Portable sequencer in the fight against infectious disease

Mongan, Arthur E.; Tuda, Josef S. B.; Runtuwene, Lucky Ronald

doi:10.1038/s10038-019-0675-4

Cited by 37 publications

(33 citation statements)

References 75 publications

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“…The application of tNGS on portable, solid-state sequencing devices holds enormous promise for precision global health in the management of DR-TB, where sequencing data obtained from direct clinical samples could inform clinical decision systems supporting individual treatment decisions and large-scale programmatic molecular DST ( 26 ). More broadly, portable and compact sequencing technologies are demonstrating their valuable role in the fight against emerging infectious diseases ( 27 ).…”

Section: Discussionmentioning

confidence: 99%

Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples

et al. 2020

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Targeted Next Generation Sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug resistant TB (DR-TB). However, the complexity of sequencing platforms has limited their uptake in low-resource settings. The goal of this study was to evaluate the use of tNGS-based DST solution: Genoscreen Deeplex Myc-TB, for use on the compact, low-cost Oxford Nanopore Technologies MinION sequencer. One hundred four DNA samples extracted from smear-positive sputum sediments, previously sequenced using the Deeplex assay on an Illumina MiniSeq, were re-sequenced on MinION after applying a custom library preparation. MinION read quality, mapping statistics and variant calling were computed using an in-house pipeline and compared to the reference Miniseq data. The average percentage of MinION reads mapped to an H37RV reference genome was 90.8%, versus 99.5% on MiniSeq. The mean depth of coverage was 4151x and 4177x on MinION and MiniSeq, respectively, with heterogeneous distribution across targeted genes. Composite reference coverage breadth was >99% for both platforms. We observed full concordance between technologies in reporting the clinically relevant drug resistant markers, including full gene deletions. We demonstrated that the workflow and sequencing data obtained from Deeplex on MinION are comparable to the MiniSeq, despite the higher raw error rates on MinION, with the added advantage of MinION's portability, versatility and low capital costs. Targeted NGS on MinION is a promising DST solution for rapidly providing clinically relevant data to manage complex DR-TB cases.

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Section: Discussionmentioning

confidence: 99%

Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples

et al. 2020

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“…Powered by USB, this nanopore sequencing instrument is capable of up to 20 GB of long read sequence data that can provide more information for species differentiation [ 215 ]. The MinION has been transported all over the globe from rainforests to the artic [ 216 ], was deployed to Brazil to help with Zika virus surveillance during the 2016 outbreak [ 217 ], and has even been tested on the International Space Station [ 218 ]. To date, use of this platform has been commonly applied to pathogen discovery and identification [ 219 ], but has also demonstrated efficacy in Cyt b sequencing from wildlife samples [ 220 ] which may also imply utility for field-based arthropod blood meal identifications.…”

Section: Advances In Portability and Field-forward Technologiesmentioning

confidence: 99%

“…Furthermore, the MinION holds great potential for simultaneous identification of arthropod, pathogens, and bloodmeal source. This technology eliminates the complications associated with sample storage, including freeze/thaw cycles that can damage precious pathogen and host DNA in arthropod bloodmeals, making it a valuable addition to the technological arsenal available for research studies [ 216 ].…”

Section: Advances In Portability and Field-forward Technologiesmentioning

confidence: 99%

Modernizing the Toolkit for Arthropod Bloodmeal Identification

Borland

Kading

2021

Insects

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Understanding vertebrate–vector interactions is vitally important for understanding the transmission dynamics of arthropod-vectored pathogens and depends on the ability to accurately identify the vertebrate source of blood-engorged arthropods in field collections using molecular methods. A decade ago, molecular techniques being applied to arthropod blood meal identification were thoroughly reviewed, but there have been significant advancements in the techniques and technologies available since that time. This review highlights the available diagnostic markers in mitochondrial and nuclear DNA and discusses their benefits and shortcomings for use in molecular identification assays. Advances in real-time PCR, high resolution melting analysis, digital PCR, next generation sequencing, microsphere assays, mass spectrometry, and stable isotope analysis each offer novel approaches and advantages to bloodmeal analysis that have gained traction in the field. New, field-forward technologies and platforms have also come into use that offer promising solutions for point-of-care and remote field deployment for rapid bloodmeal source identification. Some of the lessons learned over the last decade, particularly in the fields of DNA barcoding and sequence analysis, are discussed. Though many advancements have been made, technical challenges remain concerning the prevention of sample degradation both by the arthropod before the sample has been obtained and during storage. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification and reviews how advances in molecular technology over the past decade have been applied in this unique biomedical context.

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“…Infectious diseases are still a major threat in the world today 1 . The diagnosis and real-time tracking of both emerging 2 and re-emerging infectious diseases must be reliable, fast, and affordable.…”

Section: Introductionmentioning

confidence: 99%

Current and emerging diagnostic tests available for the novel COVID-19 global pandemic

Mboowa

2020

AAS Open Res

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On March 11, 2020 the World Health Organization (WHO) upgraded the status of the coronavirus disease 2019 (COVID-19) outbreak from epidemic to a global pandemic. This infection is caused by a novel coronavirus, SARS-CoV-2. Several rapid diagnostic tests have been developed at an astonishing pace; however, COVID-19 requires more highly specific rapid point-of-care diagnostic tests. This review describes the currently available testing approaches, as well as the available test assays including the Xpert® Xpress SARS-CoV-2 test (takes ~45 min) and Abbott ID COVID-19 test (5 min) as easy to use point-of-care tests for diagnosis of novel COVID-19 that have so far received the US Food and Drug Administration emergency use authorizations clearance. This review is correct as of the date published and will be updated as more diagnostic tests come to light.

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Portable sequencer in the fight against infectious disease

Cited by 37 publications

References 75 publications

Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples

Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples

Modernizing the Toolkit for Arthropod Bloodmeal Identification

Current and emerging diagnostic tests available for the novel COVID-19 global pandemic

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