ArticleNature communications2024
Using big sequencing data to identify chronic SARS-Coronavirus-2 infections.
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 21 papers.
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Who cites it
21 citing papers in PubMed.
- SARS-CoV-2 saltational events are recurrent and trace to persistent human infections.bioRxiv : the preprint server for biology · 2026Article
- Molecular Characterization of Persistent SARS-CoV-2 Infections in Immunocompromised Patients.Viruses · 2026Article
- Slowdown of synonymous substitution rate preceding the emergence of multiple SARS-CoV-2 variants.Virus evolution · 2026Article
- TempSnap-Trace: A temporal snapshot-based framework for haplotype network tracing.Biosafety and health · 2025Article
- Genomic and epidemiologic characteristics of SARS-CoV-2 persistent infections in California, January 2021 - July 2023.PLoS pathogens · 2025Article
- Intra-Host Evolution of SARS-CoV-2 During Persistent Infection of Pediatric COVID-19 Patients.Viruses · 2025Article
- SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study.The Lancet. Microbe · 2025Observational
- The consequences of SARS-CoV-2 within-host persistence.Nature reviews. Microbiology · 2025Review
- Determinants of SARS-CoV-2 outcomes in patients with cancer vs controls without cancer: a multivariable meta-analysis with genomic imputation.EClinicalMedicine · 2025Article
- Adaptive evolution of SARS-CoV-2 during a persistent infection for 521 days in an immunocompromised patient.NPJ genomic medicine · 2025Article
- Phylogenetic meta-analysis of persistent SARS-CoV-2 infections in immunocompromised individuals highlights the challenges of robust evolutionary rate estimation caused by low genetic diversity.Virus evolution · 2025Article
- Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients.Virus evolution · 2025Article
- Machine Learning Early Detection of SARS-CoV-2 High-Risk Variants.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Characterisation of the antibody-mediated selective pressure driving intra-host evolution of SARS-CoV-2 in prolonged infection.PLoS pathogens · 2024Article
- Case reports of persistent SARS-CoV-2 infection outline within-host viral evolution in immunocompromised patients.Virology journal · 2024Article
- Article
- Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution.Nature communications · 2024Article
- SARS-CoV-2 shedding and evolution in patients who were immunocompromised during the omicron period: a multicentre, prospective analysis.The Lancet. Microbe · 2024Article
- Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection.Virus evolution · 2024Article
- VIPERA: Viral Intra-Patient Evolution Reporting and Analysis.Virus evolution · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants. One leading hypothesis suggests these variants may have emerged during chronic infections of immunocompromised individuals, but limited data from these cases hinders comprehensive analyses. Here, we harnessed millions of SARS-CoV-2 genomes to identify potential chronic infections and used language models (LM) to infer chronic-associated mutations. First, we mined the SARS-CoV-2 phylogeny and identified chronic-like clades with identical metadata (location, age, and sex) spanning over 21 days, suggesting a prolonged infection. We inferred 271 chronic-like clades, which exhibited characteristics similar to confirmed chronic infections. Chronic-associated mutations were often high-fitness immune-evasive mutations located in the spike receptor-binding domain (RBD), yet a minority were unique to chronic infections and absent in global settings. The probability of observing high-fitness RBD mutations was 10-20 times higher in chronic infections than in global transmission chains. The majority of RBD mutations in BA.1/BA.2 chronic-like clades bore predictive value, i.e., went on to display global success. Finally, we used our LM to infer hundreds of additional chronic-like clades in the absence of metadata. Our approach allows mining extensive sequencing data and providing insights into future evolutionary patterns of SARS-CoV-2.
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