ArticleMolecular biology and evolution2022
Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Likelihoods for a general class of ARGs under the SMC.Genetics · 2026Article
- Human ancestries simulation and inference: a review of ancestral recombination graph-based approaches.Frontiers in bioinformatics · 2026Review
- A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.bioRxiv : the preprint server for biology · 2025Article
- The promise and challenge of spatial inference with the full ancestral recombination graph under Brownian motion.G3 (Bethesda, Md.) · 2025Article
- Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes.Nature genetics · 2025Article
- Likelihoods for a general class of ARGs under the SMC.bioRxiv : the preprint server for biology · 2025Article
- Leveraging graphical model techniques to study evolution on phylogenetic networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Review
- Review
- Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein.Virus evolution · 2025Article
- Data-driven recombination detection in viral genomes.Nature communications · 2024Article
- Long-range linkage effects in adapting sexual populations.Scientific reports · 2023Article
- COVID-19 annual update: a narrative review.Human genomics · 2023Review
- The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection.BMC genomics · 2023Article
- Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies.Communications medicine · 2023Review
- Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.PLoS pathogens · 2023Review
- Review
- Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Characterization of SARS-CoV-2 recombinants and emerging Omicron sublineages.International journal of medical sciences · 2023Review
- Quasispecies Analysis of SARS-CoV-2 of 15 Different Lineages during the First Year of the Pandemic Prompts Scratching under the Surface of Consensus Genome Sequences.International journal of molecular sciences · 2022Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The evolutionary process of genetic recombination has the potential to rapidly change the properties of a viral pathogen, and its presence is a crucial factor to consider in the development of treatments and vaccines. It can also significantly affect the results of phylogenetic analyses and the inference of evolutionary rates. The detection of recombination from samples of sequencing data is a very challenging problem and is further complicated for SARS-CoV-2 by its relatively slow accumulation of genetic diversity. The extent to which recombination is ongoing for SARS-CoV-2 is not yet resolved. To address this, we use a parsimony-based method to reconstruct possible genealogical histories for samples of SARS-CoV-2 sequences, which enables us to pinpoint specific recombination events that could have generated the data. We propose a statistical framework for disentangling the effects of recurrent mutation from recombination in the history of a sample, and hence provide a way of estimating the probability that ongoing recombination is present. We apply this to samples of sequencing data collected in England and South Africa and find evidence of ongoing recombination.
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