Related Experiment Video
Updated: Oct 11, 2025
10:34
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
4.6K
Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2.
Matteo Calcagnile1, Tiziano Verri1, Maurizio Salvatore Tredici1
1Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy.
One Health (Amsterdam, Netherlands)
|November 29, 2021
Summary
This study reveals SARS-CoV-2 evolution, showing viral variants bind animal ACE2 receptors better than human ones. This highlights the need for a mutation tracking system for One Health strategies.
Area of Science:
- Virology
- Molecular Biology
- Genomics
Background:
- A One Health strategy requires predicting SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) infection susceptibility in both humans and animals.
- Developing a robust SARS-CoV-2 mutation tracking system is crucial for this strategy.
Purpose of the Study:
- To investigate the molecular evolution of SARS-CoV-2.
- To analyze the binding affinity of viral variants to vertebrate ACE2 receptors.
- To understand the timeline and drivers of SARS-CoV-2 evolution.
Main Methods:
- Phylogenetic analysis of ACE2 receptors.
- Binding energy calculations for viral spike protein-ACE2 interactions.
- Codon usage analysis of viral variants.
- Tracking the prevalence of the D614G mutation over time.
Main Results:
- Phylogenetic proximity of vertebrate ACE2 receptors does not influence binding energy with the viral spike protein.
- Viral variants exhibit enhanced binding to animal ACE2 receptors compared to human ACE2.
- Codon usage patterns indicate SARS-CoV-2 evolution began in early 2020, with variants like Alpha, Beta, and Delta sharing similarities with a January 2020 sample.
- The host-specific D614G mutation became prevalent starting March 2020.
Conclusions:
- SARS-CoV-2 undergoes molecular evolution, initially optimizing codon usage and subsequently enhancing spike protein function.
- Viral evolution favors better binding to animal ACE2 receptors, with implications for interspecies transmission.
- Understanding these evolutionary dynamics is key for developing effective One Health surveillance and control strategies.
Related Concept Videos
02:05Gene Evolution - Fast or Slow?
7.5K
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...
7.5K
01:05Single Nucleotide Polymorphisms-SNPs
16.8K
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,...
16.8K
01:49Conserved Binding Sites
4.7K
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...
4.7K
02:28Leaky Scanning
5.3K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.3K
00:36Viral Mutations
34.7K
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...
34.7K
02:54Evolutionary Relationships through Genome Comparisons
6.4K
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...
6.4K