Related Experiment Video
Updated: Mar 21, 2026
06:08
Author Spotlight: A Pseudotype Virus System for Assessing Omicron Subvariants and Neutralizing Antibodies in SARS-CoV-2 Research
Published on: September 8, 2023
1.8K
Genomic evolution of SARS-CoV-2 delta variants pre- and post-omicron emergence using alignment-free machine learning
Sathish Sankar1, Kaushika Anandharaman2, Pradeesh Selvam2
1Department of Microbiology, Center for Infectious Diseases, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India.
Plos One
|March 19, 2026
Summary
The SARS-CoV-2 Delta variant evolved after Omicron emerged, showing new genomic changes. Alignment-free methods detected these subtle mutations, improving our understanding of viral evolution and surveillance.
Area of Science:
- Genomics
- Virology
- Computational Biology
Background:
- The SARS-CoV-2 Delta variant (B.1.617.2) exhibited high transmissibility and immune evasion.
- Subsequent genomic alterations in the Delta variant occurred post-Omicron (B.1.1.529) emergence.
Purpose of the Study:
- To investigate genomic differences in SARS-CoV-2 Delta variant spike genes before and after the Omicron variant emerged.
- To evaluate the efficacy of alignment-free methods combined with machine learning for variant analysis.
Main Methods:
- Analysis of 190 SARS-CoV-2 Delta variant spike gene sequences using an alignment-free approach.
- K-mer-based feature extraction coupled with machine learning models (CNN, K-means, Random Forest).
Main Results:
- The Random Forest model achieved 93% accuracy in distinguishing Delta variant groups.
- Comparative analysis identified 157 persistent and 4 vanished mutations in the post-Omicron Delta group.
- Cluster analysis revealed stable yet evolving genomic patterns over time.
Conclusions:
- Alignment-free methods are advantageous for detecting subtle SARS-CoV-2 sequence variations.
- Findings enhance understanding of SARS-CoV-2 evolution and provide a framework for public health genomic surveillance.
- Methodology supports variant surveillance, vaccine design, and preparedness for future viral emergence.
More Related Videos
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
7.2K
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...
7.2K
00:36Viral Mutations
40.6K
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...
40.6K
01:05Single Nucleotide Polymorphisms-SNPs
19.7K
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,...
19.7K
01:08Evolution of Microbial Genome
2
Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
2
02:05Gene Evolution - Fast or Slow?
8.3K
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...
8.3K
02:05Gene Evolution - Fast or Slow?
3.8K
3.8K