Use of Unamplified RNA/cDNA–Hybrid Nanopore Sequencing for Rapid Detection and Characterization of RNA Viruses

Kilianski, Andy; Roth, Pierce A.; Liem, Alvin T.; Hill, Jessica M.; Willis, Kristen L.; Rossmaier, Rebecca D.; Marinich, Andrew V.; Maughan, Michele N.; Karavis, Mark A.; Kuhn, Jens H.; Honko, Anna N.; Rosenzweig, C. Nicole

doi:10.3201/eid2208.160270

Cited by 36 publications

(21 citation statements)

References 15 publications

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“…134 MinION has already identified bacteria and viruses. [134][135][136] NEW MOLECULAR TECHNIQUES ARE NOT PERFECT Even with improvements in sensitivity, many infectious diseases do not release pathogen genetic material in the bloodstream in sufficient quantities to be diagnosed by NAAT using blood or serum samples. Blood culture theoretically can detect as little as one bacterium in a large volume culture bottle.…”

Section: Metagenomic Sequencing Can Identify Any Pathogenmentioning

confidence: 99%

Reducing Uncertainty for Acute Febrile Illness in Resource-Limited Settings: The Current Diagnostic Landscape

Robinson

Manabe

2017

The American Society of Tropical Medicine and Hygiene

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Diagnosing the cause of acute febrile illness in resource-limited settings is important-to give the correct antimicrobials to patients who need them, to prevent unnecessary antimicrobial use, to detect emerging infectious diseases early, and to guide vaccine deployment. A variety of approaches are yielding more rapid and accurate tests that can detect more pathogens in a wider variety of settings. After decades of slow progress in diagnostics for acute febrile illness in resource-limited settings, a wave of converging advancements will enable clinicians in resource-limited settings to reduce uncertainty for the diagnosis of acute febrile illness.

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Section: Metagenomic Sequencing Can Identify Any Pathogenmentioning

confidence: 99%

Reducing Uncertainty for Acute Febrile Illness in Resource-Limited Settings: The Current Diagnostic Landscape

Robinson

Manabe

2017

The American Society of Tropical Medicine and Hygiene

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“…The entire genome of a parapoxvirus isolated from a seal was obtained by combining data from Illumina next-generation sequencing with nanopore sequencing data 23 . One study has reported the detection of Venezuelan equine encephalitis virus from unamplified cDNA created from poly-A tailed RNA using cell culture grown viruses 24 . To the author's knowledge, the present study is the first using MinION as an aid in porcine health management.…”

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confidence: 99%

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

Theuns

Vanmechelen

Bernaert

et al. 2018

Sci Rep

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Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. The capacities of nanopore sequencing for viral diagnostics were investigated here. First, cell culture-grown porcine epidemic diarrhea virus and rotavirus A were pooled and sequenced on a MinION. Reads were already detected at 7 seconds after start of sequencing, resulting in high sequencing depths (19.2 to 103.5X) after 3 h. Next, diarrheic feces of a one-week-old piglet was analyzed. Almost all reads (99%) belonged to bacteriophages, which may have reshaped the piglet’s microbiome. Contigs matched Bacteroides, Escherichia and Enterococcus phages. Moreover, porcine kobuvirus was discovered in the feces for the first time in Belgium. Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (106.42–107.01 copies/swab) and diarrheic signs was not observed during a follow-up study. Retrospective analysis showed the widespread (n = 25, 56.8% positive) of genetically moderately related kobuviruses among Belgian diarrheic piglets. MinION enables rapid detection of enteric viruses. Such new methodologies will change diagnostics, but more extensive validations should be conducted. The true enteric pathogenicity of porcine kobuvirus should be questioned, while its subclinical importance cannot be excluded.

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“…MinION has been extensively used in detecting known [177][178][179][180][181] and new [182] pathogen strains, for instance, of Ebola virus [183], Begomovirus [184] and Papillomavirus [185]. Curiously, MinION allows samples to be detected and genotyped within mere hours from sample collection, even "in the field", sometimes literally [186,187]. It has also been successfully used for rapid investigation of Dengue virus outbreak in Angola [188] and Ebola epidemic in Guinea [189].…”

Section: Long Read Sequencingmentioning

confidence: 99%

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

Kiselev

Matsvay

Абрамов

et al. 2020

Viruses

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Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.

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Use of Unamplified RNA/cDNA–Hybrid Nanopore Sequencing for Rapid Detection and Characterization of RNA Viruses

Cited by 36 publications

References 15 publications

Reducing Uncertainty for Acute Febrile Illness in Resource-Limited Settings: The Current Diagnostic Landscape

Reducing Uncertainty for Acute Febrile Illness in Resource-Limited Settings: The Current Diagnostic Landscape

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

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