AI Summary
and drug resistance. The ability to accurately detect recombination events in viral genomes is crucial for understanding viral evolution, transmission dynamics, and vaccine design. The proposed method, RecombinHunt, demonstrates high accuracy, specificity, and sensitivity in identifying recombinant genomes in SARS-CoV-2 and other viruses, showing promising potential for application in tracking and studying viral epidemics and pandemics.
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.
Recombination is a key molecular mechanism used by RNA viruses to boost their evolution. Recombination occurs both in viruses with segmented and non-segmented genomes; parental strains to a recombinant virus are referred to as “donor” and “acceptor.” Recombination requires co-circulation and co-infection in the same host; the clinical and epidemiological relevance is substantial since recombinant viral strains have been associated with altered viral host tropism, enhanced virulence, host immune evasion,