction partners [31]. For RNA, its poor structural predictability hampers a reliable judgement of preservation or modulation of RNA element structure upon changes in sequence throughout evolution [32,33], and it requires sophisticated bioinformatic approaches to also take co-variation into account [34]. Co-evolution of cis-trans pairs has led to specialized binding interfaces [35], implying beneficial functions for the organism, and was found to occur even over comparably short time periods [36]. ...

Archaeological approaches to RNA virus evolution

... In the present study, we evaluated the expression profile of miRNAs encapsulated in EVs because EVs are relatively stable in the bloodstream, whereas miRNAs have a short half-life in circulation [6]. However, discrepancies in EV-miRNA and EV proteomic patterns are frequent among studies, which may be partly due to differences in the sample type from which EVs are derived (i.e., plasma or serum) and methodological differences in EV isolation, miRNA profiling, and expression normalization [20][21][22][23]. It is important to develop reproducible methods for isolating EVs from biological samples with high yield and purity. ...

Comparison of Extracellular Vesicle Isolation Methods for miRNA Sequencing

International Journal of Molecular Sciences

... The histone acetylation and host acetyltransferases are also important factors in various DNA virus infections (29)(30)(31)(32)(33). The entering viral DNAs in host cells are wrapped around host histones and densely compacted into repressive heterochromatin, which is not accessible to the transcription machinery, resulting in the silencing of viral DNA (34,35). ...

Hepatitis C virus fitness can influence the extent of infection-mediated epigenetic modifications in the host cells

... The latter scenario has been suggested for molnupiravir treatments as the possible origin of SARS-CoV-2 mutants when the drug is administered to immunocompromised patients that exhibited a debilitated immune response, thus allowing large replicating viral loads 126,127 . Virological, biochemical and structural studies suggest that lethal mutagenesis is, at least in part, the mechanism of some antiviral agents currently used to treat COVID-19 115,[128][129][130] . ...

Atypical Mutational Spectrum of SARS-CoV-2 Replicating in the Presence of Ribavirin