Data-driven recombination detection in viral genomes
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 fo...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-04-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-47464-5 |
| _version_ | 1797199312883548160 |
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| author | Tommaso Alfonsi Anna Bernasconi Matteo Chiara Stefano Ceri |
| author_facet | Tommaso Alfonsi Anna Bernasconi Matteo Chiara Stefano Ceri |
| author_sort | Tommaso Alfonsi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-24T07:13:46Z |
| format | Article |
| id | doaj.art-1d8a2764265a4dca9115d18cd9ab656c |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-24T07:13:46Z |
| publishDate | 2024-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-1d8a2764265a4dca9115d18cd9ab656c2024-04-21T11:24:22ZengNature PortfolioNature Communications2041-17232024-04-0115111610.1038/s41467-024-47464-5Data-driven recombination detection in viral genomesTommaso Alfonsi0Anna Bernasconi1Matteo Chiara2Stefano Ceri3Department of Electronics, Information, and Bioengineering, Politecnico di MilanoDepartment of Electronics, Information, and Bioengineering, Politecnico di MilanoDepartment of Biosciences, Università degli Studi di MilanoDepartment of Electronics, Information, and Bioengineering, Politecnico di MilanoAbstract 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.https://doi.org/10.1038/s41467-024-47464-5 |
| spellingShingle | Tommaso Alfonsi Anna Bernasconi Matteo Chiara Stefano Ceri Data-driven recombination detection in viral genomes Nature Communications |
| title | Data-driven recombination detection in viral genomes |
| title_full | Data-driven recombination detection in viral genomes |
| title_fullStr | Data-driven recombination detection in viral genomes |
| title_full_unstemmed | Data-driven recombination detection in viral genomes |
| title_short | Data-driven recombination detection in viral genomes |
| title_sort | data driven recombination detection in viral genomes |
| url | https://doi.org/10.1038/s41467-024-47464-5 |
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