Related Experiment Video
Updated: Jul 23, 2025
07:15
Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
Published on: January 16, 2019
11.0K
Paired associated SARS-CoV-2 spike variable positions: a network analysis approach to emerging variants
Yiannis Manoussopoulos1,2, Cleo Anastassopoulou1, John P A Ioannidis3,4,5,6
1Department of Microbiology, Medical School, National and Kapodistrian University of Athens , Athens, Greece.
Msystems
|July 11, 2023
Summary
Amino acid changes in the SARS-CoV-2 spike protein form complex networks, revealing evolutionary relationships between variants. This analysis helps understand virus evolution and develop control strategies.
Area of Science:
- Virology
- Computational Biology
- Genetics
Background:
- Amino acid variations at specific protein positions can be correlated, impacting protein structure and function.
- Understanding these associations is crucial for tracking virus evolution and identifying key mutations.
Purpose of the Study:
- To investigate the associations between variable amino acid positions in the SARS-CoV-2 spike protein.
- To analyze the temporal evolution and complexity of these associations using network analysis.
Main Methods:
- Exact tests of independence were applied to R x C contingency tables for SARS-CoV-2 spike protein sequences from Greece.
- Network analysis was used to visualize positional associations, with associated positions as links and positions as nodes.
- Modular analysis identified cliques and communities within the network.
Main Results:
- A complex, non-random network of 69 nodes and 252 links was identified, showing a temporal increase in positional differences and associations.
- Overconnected nodes corresponded to highly adapted variant positions, suggesting a link between network degree and functional importance.
- The analysis revealed epistatic associations among circulating variants, including Alpha, Beta, B.1.1.318, and Delta.
Conclusions:
- The study presents a novel method for understanding epistatic relationships in viral proteins.
- The findings offer insights into virus evolution, variant formation, and potential applications in virus control strategies.
- The network approach links structural network aspects to amino acid combinations, aiding virus epidemiology understanding.
More Related Videos
Related Concept Videos
01:05Single Nucleotide Polymorphisms-SNPs
15.3K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.3K
00:36Viral Mutations
32.5K
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...
32.5K
01:26Size and Structure of Viral Genomes
65
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
65
01:11Variability: Analysis
158
Measures of variability are statistical metrics that reveal the dispersion pattern within a dataset. They are pivotal in biostatistics, providing insights into the heterogeneity within health and biological data. Variability signifies the degree to which data points diverge from one another, helping researchers understand the potential range of values and associated uncertainty within the data.
The range is a simple measure of variability, indicating the difference between the highest and...
The range is a simple measure of variability, indicating the difference between the highest and...
158
02:26Comparing Copy Number Variations and SNPs
17.8K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.8K
00:57Viral Recombination
23.5K
Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
23.5K