ArticlePloS one2021
Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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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
17 citing papers in PubMed, 27 citations in OpenAlex.
- Article
- Performance of Long-Read Single-Molecule Real-Time Sequencing for SARS-CoV-2 Genotyping in Clinical Samples.Journal of medical virology · 2025Article
- Evaluation of the loading capacity and patterns of packaged DNA in AAV genomes of different sizes using long-read sequencing.Molecular therapy. Methods & clinical development · 2025Article
- An Improved Rapid and Sensitive Long Amplicon Method for Nanopore-Based RSV Whole-Genome Sequencing.Influenza and other respiratory viruses · 2025Article
- High-Throughput Sequencing Methods for the Detection of Two Strawberry Viruses in Post-Entry Quarantine.Viruses · 2024Article
- Whole genome sequencing and phylogenetic analysis of SARS-CoV-2 strains isolated during the COVID-19 pandemic in Nigeria.IJID regions · 2024Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Towards a post-pandemic future for global pathogen genome sequencing.PLoS biology · 2023Article
- A collaborative approach to improving representation in viral genomic surveillance.PLOS global public health · 2023Article
- VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples.BMC bioinformatics · 2022Article
- Identification of Genomic Variants of SARS-CoV-2 Using Nanopore Sequencing.Medicina (Kaunas, Lithuania) · 2022Article
- A collaborative approach to improve representation in viral genomic surveillance.bioRxiv : the preprint server for biology · 2022Article
- High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination.International journal of molecular sciences · 2022Article
- Direct RNA Nanopore Sequencing of SARS-CoV-2 Extracted from Critical Material from Swabs.Life (Basel, Switzerland) · 2022Article
- COVID-19 Whole-Genome Resequencing with Redundant Tiling PCR and Subtract-Based Amplicon Normalization Successfully Characterized SARS-CoV-2 Variants in Clinical Specimens.Interdisciplinary perspectives on infectious diseases · 2022Article
- STArS (STrain-Amplicon-Seq), a targeted nanopore sequencing workflow for SARS-CoV-2 diagnostics and genotyping.Biology methods & protocols · 2022Article
- Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19.Frontiers in bioengineering and biotechnology · 2022Review
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with PCR-tiling approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, including human and bacterial contamination, as well as the presence of reads derived from the viral sub-genomic RNAs.
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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.