Related Experiment Video
Updated: Sep 15, 2025

Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit
Published on: June 28, 2013
A codon usage-based approach for the stratification of Influenza A across recent spillovers
Tommaso Alfonsi1, Matteo Chiara2, Anna Bernasconi1
1Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milan, Italy.
None:
Influenza A virus (IAV) is a highly adaptable pathogen that poses a significant threat to human health. Genomic surveillance of IAVs is complex due to their broad host range, zoonotic potential, and rapid evolution. Strategies based on codon preference analysis have been successfully employed for the discrimination of IAVs with different host specificity in the past. Hence, monitoring changes in codon usage offers a promising strategy for tracking IAVs' host range and identifying significant epidemiological events. In this study, we developed a computational workflow for the stratification of IAVs based on codon usage profiles by analysing recent IAV-associated epidemiological emergencies: 1) the 2009 H1N1 pandemic in North America, 2) the H7N9 epidemic in China (2013-2017), and 3) the long-term circulation of H5N1 in domestic birds and its subsequent spillover to dairy cows. We explore the application of codon usage metrics for capturing patterns of viral diversification and expand previous related findings in the field. Our results uncovered important differences in genomic features, which are not always reflected in the clade-based nomenclature. Interestingly, a reduced set of amino acids and associated codons was sufficient to summarize salient patterns of IAV genomes across the 3 paradigmatic cases herein considered, suggesting shared evolutionary signatures across IAV serotypes. Codon usage-based stratification effectively highlighted key epidemiological events and enabled detailed comparisons of genomic features across IAV serotypes. The approach developed in this work provides a scalable framework for IAV genomic surveillance, offering insights into viral evolution and shared patterns of codon usage preferences. Its general applicability makes it suitable for extending to other Influenza A serotypes, particularly those for which available genomic data are limited or a reference nomenclature is not established.
More Related Videos
08:16Identifying Caspases and their Motifs that Cleave Proteins During Influenza A Virus Infection
Published on: July 21, 2022
09:31Fluorescence-based Neuraminidase Inhibition Assay to Assess the Susceptibility of Influenza Viruses to The Neuraminidase Inhibitor Class of Antivirals
Published on: April 15, 2017
Related Concept Videos
Leaky Scanning
Single Nucleotide Polymorphisms-SNPs
Viral Mutations
Viral Recombination
Viruses with RNA Genomes
Point and Frameshift Mutations