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Related Experiment Video

Updated: Oct 5, 2025

Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization

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Published on: December 23, 2020

Temporal evolution and adaptation of SARS-CoV-2 codon usage.

Elisa Posani¹, Maddalena Dilucca^1,2, Sergio Forcelloni^1,3

¹Physics Department, Sapienza University of Rome, 00185 Rome, Italy.

Frontiers in Bioscience (Landmark Edition)

|January 29, 2022

Summary

This summary is machine-generated.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) adapts to humans by evolving towards suboptimal codon usage, favoring host survival and spread. Genes for N and S proteins mutate faster, while S and RdRp face increased purifying pressure, limiting future mutations.

Keywords:

Codon usage bias ENC plot Forsdyke plot SARS-CoV-2 Similarity index Viral adaptation

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Area of Science:

Genomics and Evolutionary Biology
Virology
Molecular Biology

Background:

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019 and has since undergone mutations for human host adaptation.
Tracking SARS-CoV-2 genetic variants is critical for monitoring global spread and understanding viral evolution.

Purpose of the Study:

To analyze codon usage patterns in key SARS-CoV-2 genes over time.
To investigate the evolutionary trends and adaptation mechanisms of SARS-CoV-2 in the human host.

Main Methods:

Comparative genomic analysis of 320,338 SARS-CoV-2 genomes against the reference Wuhan strain.
Analysis of codon usage bias in genes encoding structural proteins (M, E, S, N) and RNA-dependent RNA polymerase (RdRp) and ORF1ab.

Main Results:

Nucleoprotein (N) and Spike (S) genes exhibited rapid divergence through mutation accumulation.
All analyzed SARS-CoV-2 genes showed a deoptimization of codon usage relative to the human host.
Proteins S and RdRp are under increasing purifying selection, suggesting reduced mutation acceptance, while N and M proteins evolve under mutational bias.

Conclusions:

SARS-CoV-2 exhibits an evolutionary trend towards suboptimal codon usage, potentially balancing viral spread with host survival.
Understanding these evolutionary patterns aids in predicting future mutation dynamics and the emergence of novel SARS-CoV-2 variants.