ArticleGenetics2021
Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie.
Article in Genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it, 72 citations in OpenAlex.
- SARS-CoV-2 natural infection in animals: a systematic review of studies and case reports and series.The veterinary quarterly · 2021Pooled it
- Longitudinal characterization of mixed-genotype SARS-CoV-2 infections in a military cohort reveals compartmentalized viral populations.Microbiology spectrum · 2026Article
- Hidden Markov models detect recombination and ancestry of SARS-CoV-2.bioRxiv : the preprint server for biology · 2026Article
- A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.bioRxiv : the preprint server for biology · 2025Article
- Coinfection and nonrandom recombination drive the evolution of swine enteric coronaviruses.Emerging microbes & infections · 2024Article
- Review
- Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses.Biology · 2024Article
- Data-driven recombination detection in viral genomes.Nature communications · 2024Article
- Comprehensive detection and dissection of interlineage recombination events in the SARS-CoV-2 pandemic.Virus evolution · 2024Article
- SARS-CoV-2 Recombination and Coinfection Events Identified in Clinical Samples in Russia.Viruses · 2023Article
- Review
- Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2.PLoS computational biology · 2023Article
- Using Haplotype-Based Artificial Intelligence to Evaluate SARS-CoV-2 Novel Variants and Mutations.JAMA network open · 2023Article
- 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
- Genomic surveillance and sequencing of SARS-CoV-2 across South America.Revista panamericana de salud publica = Pan American journal of public health · 2023Article
- Unraveling the genetic evolution of SARS-CoV-2 Recombinants using mutational dynamics across the different lineages.Frontiers in medicine · 2023Article
- Evaluation of recombination detection methods for viral sequencing.Virus evolution · 2023Article
- The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2.Frontiers in microbiology · 2023Review
- Characterization of SARS-CoV-2 recombinants and emerging Omicron sublineages.International journal of medical sciences · 2023Review
- Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination.Med (New York, N.Y.) · 2022Article
Corrections and comments
- Update of
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies. However, in case of the SARS-CoV-2, the low divergence of near-identical genomes sequenced over a short period of time makes conventional analysis infeasible. Using a novel method, we identified 225 anomalous SARS-CoV-2 genomes of likely recombinant origins out of the first 87,695 genomes to be released, several of which have persisted in the population. Bolotie is specifically designed to perform a rapid search for inter-clade recombination events over extremely large datasets, facilitating analysis of novel isolates in seconds. In cases where raw sequencing data were available, we were able to rule out the possibility that these samples represented co-infections by analyzing the underlying sequence reads. The Bolotie software and other data from our study are available at https://github.com/salzberg-lab/bolotie.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.