ArticleMicrobial informatics and experimentation2014
Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions.
Article in Microbial informatics and experimentation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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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
39 citing papers in PubMed.
- Understanding Basic Concepts of Viral Quasispecies: From Evolutionary Dynamics to Clinical Relevance.Pathogens (Basel, Switzerland) · 2026Review
- Genomic Evolution of the Marine Bacterium Phaeobacter inhibens during Biofilm Growth.Applied and environmental microbiology · 2021Article
- Clinically relevant mutations in core metabolic genes confer antibiotic resistance.Science (New York, N.Y.) · 2021Article
- Stability of SARS-CoV-2 phylogenies.PLoS genetics · 2020Article
- Article
- Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects.PloS one · 2020Article
- A binning tool to reconstruct viral haplotypes from assembled contigs.BMC bioinformatics · 2019Article
- DISSEQT-DIStribution-based modeling of SEQuence space Time dynamics.Virus evolution · 2019Article
- Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation.PLoS computational biology · 2019Article
- Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma.Journal of virology · 2019Article
- Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.PLoS computational biology · 2018Article
- Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus.Journal of the International AIDS Society · 2018Article
- Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues.Journal of neurovirology · 2018Article
- Prevalence of mixed genotype hepatitis C virus infections in the UK as determined by genotype-specific PCR and deep sequencing.Journal of viral hepatitis · 2018Article
- Comparative genomics reveals new single-nucleotide polymorphisms that can assist in identification of adherent-invasive Escherichia coli.Scientific reports · 2018Article
- Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.Virus evolution · 2018Article
- MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data.Biology · 2017Article
- A random forest classifier for detecting rare variants in NGS data from viral populations.Computational and structural biotechnology journal · 2017Article
- Article
- Recent advances in understanding HIV evolution.F1000Research · 2017Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deep sequencing harnesses the high throughput nature of next generation sequencing technologies to generate population samples, treating information contained in individual reads as meaningful. Here, we review applications of deep sequencing to pathogen evolution. Pioneering deep sequencing studies from the virology literature are discussed, such as whole genome Roche-454 sequencing analyses of the dynamics of the rapidly mutating pathogens hepatitis C virus and HIV. Extension of the deep sequencing approach to bacterial populations is then discussed, including the impacts of emerging sequencing technologies. While it is clear that deep sequencing has unprecedented potential for assessing the genetic structure and evolutionary history of pathogen populations, bioinformatic challenges remain. We summarise current approaches to overcoming these challenges, in particular methods for detecting low frequency variants in the context of sequencing error and reconstructing individual haplotypes from short reads.
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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.