ArticleBMC genomics2022
Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Rapid and precise amplicon-based genome sequencing to preparedness and response chikungunya virus outbreaks.Emerging microbes & infections · 2026Article
- Evaluation of amplicon-based nanopore sequencing for foot-and-mouth disease viruses in clinical and environmental samples.Microbiology spectrum · 2026Article
- Direct comparison of clear DX Nanopore and Illumina sequencing of SARS-CoV-2.Microbiology spectrum · 2025Article
- Performance of Long-Read Single-Molecule Real-Time Sequencing for SARS-CoV-2 Genotyping in Clinical Samples.Journal of medical virology · 2025Article
- Enhancing public health surveillance: a comparative study of platform-specific and hybrid assembly approaches in SARS-CoV-2 genome sequencing.Microbial genomics · 2025Article
- Influence of Sequencing Technology on Pangenome-Level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens.Open forum infectious diseases · 2025Article
- Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant.OBM genetics · 2025Article
- SARS-COV-2 mutations in North Rift, Kenya.PloS one · 2025Article
- Analytical Performance of a Novel Nanopore Sequencing for SARS-CoV-2 Genomic Surveillance.Journal of medical virology · 2024Article
- Improved sub-genomic RNA prediction with the ARTIC protocol.Nucleic acids research · 2024Article
- Combining Short- and Long-Read Sequencing Technologies to Identify SARS-CoV-2 Variants in Wastewater.Viruses · 2024Article
- Single-Cell Sequencing Technology and Its Application in the Study of Central Nervous System Diseases.Cell biochemistry and biophysics · 2024Review
- Investing in health preparedness, response and resilience: a genomics costing tool focused on next generation sequencing.Frontiers in public health · 2024Article
- ONT sequencing identifies a high prevalence ofFrontiers in genetics · 2024Article
- Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater.International journal of molecular sciences · 2023Article
- Domestic and wild animal samples and diagnostic testing for SARS-CoV-2.The veterinary quarterly · 2023Review
- The application of long-read sequencing in clinical settings.Human genomics · 2023Review
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting.Scientific reports · 2023Article
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Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOver 4 million SARS-CoV-2 genomes have been sequenced globally in the past 2 years. This has been crucial in elucidating transmission chains within communities, the development of new diagnostic methods, vaccines, and antivirals. Although several sequencing technologies have been employed, Illumina and Oxford Nanopore remain the two most commonly used platforms. The sequence quality between these two platforms warrants a comparison of the genomes produced by the two technologies. Here, we compared the SARS-CoV-2 consensus genomes obtained from the Oxford Nanopore Technology GridION and the Illumina MiSeq for 28 sequencing runs.
resultsOur results show that the MiSeq had a significantly higher number of consensus genomes classified by Nextclade as good and mediocre compared to the GridION. The MiSeq also had a significantly higher genome coverage and mutation counts than the GridION.
conclusionDue to the low genome coverage, high number of indels, and sensitivity to SARS-CoV-2 viral load noted with the GridION when compared to MiSeq, we can conclude that the MiSeq is more favourable for SARS-CoV-2 genomic surveillance, as successful genomic surveillance is dependent on high quality, near-whole consensus genomes.
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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.