ArticleMicroorganisms2021
Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses.
Article in Microorganisms, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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
24 citing papers in PubMed.
- Unraveling the intra-species genomic diversity of sweetpotato-infecting CRESS-DNA and RNA viruses in Burkina Faso using Oxford Nanopore sequencing.Frontiers in microbiology · 2026Article
- Geminivirus diversity and community structure at the scale of agro-ecological systems in two localities of Burkina Faso.ISME communications · 2026Article
- Dataset of rolling circle amplification (RCA) enriched metagenome of Cassava obtained through nanopore sequencing.Data in brief · 2025Article
- Oxford nanopore sequencing as a useful tool for investigating the population dynamics of invasive begomoviruses in Sicily.Microbial genomics · 2025Article
- Improvement of Nanopore sequencing provides access to high quality genomic data for multi-component CRESS-DNA plant viruses.Virology journal · 2025Article
- Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host.PloS one · 2025Article
- Article
- High-throughput Sequencing (HTS)-Based Diagnosis of Geminiviruses.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.Microbiome · 2024Article
- Identification of Viruses InfectingInternational journal of molecular sciences · 2024Article
- Increase of niche filling with increase of host richness for plant-infecting mastreviruses.Virus evolution · 2024Article
- Evaluation of sequencing and PCR-based methods for the quantification of the viral genome formula.Virus research · 2023Article
- NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection.Frontiers in microbiology · 2023Article
- Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly.Microbial genomics · 2022Article
- Nanopore Metagenomics Sequencing for Rapid Diagnosis and Characterization of Lily Viruses.The plant pathology journal · 2022Article
- A balanced gut microbiota is essential to maintain health in captive sika deer.Applied microbiology and biotechnology · 2022Article
- Rapid and Routine Molecular Typing Using Multiplex Polymerase Chain Reaction and MinION Sequencer.Frontiers in microbiology · 2022Article
- Nanopore sequencing technology and its application in plant virus diagnostics.Frontiers in microbiology · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
Next-generation sequencing (NGS), through the implementation of metagenomic protocols, has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocols are still laborious and costly to implement, and the technique has not yet become routine for everyday virus characterization. Within the context of CRESS DNA virus studies, we implemented two alternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledge of the viral genome) and the other that use specific primers to target a virus (with a priori). Agnostic and specific long read NGS-based assembled genomes of two capulavirus strains were compared to those obtained using the gold standard technique of Sanger sequencing. Both protocols allowed the detection and accurate full genome characterization of both strains. Globally, the assembled genomes were very similar (99.5-99.7% identity) to the Sanger sequences consensus, but differences in the homopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGS approach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has proven to be a credible alternative in the context of CRESS DNA virus study and could offer a new range of applications not previously accessible.
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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.