ArticleVirus evolution2017
On the effective depth of viral sequence data.
Article in Virus evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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
31 citing papers in PubMed.
- Rapid and precise amplicon-based genome sequencing to preparedness and response chikungunya virus outbreaks.Emerging microbes & infections · 2026Article
- Optimal sequencing depth for measuring the concentrations of molecular barcodes.Nucleic acids research · 2025Article
- Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity.Annual review of virology · 2024Review
- Refining SARS-CoV-2 intra-host variation by leveraging large-scale sequencing data.NAR genomics and bioinformatics · 2024Article
- Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses.PLoS genetics · 2024Article
- A laboratory framework for ongoing optimization of amplification-based genomic surveillance programs.Microbiology spectrum · 2023Article
- Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations.The Journal of general virology · 2023Article
- Article
- Oral Rabies Vaccine Strain SPBN GASGAS: Genetic Stability after Serial In Vitro and In Vivo Passaging.Viruses · 2022Article
- A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events.Molecular biology and evolution · 2022Article
- Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat.bioRxiv : the preprint server for biology · 2022Article
- Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat.Virus evolution · 2022Article
- Genetic Diversity and Spatiotemporal Dynamics of Chikungunya Infections in Mexico during the Outbreak of 2014-2016.Viruses · 2021Article
- Article
- Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children.eLife · 2021Article
- Article
- Drivers of within-host genetic diversity in acute infections of viruses.PLoS pathogens · 2020Article
- Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses.Applied and environmental microbiology · 2020Review
- Within-Host Viral Diversity: A Window into Viral Evolution.Annual review of virology · 2020Review
- A large effective population size for established within-host influenza virus infection.eLife · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome sequence data are of great value in describing evolutionary processes in viral populations. However, in such studies, the extent to which data accurately describes the viral population is a matter of importance. Multiple factors may influence the accuracy of a dataset, including the quantity and nature of the sample collected, and the subsequent steps in viral processing. To investigate this phenomenon, we sequenced replica datasets spanning a range of viruses, and in which the point at which samples were split was different in each case, from a dataset in which independent samples were collected from a single patient to another in which all processing steps up to sequencing were applied to a single sample before splitting the sample and sequencing each replicate. We conclude that neither a high read depth nor a high template number in a sample guarantee the precision of a dataset. Measures of consistency calculated from within a single biological sample may also be insufficient; distortion of the composition of a population by the experimental procedure or genuine within-host diversity between samples may each affect the results. Where it is possible, data from replicate samples should be collected to validate the consistency of short-read sequence data.
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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.