ArticleNature communications2024
Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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.
The trial behind it
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
24 citing papers in PubMed, 28 citations in OpenAlex.
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- Comprehensive profiling of humoral immune responses to pan-respiratory pathogens: Insights from diverse cohorts.iScience · 2026Article
- Double trouble: how co- and superinfections shape viral dynamics and host responses.Journal of virology · 2026Review
- Integrating Genomic Data into Test-negative Designs for Estimating Lineage-specific COVID-19 Vaccine Effectiveness.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases.Microbial genomics · 2026Article
- Targeted and untargeted cross-sectional study for sex-specific identification of plasma biomarkers of COVID-19 severity.Analytical and bioanalytical chemistry · 2026Article
- SARS-CoV-2 Intra-host Variation Shows Evidence of Transmission and Convergent Evolution in a University Surveillance Cohort.bioRxiv : the preprint server for biology · 2025Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Molecular mechanisms of co-infections.EMBO reports · 2025Review
- Recombinants Are the Key Drivers of Recent PRRSV-2 Evolution.Pathogens (Basel, Switzerland) · 2025Article
- Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population.Journal of virology · 2025Article
- Genomics-based approach for detection and characterization of SARS-CoV-2 co-infections and diverse viral populations.Microbiology spectrum · 2025Article
- Epidemiology, Clinical Significance, and Diagnosis of Respiratory Viruses and Their Co-Infections in the Post-COVID Era.Pathogens (Basel, Switzerland) · 2025Review
- Real-Time PCR-Based Test as a Research Tool for the Retrospective Detection and Identification of SARS-CoV-2 Variants of Concern in a Sample.International journal of molecular sciences · 2025Article
- Whole genome characterization of Torque teno sus virus 1 (TTSuV1) in wild and domestic pigs: insights into genetic classification, host differentiation, and intra-host variation.Frontiers in microbiology · 2025Article
- Patterns of Isoform Variation for N Gene Subgenomic mRNAs in Betacoronavirus Transcriptomes.Viruses · 2024Article
- High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark.Nature communications · 2024Article
- Ten-year retrospective data analysis reveals frequent respiratory co-infections in hospitalized patients in Augsburg.iScience · 2024Article
- Unveiling Inter- and Intra-Patient Sequence Variability with a Multi-Sample Coronavirus Target Enrichment Approach.Viruses · 2024Article
- Review
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
Abstract
Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.35% of the investigated cases. Two independent procedures were implemented to detect intra-host recombination. We show that sensitivity is predominantly determined by the density of lineage-defining mutations along the genome, thus we used an expanded list of mutually exclusive defining mutations of specific variant combinations to increase statistical power. We call attention to multiple challenges rendering recombinant detection difficult and provide guidelines for the reduction of false positives arising from chimeric sequences produced during PCR amplification. Additionally, we identify three recombination hotspots of Delta - Omicron BA.1 intra-host recombinants.
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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.