ArticleVirus evolution2019
Measurements of intrahost viral diversity require an unbiased diversity metric.
Article in Virus evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 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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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
49 citing papers in PubMed.
- Influenza antibody breadth and effector functions are immune correlates from acquisition of pandemic infection of children.Nature communications · 2024Trial
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- HPV16 genetic variation provides evidence of positive natural selection driven by HLA class I.Nature communications · 2026Article
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses.PLoS pathogens · 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
- Genomic evolution and minority variant dynamics of RSV during the first season of nirsevimab implementation in Italy (2024-5).Virus evolution · 2026Article
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses.bioRxiv : the preprint server for biology · 2025Article
- Changes in intra-host mycovirus population diversity after vertical and horizontal transmission.Virus evolution · 2025Article
- Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients.Virus evolution · 2025Article
- Quantifying the impact of vaccination on transmission and diversity of influenza A variants in pigs.Journal of virology · 2024Article
- High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark.Nature communications · 2024Article
- Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status.Virus evolution · 2024Article
- Unraveling the genomic landscape of piscine myocarditis virus: mutation frequencies, viral diversity and evolutionary dynamics in Atlantic salmon.Virus evolution · 2024Article
- Puzzles, challenges, and information reservoir of SARS-CoV-2 quasispecies.Journal of virology · 2023Review
- Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.Proceedings. Biological sciences · 2023Article
- Article
- Viruses of a key coral symbiont exhibit temperature-driven productivity across a reefscape.ISME communications · 2023Article
- Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals.Nature communications · 2023Article
- Article
- Atypical Mutational Spectrum of SARS-CoV-2 Replicating in the Presence of Ribavirin.Antimicrobial agents and chemotherapy · 2023Article
Corrections and comments
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2 authors.
Funding
Abstract
Viruses exist within hosts at large population sizes and are subject to high rates of mutation. As such, viral populations exhibit considerable sequence diversity. A variety of summary statistics have been developed which describe, in a single number, the extent of diversity in a viral population; such measurements allow the diversities of different populations to be compared, and the effect of evolutionary forces on a population to be assessed. Here we highlight statistical artefacts underlying some common measures of sequence diversity, whereby variation in the depth of genome sequencing may substantially affect the extent of diversity measured in a viral population, making comparisons of population diversity invalid. Specifically, naive estimation of sequence entropy provides a systematically biased metric, a lower read depth being expected to produce a lower estimate of diversity. The number of polymorphic loci per kilobase of genome is more unpredictably affected by read depth, giving potentially flawed results at lower sequencing depths. We show that the nucleotide diversity statistic
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