Dataset Information

Metagenome of a Bronchoalveolar Lavage Fluid Sample from a Confirmed COVID-19 Case in Quito, Ecuador, Obtained Using Oxford Nanopore MinION Technology.

ABSTRACT: We report the metagenome analysis of a bronchoalveolar lavage (BAL) fluid sample from a confirmed coronavirus disease 2019 (COVID-19) case in Quito, Ecuador. Sequencing was performed using MinION technology.

SUBMITTER: Marquez S

PROVIDER: S-EPMC7545292 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Metagenome of a Bronchoalveolar Lavage Fluid Sample from a Confirmed COVID-19 Case in Quito, Ecuador, Obtained Using Oxford Nanopore MinION Technology.

Márquez Sully S Prado-Vivar Belén B Guadalupe Juan José JJ Gutierrez Bernardo B Becerra-Wong Mónica M Jibaja Manuel M Tobar Milton M Barragán Verónica V Rojas-Silva Patricio P Coloma Josefina J Trueba Gabriel G Grunauer Michelle M Cárdenas Paúl P

Microbiology resource announcements 20201008 41

We report the metagenome analysis of a bronchoalveolar lavage (BAL) fluid sample from a confirmed coronavirus disease 2019 (COVID-19) case in Quito, Ecuador. Sequencing was performed using MinION technology. ...[more]

PMID: 33033138

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Project description:BackgroundSequence verification is essential for plasmids used as critical reagents or therapeutic products. Typically, high-quality plasmid sequence is achieved through capillary-based Sanger sequencing, requiring customized sets of primers for each plasmid. This process can become expensive, particularly for applications where the validated sequence needs to be produced within a regulated and quality-controlled environment for downstream clinical research applications.ResultsHere, we describe a cost-effective and accurate plasmid sequencing and consensus generation procedure using the Oxford Nanopore Technologies' MinION device as an alternative to capillary-based plasmid sequencing options. This procedure can verify the identity of a pure population of plasmid, either confirming it matches the known and expected sequence, or identifying mutations present in the plasmid if any exist. We use a full MinION flow cell per plasmid, maximizing available data and allowing for stringent quality filters. Pseudopairing reads for consensus base calling reduces read error rates from 5.3 to 0.53%, and our pileup consensus approach provides per-base counts and confidence scores, allowing for interpretation of the certainty of the resulting consensus sequences. For pure plasmid samples, we demonstrate 100% accuracy in the resulting consensus sequence, and the sensitivity to detect small mutations such as insertions, deletions, and single nucleotide variants. In test cases where the sequenced pool of plasmids contains subclonal templates, detection sensitivity is similar to that of traditional capillary sequencing.ConclusionsOur pipeline can provide significant cost savings compared to outsourcing clinical-grade sequencing of plasmids, making generation of high-quality plasmid sequence for clinical sequence verification more accessible. While other long-read-based methods offer higher-throughput and less cost, our pipeline produces complete and accurate sequence verification for cases where absolute sequence accuracy is required.

Dataset Information

Metagenome of a Bronchoalveolar Lavage Fluid Sample from a Confirmed COVID-19 Case in Quito, Ecuador, Obtained Using Oxford Nanopore MinION Technology.

Publications

Metagenome of a Bronchoalveolar Lavage Fluid Sample from a Confirmed COVID-19 Case in Quito, Ecuador, Obtained Using Oxford Nanopore MinION Technology.

Similar Datasets

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