ReviewInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2015
Within-host nucleotide diversity of virus populations: insights from next-generation sequencing.
Review in Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 1 of them a synthesis that pooled it.
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
61 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing.Briefings in bioinformatics · 2020Guideline
- Distinct patterns of within-host virus populations between two subgroups of human respiratory syncytial virus.Nature communications · 2021Trial
- Intrahost Dynamics of Human Cytomegalovirus Variants Acquired by Seronegative Glycoprotein B Vaccinees.Journal of virology · 2019Trial
- Integrated multi-population selection-signature scans identify putative functional genes influencing litter size in jishen black pigs.BMC genomics · 2026Article
- HPV16 genetic variation provides evidence of positive natural selection driven by HLA class I.Nature communications · 2026Article
- A recurrent adaptive mutation in the transmembrane 2B protein of an insect picorna-like virus in a nonnative host.Journal of virology · 2026Article
- An emerging PB2-627 polymorphism increases the zoonotic risk of avian influenza virus by overcoming ANP32 host restriction in mammalian and avian hosts.Journal of virology · 2025Article
- Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.Nature communications · 2025Article
- Article
- Genetic diversity of murine norovirus associated with ethanol sensitivity.Applied microbiology and biotechnology · 2025Article
- Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients.Viruses · 2025Article
- Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome.Nucleic acids research · 2024Article
- Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.bioRxiv : the preprint server for biology · 2024Article
- Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity.Annual review of virology · 2024Review
- Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation.American journal of human genetics · 2024Article
- Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data.Nature communications · 2024Article
- Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status.Virus evolution · 2024Article
- Genetic diversity of murine norovirus populations less susceptible to chlorine.Frontiers in microbiology · 2024Article
- Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus.Virus evolution · 2024Article
- Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Next-generation sequencing (NGS) technology offers new opportunities for understanding the evolution and dynamics of viral populations within individual hosts over the course of infection. We review simple methods for estimating synonymous and nonsynonymous nucleotide diversity in viral genes from NGS data without the need for inferring linkage. We discuss the potential usefulness of these data for addressing questions of both practical and theoretical interest, including fundamental questions regarding the effective population sizes of within-host viral populations and the modes of natural selection acting on them.
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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.