ArticleBMC infectious diseases2020
Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses.
Article in BMC infectious diseases, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic Review of New, Enhanced Surveillance Systems and Methodologies for Zoonotic Influenza Viruses in Animals and Human-Animal Interface.Influenza and other respiratory viruses · 2025Pooled it
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- Adaptation and validation of an influenza a subtyping panel for detection of H1pdm09, H3 and H5 on a high-throughput RT-qPCR system.Scientific reports · 2026Article
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- Multiplex PCR and nanopore sequencing reveal the genetic stability of Hantaan virus in Xi'an, China.Archives of virology · 2026Article
- Development of a portable avian influenza virus characterisation system: bringing the inside-out.Scientific reports · 2025Article
- Whole-genome analysis of influenza A(H1N1)pdm09 viruses in Cameroon (2019-2024) using nanopore sequencing.BMC infectious diseases · 2025Article
- High serological barriers may contribute to restricted Influenza-A-virus transmission between pigs and humans.One health (Amsterdam, Netherlands) · 2025Article
- Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus.Genome medicine · 2025Article
- Emerging Highly Pathogenic Avian Influenza H5N1 Clade 2.3.4.4b Causes Neurological Disease and Mortality in Scavenging Ducks in Bangladesh.Veterinary sciences · 2025Article
- Swine influenza virus surveillance programme pilot to assess the risk for animal and public health, the Netherlands, 2022 to 2023.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza.Virus evolution · 2025Article
- Wild passerines as potential carriers and sources of avian influenza viruses in Ukraine.Frontiers in microbiology · 2025Article
- Article
- Article
- Out of the blue: detection of a unique highly pathogenic avian influenza virus of subtype H7N5 in Germany.Emerging microbes & infections · 2024Article
- Avian raptors are indicator species and victims of high pathogenicity avian influenza virus HPAIV H5N1 (clade 2.3.4.4b) in Germany.Scientific reports · 2024Article
- Dominant HPAIV H5N1 genotypes of Germany 2021/2022 are linked to high virulence in Pekin ducklings.Npj viruses · 2024Article
- Identification of Rotavirus Genotypes in Children under Five Years in the United Arab Emirates Using Nanopore Sequencing Technology.Journal of medical virology · 2024Article
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Authors and funding
4 authors.
Funding
Abstract
backgroundDue to the frequent reassortment and zoonotic potential of influenza A viruses, rapid gain of sequence information is crucial. Alongside established next-generation sequencing protocols, the MinION sequencing device (Oxford Nanopore Technologies) has become a serious competitor for routine whole-genome sequencing. Here, we established a novel, rapid and high-throughput MinION multiplexing workflow based on a universal RT-PCR.
methodsTwelve representative influenza A virus samples of multiple subtypes were universally amplified in a one-step RT-PCR and subsequently sequenced on the MinION instrument in conjunction with a barcoding library preparation kit from the rapid family and the MinIT performing live base-calling. The identical PCR products were sequenced on an IonTorrent platform and, after final consensus assembly, all data was compared for validation. To prove the practicability of the MinION-MinIT method in human and veterinary diagnostics, we sequenced recent and historical influenza strains for further benchmarking.
resultsThe MinION-MinIT combination generated over two million reads for twelve samples in a six-hour sequencing run, from which a total of 72% classified as quality screened, trimmed and mapped influenza reads to produce full genome sequences. Identities between the datasets of > 99.9% were achieved, with 100% coverage of all segments alongside a sufficient confidence and 4492fold mean depth. From RNA extraction to finished sequences, only 14 h were required.
conclusionsOverall, we developed and validated a novel and rapid multiplex workflow for influenza A virus sequencing. This protocol suits both clinical and academic settings, aiding in real time diagnostics and passive surveillance.
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