ArticleJournal of medical virology2022
Assessment of two-pool multiplex long-amplicon nanopore sequencing of SARS-CoV-2.
Article in Journal of medical virology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 29 citations in OpenAlex.
- Multiplex PCR and nanopore sequencing reveal the genetic stability of Hantaan virus in Xi'an, China.Archives of virology · 2026Article
- Comparative Analysis of Next- and Third-Generation Sequencing Platforms for Chikungunya Virus Whole-Genome Sequencing Using a Lineage-Inclusive Primer Set During the 2025 Foshan Outbreak.Tropical medicine and infectious disease · 2026Article
- Oxford Nanopore Sequencing in pediatric emergency infectious diseases: from rapid diagnosis to precision medicine.Frontiers in cellular and infection microbiology · 2026Review
- Cost-effective and flexible preimplantation genetic testing (PGT) by nanopore adaptive sampling.Journal of nanobiotechnology · 2025Article
- Development and validation of a carnitine cycle and transport disorders (CCD) panel: an ONT-compatible multi-gene diagnostic kit for newborn and selective screening.Orphanet journal of rare diseases · 2025Article
- An Improved Rapid and Sensitive Long Amplicon Method for Nanopore-Based RSV Whole-Genome Sequencing.Influenza and other respiratory viruses · 2025Article
- Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing.GigaScience · 2025Article
- An Oxford Nanopore Technologies-Based Sequencing Assay for Molecular Diagnosis of Phenylketonuria and Variant Frequencies in a Turkish Cohort.International journal of genomics · 2025Article
- Analytical Performance of a Novel Nanopore Sequencing for SARS-CoV-2 Genomic Surveillance.Journal of medical virology · 2024Article
- ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.Briefings in bioinformatics · 2024Article
- An amplicon-based sequencing approach for Usutu virus characterization.Virology journal · 2024Article
- Target enrichment metaviromics enables comprehensive surveillance of coronaviruses in environmental and animal samples.Heliyon · 2024Article
- Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples.Nature communications · 2024Article
- Structural and genomic evolutionary dynamics of Omicron variant of SARS-CoV-2 circulating in Madhya Pradesh, India.Frontiers in medicine · 2024Article
- Article
- A collaborative approach to improving representation in viral genomic surveillance.PLOS global public health · 2023Article
- The continuing evolution of barcode applications: Functional toxicology to cell lineage.Experimental biology and medicine (Maywood, N.J.) · 2022Review
- Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms.International journal of molecular sciences · 2022Article
- A collaborative approach to improve representation in viral genomic surveillance.bioRxiv : the preprint server for biology · 2022Article
- Targeted Whole Genome Sequencing (TWG-Seq) of Cucumber Green Mottle Mosaic Virus Using Tiled Amplicon Multiplex PCR and Nanopore Sequencing.Plants (Basel, Switzerland) · 2022Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an important role in COVID-19 pandemic control and elimination efforts, especially by elucidating its global transmission network and illustrating its viral evolution. The deployment of multiplex PCR assays that target SARS-CoV-2 followed by either massively parallel or nanopore sequencing is a widely-used strategy to obtain genome sequences from primary samples. However, multiplex PCR-based sequencing carries an inherent bias of sequencing depth among different amplicons, which may cause uneven coverage. Here we developed a two-pool, long-amplicon 36-plex PCR primer panel with ~1000-bp amplicon lengths for full-genome sequencing of SARS-CoV-2. We validated the panel by assessing nasopharyngeal swab samples with a <30 quantitative reverse transcription PCR cycle threshold value and found that ≥90% of viral genomes could be covered with high sequencing depths (≥20% mean depth). In comparison, the widely-used ARTIC panel yielded 79%-88% high-depth genome regions. We estimated that ~5 Mbp nanopore sequencing data may ensure a >95% viral genome coverage with a ≥10-fold depth and may generate reliable genomes at consensus sequence levels. Nanopore sequencing yielded false-positive variations with frequencies of supporting reads <0.8, and the sequencing errors mostly occurred on the 5' or 3' ends of reads. Thus, nanopore sequencing could not elucidate intra-host viral diversity.
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