ArticleNature communications2023
Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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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
33 citing papers in PubMed.
- Phylodynamic reconstruction of H1N1pdm09 influenza virus transmission in Brazil: a decade of evolutionary dynamics.Emerging microbes & infections · 2026Article
- Transmission of mutated SARS-CoV-2 variants is favored by relatively prolonged infections due to delayed immunity.bioRxiv : the preprint server for biology · 2026Article
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- Dose-dependent effects of recombinant spike protein-based vaccination on SARS-CoV-2 evolutionary dynamics and the emergence of variants in hamster models.The Journal of general virology · 2026Article
- Within-host SARS-CoV-2 diversity in immunocompromised patients during acute infection.Journal of virology · 2026Article
- Large-scale genomic surveillance reveals immunosuppression drives mutation dynamics in persistent SARS-CoV-2 infections.Nature communications · 2026Article
- SARS-CoV-2 intra-host viral diversity associated with host innate and vaccine-induced immunity in an obese mouse model.BMC infectious diseases · 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
- Selection Estimation from Genetic Time-Series Data: Effects of Limited Sampling and Genetic Drift.Molecular biology and evolution · 2025Article
- Case-based evidence links increased SARS-CoV-2 diversity to impaired IFN-I response in severe COVID-19.Journal of human immunity · 2025Article
- Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks.PLoS biology · 2025Article
- Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore.Emerging infectious diseases · 2025Article
- Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks.bioRxiv : the preprint server for biology · 2025Article
- Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population.Journal of virology · 2025Article
- The impact of pre-existing immunity on the emergence of within-host immune-escape mutations in Omicron lineages.The Journal of general virology · 2025Article
- In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants.PLoS pathogens · 2025Article
- Article
- Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time.Nucleic acids research · 2025Article
- Predicting pathogen evolution and immune evasion in the age of artificial intelligence.Computational and structural biotechnology journal · 2025Review
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Abstract
Viral and host factors can shape SARS-CoV-2 evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here, we analysed deep sequencing data from 2,820 SARS-CoV-2 respiratory samples with different viral lineages to describe the patterns of within-host diversity under different conditions, including vaccine-breakthrough infections. In unvaccinated individuals, variant of Concern (VOC) Alpha, Delta, and Omicron respiratory samples were found to have higher within-host diversity and were under neutral to purifying selection at the full genome level compared to non-VOC SARS-CoV-2. Breakthrough infections in 2-dose or 3-dose Comirnaty and CoronaVac vaccinated individuals did not increase levels of non-synonymous mutations and did not change the direction of selection pressure. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 sequence diversification. Our findings suggest that vaccination does not increase exploration of SARS-CoV-2 protein sequence space and may not facilitate emergence of viral variants.
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