ArticleVirology journal2018
Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing.
Article in Virology journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 49 citations in OpenAlex.
- Toward Precision Vaccinology for Mpox: Rational Antigen Design, Next-Generation Platforms, and Immune Correlates of Protection.Tropical medicine and infectious disease · 2026Review
- Targeted sequence capture of coxsackievirus A6 using nanopore sequencing directly from clinical specimens.Microbiology spectrum · 2026Article
- Unlocking the full potential of nanopore sequencing: tips, tricks, and advanced data analysis techniques.Nucleic acids research · 2026Review
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples.Veterinary sciences · 2023Review
- Molecular characterization of Newcastle disease virus obtained from Mawenzi live bird market in Morogoro, Tanzania in 2020-2021.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2023Article
- Genetic diversity of Newcastle disease viruses circulating in wild and synanthropic birds in Ukraine between 2006 and 2015.Frontiers in veterinary science · 2023Article
- Rapid genotyping of porcine reproductive and respiratory syndrome virus (PRRSV) using MinION nanopore sequencing.PloS one · 2023Article
- Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms.Nanomaterials (Basel, Switzerland) · 2022Review
- Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples.Frontiers in veterinary science · 2022Article
- Randomly primed, strand-switching, MinION-based sequencing for the detection and characterization of cultured RNA viruses.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2021Article
- Article
- Molecular Characterization of Newcastle Disease Viruses Isolated from Chickens in Tanzania and Ghana.Viruses · 2020Article
- Simultaneous detection and comprehensive analysis of HPV and microbiome status of a cervical liquid-based cytology sample using Nanopore MinION sequencing.Scientific reports · 2019Article
- Biotic concerns in generating molecular diagnosis matrixes for 4 avian viruses with emphasis on Marek's disease virus.Journal of virological methods · 2019Review
- Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology.Scientific reports · 2019Article
- Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells.Genes · 2019Article
- Presence of Newcastle disease viruses of sub-genotypes Vc and VIn in backyard chickens and in apparently healthy wild birds from Mexico in 2017.Virus genes · 2019Article
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Authors and funding
11 authors at 5 institutions in 1 country.
Funding
Abstract
backgroundNewcastle disease (ND) outbreaks are global challenges to the poultry industry. Effective management requires rapid identification and virulence prediction of the circulating Newcastle disease viruses (NDV), the causative agent of ND. However, these diagnostics are hindered by the genetic diversity and rapid evolution of NDVs.
methodsAn amplicon sequencing (AmpSeq) workflow for virulence and genotype prediction of NDV samples using a third-generation, real-time DNA sequencing platform is described here. 1D MinION sequencing of barcoded NDV amplicons was performed using 33 egg-grown isolates, (15 NDV genotypes), and 15 clinical swab samples collected from field outbreaks. Assembly-based data analysis was performed in a customized, Galaxy-based AmpSeq workflow. MinION-based results were compared to previously published sequences and to sequences obtained using a previously published Illumina MiSeq workflow.
resultsFor all egg-grown isolates, NDV was detected and virulence and genotype were accurately predicted. For clinical samples, NDV was detected in ten of eleven NDV samples. Six of the clinical samples contained two mixed genotypes as determined by MiSeq, of which the MinION method detected both genotypes in four samples. Additionally, testing a dilution series of one NDV isolate resulted in NDV detection in a dilution as low as 10
conclusionThe depth of sequencing, fast sequencing capabilities, accuracy of the consensus sequences, and the low cost of multiplexing allowed for effective virulence prediction and genotype identification of NDVs currently circulating worldwide. The sensitivity of this protocol was preliminary tested using only one genotype. After more extensive evaluation of the sensitivity and specificity, this protocol will likely be applicable to the detection and characterization of NDV.
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