ArticleJournal of virology2011
Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing.
Article in Journal of virology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 1 of them a synthesis that pooled it.
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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
79 citing papers in PubMed, 1 synthesis or guideline pooled it, 140 citations in OpenAlex.
- A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing.Briefings in bioinformatics · 2020Guideline
- Distinct mutations emerge in the genome of serotype O foot-and-mouth disease virus during persistence in cattle.Journal of virology · 2025Article
- Advances in bioinformatics and multi-omics integration: transforming viral infectious disease research in veterinary medicine.Virology journal · 2025Review
- Direct RNA Sequencing of Foot-and-mouth Disease Virus Genome Using a Flongle on MinION.Bio-protocol · 2024Article
- Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.Viruses · 2023Article
- Epidemiological Dynamics of Foot-and-Mouth Disease in the Horn of Africa: The Role of Virus Diversity and Animal Movement.Viruses · 2023Review
- Laboratory diagnosis of nonpolio enteroviruses: A review of the current literature.Biosafety and health · 2023Review
- Genetic diversity through social heterosis can increase virulence in RNA viral infections and cancer progression.Royal Society open science · 2021Article
- SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.Genome research · 2021Article
- VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples.Patterns (New York, N.Y.) · 2021Article
- A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity.Frontiers in microbiology · 2021Article
- Article
- Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission.bioRxiv : the preprint server for biology · 2020Article
- Into the Deep (Sequence) of the Foot-and-Mouth Disease Virus Gene Pool: Bottlenecks and Adaptation during Infection in Naïve and Vaccinated Cattle.Pathogens (Basel, Switzerland) · 2020Article
- Estimating viral bottleneck sizes for FMDV transmission within and between hosts and implications for the rate of viral evolution.Interface focus · 2020Article
- Persistent Infection of African Buffalo (Syncerus caffer) with Foot-and-Mouth Disease Virus: Limited Viral Evolution and No Evidence of Antibody Neutralization Escape.Journal of virology · 2019Article
- Intrahost Selection Pressure Drives Equine Arteritis Virus Evolution during Persistent Infection in the Stallion Reproductive Tract.Journal of virology · 2019Article
- Article
- Diagnosing bluetongue virus in domestic ruminants: current perspectives.Veterinary medicine (Auckland, N.Z.) · 2019Review
- Article
19 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
8 authors at 3 institutions in 3 countries.
Funding
Abstract
The diverse sequences of viral populations within individual hosts are the starting material for selection and subsequent evolution of RNA viruses such as foot-and-mouth disease virus (FMDV). Using next-generation sequencing (NGS) performed on a Genome Analyzer platform (Illumina), this study compared the viral populations within two bovine epithelial samples (foot lesions) from a single animal with the inoculum used to initiate experimental infection. Genomic sequences were determined in duplicate sequencing runs, and the consensus sequence of the inoculum determined by NGS was identical to that previously determined using the Sanger method. However, NGS revealed the fine polymorphic substructure of the viral population, from nucleotide variants present at just below 50% frequency to those present at fractions of 1%. Some of the higher-frequency polymorphisms identified encoded changes within codons associated with heparan sulfate binding and were present in both foot lesions, revealing intermediate stages in the evolution of a tissue culture-adapted virus replicating within a mammalian host. We identified 2,622, 1,434, and 1,703 polymorphisms in the inoculum and in the two foot lesions, respectively: most of the substitutions occurred in only a small fraction of the population and represented the progeny from recent cellular replication prior to onset of any selective pressures. We estimated the upper limit for the genome-wide mutation rate of the virus within a cell to be 7.8 × 10(-4) per nucleotide. The greater depth of detection achieved by NGS demonstrates that this method is a powerful and valuable tool for the dissection of FMDV populations within hosts.
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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.