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Data-driven recombination detection in viral genomes

Author

Listed:
  • Tommaso Alfonsi

    (Politecnico di Milano)

  • Anna Bernasconi

    (Politecnico di Milano)

  • Matteo Chiara

    (Università degli Studi di Milano)

  • Stefano Ceri

    (Politecnico di Milano)

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.

Suggested Citation

  • Tommaso Alfonsi & Anna Bernasconi & Matteo Chiara & Stefano Ceri, 2024. "Data-driven recombination detection in viral genomes," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47464-5
    DOI: 10.1038/s41467-024-47464-5
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    References listed on IDEAS

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    1. Nicola F. Müller & Kathryn E. Kistler & Trevor Bedford, 2022. "A Bayesian approach to infer recombination patterns in coronaviruses," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    2. Freda Kreier, 2022. "Deltacron: the story of the variant that wasn’t," Nature, Nature, vol. 602(7895), pages 19-19, February.
    3. Rebecca J. Rockett & Jenny Draper & Mailie Gall & Eby M. Sim & Alicia Arnott & Jessica E. Agius & Jessica Johnson-Mackinnon & Winkie Fong & Elena Martinez & Alexander P. Drew & Clement Lee & Christine, 2022. "Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    4. Joel O. Wertheim & Jade C. Wang & Mindy Leelawong & Darren P. Martin & Jennifer L. Havens & Moinuddin A. Chowdhury & Jonathan E. Pekar & Helly Amin & Anthony Arroyo & Gordon A. Awandare & Hoi Yan Chow, 2022. "Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
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