ArticleNature communications2022
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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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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Who cites it
32 citing papers in PubMed.
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases.Microbial genomics · 2026Article
- Intra-host diversity of SARS-CoV-2 in children with long-term and short-term excretion in nasopharyngeal samples.BMC infectious diseases · 2025Article
- Screening bacterial effectors and human virus proteins in yeast to identify host factors driving tombusvirus RNA recombination: a role for autophagy and membrane phospholipid content.Journal of virology · 2025Article
- Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population.Journal of virology · 2025Article
- Co-opted SUMO machinery promotes condensate formation associated with membranous replication organelles of a positive-strand RNA virus.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SARS-CoV-2 cellular coinfection is limited by superinfection exclusion.Journal of virology · 2025Article
- Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data.PLoS pathogens · 2025Article
- Genomic epidemiology and immune escape of SARS-CoV-2 recombinant strains circulating in Botswana.IJID regions · 2024Article
- Refining SARS-CoV-2 intra-host variation by leveraging large-scale sequencing data.NAR genomics and bioinformatics · 2024Article
- Publication-ready single nucleotide polymorphism visualization with snipit.Bioinformatics (Oxford, England) · 2024Article
- SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection.Genome medicine · 2024Article
- Data-driven recombination detection in viral genomes.Nature communications · 2024Article
- Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples.Nature communications · 2024Article
- Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient.Virology journal · 2023Article
- "Nano COVID-19": Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern.Experimental biology and medicine (Maywood, N.J.) · 2023Article
- Coinfections and Superinfections Associated with COVID-19 in Colombia: A Narrative Review.Medicina (Kaunas, Lithuania) · 2023Review
- Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.Viruses · 2023Article
- Adaptive Evolution of the Spike Protein in Coronaviruses.Molecular biology and evolution · 2023Article
- Effect of Transmission and Vaccination on Time to Dominance of Emerging Viral Strains: A Simulation-Based Study.Microorganisms · 2023Article
Corrections and comments
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Authors and funding
24 authors.
Funding
Abstract
Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination is only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts reveals that Alpha variant alleles comprise around 75% of the genomes, whereas the Epsilon variant alleles comprise around 20% of the sample. Further investigation reveals the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.
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