Related Experiment Video
Updated: Jun 28, 2025

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
Data-driven recombination detection in viral genomes
Tommaso Alfonsi1, Anna Bernasconi2, Matteo Chiara3
1Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Via Ponzio 34/5, 20133, Milan, Italy.
Abstract:
Recombination is a key molecular mechanism for the evolution and adaptation of viruses. The first recombinant SARS-CoV-2 genomes were recognized in 2021; as of today, more than ninety SARS-CoV-2 lineages are designated as recombinant. In the wake of the COVID-19 pandemic, several methods for detecting recombination in SARS-CoV-2 have been proposed; however, none could faithfully confirm manual analyses by experts in the field. We hereby present RecombinHunt, an original data-driven method for the identification of recombinant genomes, capable of recognizing recombinant SARS-CoV-2 genomes (or lineages) with one or two breakpoints with high accuracy and within reduced turn-around times. ReconbinHunt shows high specificity and sensitivity, compares favorably with other state-of-the-art methods, and faithfully confirms manual analyses by experts. RecombinHunt identifies recombinant viral genomes from the recent monkeypox epidemic in high concordance with manually curated analyses by experts, suggesting that our approach is robust and can be applied to any epidemic/pandemic virus.
Related Concept Videos
Viral Recombination
Viral Mutations
Conservative Site-specific Recombination and Phase Variation
The recognition sites for Cre recombinase called LoxP...
Homologous Recombination

