Related Experiment Video
Updated: Dec 3, 2025
18:10
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
29.9K
Dissimilar Conservation Pattern in Hepatitis C Virus Mutant Spectra, Consensus Sequences, and Data Banks
Carlos García-Crespo1, María Eugenia Soria1,2, Isabel Gallego1,3
1Department of Interactions with the environment, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
Journal of Clinical Medicine
|October 30, 2020
Summary
Viral quasispecies dynamics significantly impact virus evolution, challenging assumptions about sequence conservation. Short-term residue conservation differs from long-term data, affecting universal antiviral design.
Area of Science:
- Virology
- Evolutionary Biology
- Computational Biology
Background:
- Quasispecies dynamics are crucial for viral evolution but their influence on long-term diversification remains unclear.
- Current strategies for universal antiviral design rely on assumed long-term sequence conservation, potentially overlooking short-term variations.
- The relationship between intra-host variation in quasispecies and observed consensus or database sequences is not well understood.
Purpose of the Study:
- To investigate the influence of quasispecies dynamics on viral diversification and sequence conservation.
- To compare intra-host nucleotide and amino acid variation within quasispecies against consensus sequences and database alignments.
- To evaluate the adequacy of current assumptions about viral sequence conservation for designing universal antiviral agents.
Main Methods:
- Analysis of mutant frequencies from hepatitis C virus (HCV) populations in cell culture and patients.
- Comparison of residue conservation in mutant spectra with conservation in consensus sequences and the Los Alamos HCV database.
- Utilizing genome conservation and dynamics simulations.
Main Results:
- Nucleotide and amino acid conservation in consensus sequences and databases did not align with residue conservation observed in mutant spectra.
- Quasispecies dynamics exhibit relaxed mutational restrictions, leading to higher short-term than long-term evolutionary rates.
- Residue invariance in databases is an insufficient basis for designing universal viral ligands.
Conclusions:
- Viral sequence conservation is a more dynamic concept than previously assumed, influenced by short-term quasispecies dynamics.
- Current approaches to designing universal vaccines and antivirals may be limited by not fully accounting for quasispecies-driven variations.
- Future antiviral strategies should consider the impact of quasispecies dynamics on viral evolution for improved efficacy.
Related Concept Videos
02:51Multi-species Conserved Sequences
4.5K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.5K
01:49Conserved Binding Sites
4.9K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.9K
00:36Viral Mutations
38.4K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
38.4K
02:26Conservation of Protein Domains Over Different Proteins
13.8K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
13.8K
02:26Conservation of Protein Domains
3.7K
3.7K
02:54Evolutionary Relationships through Genome Comparisons
6.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.7K