OpenRecombinHunt: Automatic detection of recombination in publicly available viral sequences

Zoonotic transmission and viral spillover events pose severe threats to public health, as underscored by recent pandemics. Mitigating these risks requires robust genomic surveillance systems, supported by the growing availability of openly accessible viral genome sequences through dedicated resources such as NCBI Virus and Nextstrain/Pathogens. This wealth of data highlights the need for lightweight, automated computational tools to monitor viral evolution and spread. OpenRecombinHunt extends our previously published RecombinHunt method, originally developed to identify recombinant SARS-CoV-2 lineages, to prioritize recombination patterns in any virus for which a large corpus of sequences is publicly available. Here, we couple RecombinHunt with HaploCoV, a computational workflow that stratifies viral genomes into distinct groups based on high-frequency genomic variants, without requiring a predefined reference nomenclature. We apply this framework to openly-accessible datasets for SARS-CoV-2, Respiratory Syncytial Virus (RSV) A/B, Monkeypox, Zika, Yellow Fever, and hemagglutinin segments of H5N1 Influenza A, reporting interesting recombination patterns. OpenRecombinHunt monthly updates ensure continuous monitoring, providing temporal snapshots of viral genomes with potential mosaic structure. Our method and Web Server have the potential to unlock large-scale automated support to detection of recombination in viruses, in line with current genomic surveillance interests. The Web Server is freely available at http://gmql.eu/openrecombinhunt/.