ArticleBMC genomics2014
Next-generation sequencing reveals large connected networks of intra-host HCV variants.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 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
34 citing papers in PubMed.
- Leveraging injection networks to prevent HIV and other blood borne infections among people who inject drugs in Kenya: design and rationale.BMC infectious diseases · 2025Article
- Multiple Approaches to Genetic Sequencing to Identify Hepatitis C Virus Reinfection Among People Who Inject Drugs.The Journal of infectious diseases · 2025Article
- Article
- Genetically distinct within-host subpopulations of hepatitis C virus persist after Direct-Acting Antiviral treatment failure.PLoS pathogens · 2025Article
- Widespread hepatitis C virus transmission network among people who inject drugs in Kenya.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2024Article
- Polyvalent immunization elicits a synergistic broadly neutralizing immune response to hypervariable region 1 variants of hepatitis C virus.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Polymorphic Molecular Signatures in Variable Regions of thePathogens (Basel, Switzerland) · 2022Article
- Primary case inference in viral outbreaks through analysis of intra-host variant population.BMC bioinformatics · 2022Article
- Article
- Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.Briefings in bioinformatics · 2021Review
- Recovery of Recombinant Canine Distemper Virus That Expresses CPV-2a VP2: Uncovering the Mutation Profile of Recombinant Undergoing 50 Serial PassagesFrontiers in cellular and infection microbiology · 2021Article
- Rescuing eGFP-Tagged Canine Distemper Virus for 40 Serial Passages Separately in Ribavirin- and Non-Treated Cells: Comparative Analysis of Viral Mutation Profiles.Frontiers in cellular and infection microbiology · 2021Article
- Mutation Profiles of eGFP-Tagged Small Ruminant Morbillivirus During 45 Serial Passages in Ribavirin-Treated Cells.Frontiers in veterinary science · 2021Article
- Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections.Virus evolution · 2021Article
- Convex hulls in hamming space enable efficient search for similarity and clustering of genomic sequences.BMC bioinformatics · 2020Article
- Analysis of heterogeneous genomic samples using image normalization and machine learning.BMC genomics · 2020Article
- Graph fractal dimension and the structure of fractal networks.Journal of complex networks · 2020Article
- A Phylogenetic Analysis of Hepatitis C Virus Transmission, Relapse, and Reinfection Among People Who Inject Drugs Receiving Opioid Agonist Therapy.The Journal of infectious diseases · 2020Article
- Global transmission network of SARS-CoV-2: from outbreak to pandemic.medRxiv : the preprint server for health sciences · 2020Article
- Local immunodeficiency: Minimal networks and stability.Mathematical biosciences · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.
resultsIntra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient.
conclusionsMost intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance.
Indexed as
Identifiers
What OpenQuestion holds
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.