Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19

Moore, Shona C.; Penrice-Randal, Rebekah; Alruwaili, Muhannad; Dong, Xiaofeng; Pullan, Steven T.; Carter, Dan; Bewley, Kevin R.; Zhao, Qin; Sun, Yani; Hartley, Catherine; Zhou, En‐Min; Solomon, Tom; Beadsworth, Michael; Cruise, James; Bogaert, Debby; Crook, Derrick W.; Matthews, David A.; Davidson, Andrew D.; Mahmood, Zana H.; Aljabr, Waleed; Druce, Julian; Vipond, Richard; Ng, Lisa F. P.; Rénia, Laurent; Openshaw, Peter; Baillie, J Kenneth; Carroll, Miles W.; Semple, Malcolm G; Turtle, Lance; Hiscox, Julian A.

doi:10.1101/2020.03.05.20032011

Cited by 65 publications

(63 citation statements)

References 14 publications

(14 reference statements)

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“…Novel systems are being assessed for faster detection of key viral sequences51112 and a variety of point-of-care antigen detection devices have been developed, but their performance varies widely. Some antigen detection devices have poor sensitivity, meaning that infections are missed and infectious individuals are not managed appropriately 11…”

Section: Swab Testsmentioning

confidence: 99%

Covid-19: testing times

Beeching

Fletcher

Beadsworth

2020

BMJ

206

195

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Section: Swab Testsmentioning

confidence: 99%

Covid-19: testing times

Beeching

Fletcher

Beadsworth

2020

BMJ

206

195

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“…Several approaches have been used to sequence the SARS-CoV-2 genome, including metagenomics (Manning et al 2020) , sequence capture (Gohl et al 2020) , SISPA (Moore et al 2020) , and multiplex PCR (Gohl et al 2020;Itokawa et al 2020;Resende et al 2020;Moore et al 2020;Eden et al 2020) , followed by next generation sequencing using either the Illumina or Oxford Nanopore platforms. Due to its simplicity and economy, using multiplexed PCR amplicons is perhaps the most common approach.…”

Section: Introductionmentioning

confidence: 99%

Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding

Freed

Vlková

Faisal

et al. 2020

Preprint

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Rapid and cost-efficient whole-genome sequencing of SARS-CoV-2, the virus that causes COVID-19, is critical for understanding viral transmission dynamics. Here we show that using a new multiplexed set of primers in conjunction with the Oxford Nanopore Rapid Barcode library kit allows for faster, simpler, and less expensive SARS-CoV-2 genome sequencing. This primer set results in amplicons that exhibit lower levels of variation in coverage compared to other commonly used primer sets. Using five SARS-CoV-2 patient samples with C q values between 20 and 31, we show that high-quality genomes can be generated with as few as 10,000 reads (approximately 5 Mbp of sequence data). We also show that mis-classification of barcodes, which may be more likely when using the Oxford Nanopore Rapid Barcode library prep, is unlikely to cause problems in variant calling. This method reduces the time from RNA to genome sequence by more than half compared to the more standard ligation-based Oxford Nanopore library preparation method at considerably lower costs.

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“…However, the pandemic has also made travel and in-person learning a challenge, and therefore, GEIS is planning on development of virtual versions of the workshops to continue development of this important DoD-wide capability. In addition, Oxford Nanopore's MinION platform has increasingly been used in pathogen outbreak studies for real-time in-field analyses throughout the world, including analyses of SARS-CoV-2 (Quick et al, 2016;Faria et al, 2018;Moore et al, 2020). Although training in the wetlab and bioinformatics of this approach was not included in the workshop in Kenya to maintain simplicity and focus, the plan is to apply the modular approach for development and incorporation of a general DoD MinION-focused training for the GEIS partner laboratories.…”

Section: Discussionmentioning

confidence: 99%

A Department of Defense Laboratory Consortium Approach to Next Generation Sequencing and Bioinformatics Training for Infectious Disease Surveillance in Kenya

et al. 2020

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Epidemics of emerging and re-emerging infectious diseases are a danger to civilian and military populations worldwide. Health security and mitigation of infectious disease threats is a priority of the United States Government and the Department of Defense (DoD). Next generation sequencing (NGS) and Bioinformatics (BI) enhances traditional biosurveillance by providing additional data to understand transmission, identify resistance and virulence factors, make predictions, and update risk assessments. As more and more laboratories adopt NGS and BI technologies they encounter challenges in building local capacity. In addition to choosing the right sequencing platform and approach, considerations must also be made for the complexity of bioinformatics analyses, data storage, as well as personnel and computational requirements. To address these needs, a comprehensive training program was developed covering wet lab and bioinformatics approaches to NGS. The program is meant to be modular and adaptive to meet both common and individualized needs of medical research and public health laboratories across the DoD. The training program was first deployed internationally to the Basic Science Laboratory of the US Army Medical Research Directorate-Africa in Kisumu, Kenya, which is an overseas Lab of the Walter Reed Army Institute of Research (WRAIR). A week-long workshop with intensive focus on targeted sequencing and the bioinformatics of genome assembly (n = 24 participants) was held. Post-workshop self-assessment (completed by 21 participants

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Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19

Cited by 65 publications

References 14 publications

Covid-19: testing times

Covid-19: testing times

Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding

A Department of Defense Laboratory Consortium Approach to Next Generation Sequencing and Bioinformatics Training for Infectious Disease Surveillance in Kenya

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