Data of whole genome sequencing of five garden asparagus (Asparagus officinalis) individuals with the MinION nanopore sequencer

Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.

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In-field whole genome sequencing using the MinION nanopore sequencer to detect the presence of high-prized military targets

Australian Journal of Forensic Sciences ◽

10.1080/00450618.2019.1568562 ◽

2019 ◽

Vol 51 (sup1) ◽

pp. S86-S90 ◽

Cited By ~ 1

Author(s):

Justin Sim ◽

Brendan Chapman

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Nanopore Sequencer

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Evaluating an Upper Respiratory Disease Panel on the Portable MinION Sequencer

10.1101/436600 ◽

2018 ◽

Author(s):

Wanda J. Lyon ◽

Zachary K. Smith ◽

Brian Grier ◽

James Baldwin ◽

Clarise R. Starr

Keyword(s):

Whole Genome Sequencing ◽

Respiratory Disease ◽

Genome Sequencing ◽

Error Rate ◽

Whole Genome Amplification ◽

Targeted Sequencing ◽

Whole Genome ◽

Genome Amplification ◽

Upper Respiratory ◽

Nanopore Sequencer

AbstractThe MinION was used to evaluate upper respiratory disease infections using both whole genome amplification (WGA), targeted sequencing, and was found to have tremendous potential for field use. The MinION nanopore sequencer was been released to community testers for evaluation using a variety of sequencing applications. The MinION was used to evaluate upper respiratory disease infections using both whole genome amplification and targeted sequencing, and was found to have tremendous potential for field use. In this study, we tested the ability of the MinION nanopore sequencer to accurately identify and differentiate clinical bacterial and viral samples via targeted sequencing and whole genome sequencing. The current nanopore technology has limitations with respect to error rate but has steadily improved with development of new flow cells and kits. Upper respiratory disease organisms were successfully identified and differentiated down to the strain level with 87-98% alignment to our reference genome database. The ability to differentiate strains by amplicon and whole genome sequencing on the MinION was accomplished despite the observed average per 100-base error rate averaged 1.2E-01. This study offers evidence of the utility of sequencing to identify and differentiate both viral and bacterial species present within clinical samples.

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