Accelerating SARS-CoV-2 genomic surveillance in a routine clinical setting with nanopore sequencing

Buenestado-Serrano, Sergio; Herranz, Marta; Otero-Sobrino, Álvaro; Molero-Salinas, Andrea; Rodríguez-Grande, Cristina; Sanz-Pérez, Amadeo; Durán Galván, María José; Catalán, Pilar; Alonso, Roberto; Muñoz, Patricia; Pérez-Lago, Laura; García de Viedma, Darío

doi:10.1016/j.ijmm.2024.151599

Cited by 4 publications

(1 citation statement)

References 15 publications

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“…Their instrumentation, the corresponding chemicals, and flow cells are more affordable, and the generated data are more targeted [ 131 ]. On the other hand, as long-read techniques offer a wider genomic picture, thus providing a deeper insight into nucleic acid traits, their introduction into routine examinations has started [ 132 – 136 ] and their spreading is expected in the near future.…”

Section: Applications Of Long-read Sequencingmentioning

confidence: 99%

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

Szakállas,

Barták,

Valcz

et al. 2024

Pathol. Oncol. Res.

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The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points. The appearance of new sequencing techniques was essential to get more interpretable genomic data. In contrast to the previous short-reads, longer lengths can provide a better insight into the potential health threatening genetic abnormalities. Long-reads offer more accurate variant identification and genome assembly methods, indicating advances in nucleotide deflect-related studies. In this review, we introduce the historical background of sequencing technologies and show their benefits and limits, as well. Furthermore, we highlight the differences between short- and long-read approaches, including their unique advances and difficulties in methodologies and evaluation. Additionally, we provide a detailed description of the corresponding bioinformatics and the current applications.

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Section: Applications Of Long-read Sequencingmentioning

confidence: 99%

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

Szakállas,

Barták,

Valcz

et al. 2024

Pathol. Oncol. Res.

View full text Add to dashboard Cite

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Development of a portable multi-step microfluidic device for point-of-care nucleic acid diagnostics

Shi,

Pang,

et al. 2025

Analytica Chimica Acta

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Portable In-Field DNA Sequencing for Rapid Detection of Pathogens and Antimicrobial Resistance: A Proof-of-Concept Study

Pillay,

Calderón-Franco,

Abeel

2024

Preprint

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Purpose: Infectious diseases represent a major global health threat due to the rapid spread of pathogens, leading to widespread outbreaks. Concurrently, antimicrobial resistance (AMR) is increasing, making standard treatments less effective and complicating infection management. Effective surveillance systems are essential to address these challenges. Methods: We conducted a proof-of-concept study to evaluate a portable in-field microbial lab against a traditional molecular lab for DNA isolation, sequencing, microbial detection, antibiotic resistance gene identification, and plasmid classification. Samples from lake water, wastewater treatment plant sludge, and retail meat were selected to reflect relevant surveillance vectors. This approach provides valuable data for environmental monitoring, public health, and food safety, aiding in outbreak preparedness. We compared results using five metrics: DNA yield and purity, read N50, taxonomic classification, antibiotic resistance gene identification (ARGs), and plasmid classification. Results: Our study found that metagenomic bacterial DNA isolation from environmental and food sources is feasible with portable lab technology, producing >800ng of DNA, suitable for Nanopore sequencing. DNA from retail meat, lake, and sludge samples resulted in similar read numbers and read N50 values. Taxonomic classification was achieved at the genus and species levels. A Jaccard similarity of over 50% was observed in the top 20 most abundant species between chicken samples, and lake samples. ESKAPE pathogens were detected in chicken and lake samples. ARGs and plasmids were also identified in both retail meat and lake samples. Conclusion: This study demonstrates that in-field DNA isolation and sequencing are feasible with minimal equipment, yielding results comparable to traditional lab methods.

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Accelerating SARS-CoV-2 genomic surveillance in a routine clinical setting with nanopore sequencing

Cited by 4 publications

References 15 publications

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

Development of a portable multi-step microfluidic device for point-of-care nucleic acid diagnostics

Portable In-Field DNA Sequencing for Rapid Detection of Pathogens and Antimicrobial Resistance: A Proof-of-Concept Study

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