Trial reportPLoS pathogens2021
High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19.
Trial report in PLoS pathogens, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it, 48 citations in OpenAlex.
- Update on geographical variation and distribution of SARS-nCoV-2: A systematic review.Indian journal of pharmacologyPooled it
- Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial.Nature microbiology · 2022Trial
- A favorable follicular helper CD4+ T cell programming characterizes neutralization activity in chronic HIV infection.The Journal of clinical investigation · 2026Article
- QoALa: A comprehensive workflow for viral quasispecies diversity comparison using long-read sequencing data.PLoS computational biology · 2026Article
- Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections.Cell reports. Medicine · 2026Article
- CLAE: A High-Fidelity Nanopore Sequencing Strategy for Read-Level Viral Variant Detection and Environmental RNA Virus Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Cross-neutralizing and potent human monoclonal antibodies against historical and emerging H5Nx influenza viruses.Nature microbiology · 2025Article
- Virologic effects of broadly neutralizing antibodies VRC01LS and VRC07-523LS on chronic HIV-1 infection.JCI insight · 2025Article
- Administration of anti-HIV-1 broadly neutralizing monoclonal antibodies with increased affinity to Fcγ receptors during acute SHIVNature communications · 2024Article
- Rapid intra-host diversification and evolution of SARS-CoV-2 in advanced HIV infection.Nature communications · 2024Article
- Vascular dysfunction in hemorrhagic viral fevers: opportunities for organotypic modeling.Biofabrication · 2024Review
- Adaptation of SARS-CoV-2 to ACE2Journal of virology · 2024Article
- Identification and quantitation of multiple variants in RNA virus genomes.Biology methods & protocols · 2024Article
- Article
- SARS-CoV-2 evolves increased infection elicited cell death and fusion in an immunosuppressed individual.medRxiv : the preprint server for health sciences · 2022Article
- Article
- Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns.bioRxiv : the preprint server for biology · 2022Article
- A pair of noncompeting neutralizing human monoclonal antibodies protecting from disease in a SARS-CoV-2 infection model.European journal of immunology · 2022Article
- Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529.Science (New York, N.Y.) · 2022Article
- Designing AbhiSCoVac - A single potential vaccine for all 'corona culprits': Immunoinformatics and immune simulation approaches.Journal of molecular liquids · 2022Article
Corrections and comments
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Authors and funding
16 authors at 2 institutions in 1 country.
Funding
Abstract
Tracking evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within infected individuals will help elucidate coronavirus disease 2019 (COVID-19) pathogenesis and inform use of antiviral interventions. In this study, we developed an approach for sequencing the region encoding the SARS-CoV-2 virion surface proteins from large numbers of individual virus RNA genomes per sample. We applied this approach to the WA-1 reference clinical isolate of SARS-CoV-2 passaged in vitro and to upper respiratory samples from 7 study participants with COVID-19. SARS-CoV-2 genomes from cell culture were diverse, including 18 haplotypes with non-synonymous mutations clustered in the spike NH2-terminal domain (NTD) and furin cleavage site regions. By contrast, cross-sectional analysis of samples from participants with COVID-19 showed fewer virus variants, without structural clustering of mutations. However, longitudinal analysis in one individual revealed 4 virus haplotypes bearing 3 independent mutations in a spike NTD epitope targeted by autologous antibodies. These mutations arose coincident with a 6.2-fold rise in serum binding to spike and a transient increase in virus burden. We conclude that SARS-CoV-2 exhibits a capacity for rapid genetic adaptation that becomes detectable in vivo with the onset of humoral immunity, with the potential to contribute to delayed virologic clearance in the acute setting.
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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.