Related Experiment Video
Updated: Aug 30, 2025
18:10
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
29.7K
Sequence Similarity Network Analysis Provides Insight into the Temporal and Geographical Distribution of Mutations in
Shruti S Patil1, Helen N Catanese1, Kelly A Brayton1,2
1School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA.
Viruses
|August 26, 2022
Summary
This study analyzed SARS-CoV-2 spike protein mutations in the US, revealing transmission patterns. Directed Weighted All Nearest Neighbors (DiWANN) networks offer superior insights into viral evolution and spread.
Area of Science:
- Virology
- Computational Biology
- Epidemiology
Background:
- Severe acute respiratory syndrome-related coronavirus (SARS-CoV-2) continues to spread globally, driven by rapid mutations.
- Mutations in the spike (S) protein are critical for viral stability, transmission, and adaptability, necessitating detailed evolutionary analysis.
Purpose of the Study:
- To investigate the temporal and geographical distribution of SARS-CoV-2 S protein mutations across the US.
- To analyze mutation profiles of concerning variants and understand their transmission dynamics.
- To evaluate the effectiveness of computational network approaches for tracking viral evolution.
Main Methods:
- Multiple sequence alignment to identify key mutations and mutable regions in S protein sequences.
- Sequence similarity networks, specifically Directed Weighted All Nearest Neighbors (DiWANN), to analyze mutation profiles and transmission.
- Geographical mapping visualizations to track variant distribution and spread over 19 months (2020-2021).
Main Results:
- Identified prominent mutations and highly mutable regions within the SARS-CoV-2 S protein.
- DiWANN networks provided superior insights into variant transmission compared to traditional BLAST-based methods.
- Visualizations accurately reflected reported viral transmission statistics for the studied periods.
Conclusions:
- The study presents a robust computational framework for analyzing SARS-CoV-2 S protein mutation transmission.
- DiWANN networks offer a powerful tool for understanding viral evolution and informing public health strategies.
- This approach can be extended to study mutations in other viral proteins and pathogens.
Related Concept Videos
00:36Viral Mutations
32.8K
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...
32.8K
01:05Single Nucleotide Polymorphisms-SNPs
15.7K
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,...
15.7K
00:57Viral Recombination
23.7K
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.
23.7K
02:54Evolutionary Relationships through Genome Comparisons
6.1K
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...
6.1K
02:05Gene Evolution - Fast or Slow?
7.3K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.3K